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Sample records for neandertal mitochondrial genome

  1. A Draft Sequence of the Neandertal Genome

    Science.gov (United States)

    Green, Richard E.; Li, Heng; Zhai, Weiwei; Fritz, Markus Hsi-Yang; Hansen, Nancy F.; Durand, Eric Y.; Malaspinas, Anna-Sapfo; Jensen, Jeffrey D.; Marques-Bonet, Tomas; Alkan, Can; Prüfer, Kay; Meyer, Matthias; Burbano, Hernán A.; Good, Jeffrey M.; Schultz, Rigo; Aximu-Petri, Ayinuer; Butthof, Anne; Höber, Barbara; Höffner, Barbara; Siegemund, Madlen; Weihmann, Antje; Nusbaum, Chad; Lander, Eric S.; Russ, Carsten; Novod, Nathaniel; Affourtit, Jason; Egholm, Michael; Verna, Christine; Rudan, Pavao; Brajkovic, Dejana; Kucan, Željko; Gušic, Ivan; Doronichev, Vladimir B.; Golovanova, Liubov V.; Lalueza-Fox, Carles; de la Rasilla, Marco; Fortea, Javier; Rosas, Antonio; Schmitz, Ralf W.; Johnson, Philip L. F.; Eichler, Evan E.; Falush, Daniel; Birney, Ewan; Mullikin, James C.; Slatkin, Montgomery; Nielsen, Rasmus; Kelso, Janet; Lachmann, Michael; Reich, David; Pääbo, Svante

    2016-01-01

    Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other. PMID:20448178

  2. A functional test of Neandertal and modern human mitochondrial targeting sequences

    Energy Technology Data Exchange (ETDEWEB)

    Gralle, Matthias, E-mail: gralle@bioqmed.ufrj.br [Instituto de Bioquimica Medica, Universidade Federal do Rio de Janeiro, CCS, Ilha do Fundao, 21941-590 Rio de Janeiro (Brazil); Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig (Germany); Schaefer, Ingo; Seibel, Peter [Department of Molecular Cell Therapy, Leipzig University, Deutscher Platz 5, 04103 Leipzig (Germany); Paeaebo, Svante [Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig (Germany)

    2010-11-26

    Research highlights: {yields} Two mutations in mitochondrial targeting peptides occurred during human evolution, possibly after Neandertals split off from modern human lineage. {yields} The ancestral and modern human versions of these two targeting peptides were tested functionally for their effects on localization and cleavage rate. {yields} In spite of recent evolution, and to the contrary of other mutations in targeting peptides, these mutations had no visible effects. -- Abstract: Targeting of nuclear-encoded proteins to different organelles, such as mitochondria, is a process that can result in the redeployment of proteins to new intracellular destinations during evolution. With the sequencing of the Neandertal genome, it has become possible to identify amino acid substitutions that occurred on the modern human lineage since its separation from the Neandertal lineage. Here we analyze the function of two substitutions in mitochondrial targeting sequences that occurred and rose to high frequency recently during recent human evolution. The ancestral and modern versions of the two targeting sequences do not differ in the efficiency with which they direct a protein to the mitochondria, an observation compatible with the neutral theory of molecular evolution.

  3. Twelve Years of Neandertal Genetic Discoveries: State-of-the-Art and Future Challenges

    DEFF Research Database (Denmark)

    Orlando, Ludovic Antoine Alexandre; Hänni, Catherine

    2013-01-01

    The first mitochondrial DNA sequence from a Neandertal specimen was recovered in 1997. Now the completion of the whole Neandertal genome has been announced to be completed in the forthcoming months. About one ­million nucleotides of nuclear DNA have already been sequenced and so far 15 Neandertal...

  4. Statistical analysis of post mortem DNA damage-derived miscoding lesions in Neandertal mitochondrial DNA

    NARCIS (Netherlands)

    S. Vives (Sergi); M.T. Gilbert (Thomas); C. Arenas (Conchita); E. Gigli (Elena); O. Lao Grueso (Oscar); C. Lalueza-Fox (Carles)

    2008-01-01

    textabstractBackground. We have analysed the distribution of post mortem DNA damage derived miscoding lesions from the datasets of seven published Neandertal specimens that have extensive cloned sequence coverage over the mitochondrial DNA (mtDNA) hypervariable region 1 (HVS1). The analysis was rest

  5. Statistical analysis of post mortem DNA damage-derived miscoding lesions in Neandertal mitochondrial DNA

    OpenAIRE

    Vives, Sergi; Gilbert, Thomas; Arenas, Conchita; Gigli, Elena, 1978-; Lao Grueso, Oscar; Lalueza-Fox, Carles

    2008-01-01

    textabstractBackground. We have analysed the distribution of post mortem DNA damage derived miscoding lesions from the datasets of seven published Neandertal specimens that have extensive cloned sequence coverage over the mitochondrial DNA (mtDNA) hypervariable region 1 (HVS1). The analysis was restricted to C → T and G → A miscoding lesions (the predominant manifestation of post mortem damage) that are seen at a frequency of more than one clone among sequences from a single PCR, but do not r...

  6. Statistical analysis of post mortem DNA damage-derived miscoding lesions in Neandertal mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    Gigli Elena

    2008-07-01

    Full Text Available Abstract Background We have analysed the distribution of post mortem DNA damage derived miscoding lesions from the datasets of seven published Neandertal specimens that have extensive cloned sequence coverage over the mitochondrial DNA (mtDNA hypervariable region 1 (HVS1. The analysis was restricted to C→T and G→A miscoding lesions (the predominant manifestation of post mortem damage that are seen at a frequency of more than one clone among sequences from a single PCR, but do not represent the true endogenous sequence. Findings The data indicates an extreme bias towards C→T over G→A miscoding lesions (observed ratio of 67:2 compared to an expected ratio of 7:2, implying that the mtDNA Light strand molecule suffers proportionally more damage-derived miscoding lesions than the Heavy strand. Conclusion The clustering of Cs in the Light strand as opposed to the singleton pattern of Cs in the Heavy strand could explain the observed bias, a phenomenon that could be further tested with non-PCR based approaches. The characterization of the HVS1 hotspots will be of use to future Neandertal mtDNA studies, with specific regards to assessing the authenticity of new positions previously unknown to be polymorphic.

  7. Statistical analysis of post mortem DNA damage-derived miscoding lesions in Neandertal mitochondrial DNA

    DEFF Research Database (Denmark)

    Vives, Sergi; Gilbert, M Thomas; Arenas, Conchita

    2008-01-01

    ABSTRACT: BACKGROUND: We have analysed the distribution of post mortem DNA damage derived miscoding lesions from the datasets of seven published Neandertal specimens that have extensive cloned sequence coverage over the mitochondrial DNA (mtDNA) hypervariable region 1 (HVS1). The analysis...... was restricted to C-->T and G-->A miscoding lesions (the predominant manifestation of post mortem damage) that are seen at a frequency of more than one clone among sequences from a single PCR, but do not represent the true endogenous sequence. FINDINGS: The data indicates an extreme bias towards C-->T over G......-->A miscoding lesions (observed ratio of 67:2 compared to an expected ratio of 7:2), implying that the mtDNA Light strand molecule suffers proportionally more damage-derived miscoding lesions than the Heavy strand. CONCLUSION: The clustering of Cs in the Light strand as opposed to the singleton pattern of Cs...

  8. Lophotrochozoan mitochondrial genomes

    Energy Technology Data Exchange (ETDEWEB)

    Valles, Yvonne; Boore, Jeffrey L.

    2005-10-01

    Progress in both molecular techniques and phylogeneticmethods has challenged many of the interpretations of traditionaltaxonomy. One example is in the recognition of the animal superphylumLophotrochozoa (annelids, mollusks, echiurans, platyhelminthes,brachiopods, and other phyla), although the relationships within thisgroup and the inclusion of some phyla remain uncertain. While much ofthis progress in phylogenetic reconstruction has been based on comparingsingle gene sequences, we are beginning to see the potential of comparinglarge-scale features of genomes, such as the relative order of genes.Even though tremendous progress is being made on the sequencedetermination of whole nuclear genomes, the dataset of choice forgenome-level characters for many animals across a broad taxonomic rangeremains mitochondrial genomes. We review here what is known aboutmitochondrial genomes of the lophotrochozoans and discuss the promisethat this dataset will enable insight into theirrelationships.

  9. North African populations carry the signature of admixture with Neandertals

    DEFF Research Database (Denmark)

    Sánchez-Quinto, Federico; Botigué, Laura R; Civit, Sergi

    2012-01-01

    One of the main findings derived from the analysis of the Neandertal genome was the evidence for admixture between Neandertals and non-African modern humans. An alternative scenario is that the ancestral population of non-Africans was closer to Neandertals than to Africans because of ancient popu...

  10. North African populations carry the signature of admixture with Neandertals

    DEFF Research Database (Denmark)

    Sánchez-Quinto, Federico; Botigué, Laura R.; Civit, Sergi

    2012-01-01

    One of the main findings derived from the analysis of the Neandertal genome was the evidence for admixture between Neandertals and non-African modern humans. An alternative scenario is that the ancestral population of non-Africans was closer to Neandertals than to Africans because of ancient popu...

  11. Inheritance of the yeast mitochondrial genome

    DEFF Research Database (Denmark)

    Piskur, Jure

    1994-01-01

    Mitochondrion, extrachromosomal genetics, intergenic sequences, genome size, mitochondrial DNA, petite mutation, yeast......Mitochondrion, extrachromosomal genetics, intergenic sequences, genome size, mitochondrial DNA, petite mutation, yeast...

  12. An X-Linked Haplotype of Neandertal Origin Is Present Among All Non-African Populations

    National Research Council Canada - National Science Library

    Yotova, Vania; Lefebvre, Jean-Francois; Moreau, Claudia; Gbeha, Elias; Hovhannesyan, Kristine; Bourgeois, Stephane; Bédarida, Sandra; Azevedo, Luisa; Amorim, Antonio; Sarkisian, Tamara; Avogbe, Patrice Hodonou; Chabi, Nicodeme; Dicko, Mamoudou Hama; Kou' Santa Amouzou, Emile Sabiba; Sanni, Ambaliou; Roberts-Thomson, June; Boettcher, Barry; Scott, Rodney J; Labuda, Damian

    2011-01-01

    Recent work on the Neandertal genome has raised the possibility of admixture between Neandertals and the expanding population of Homo sapiens who left Africa between 80 and 50 Kya (thousand years ago...

  13. Ancient DNA: Would the Real Neandertal Please Stand up?

    DEFF Research Database (Denmark)

    Cooper, Alan; Drummond, Alexei J.; Willerslev, Eske

    2004-01-01

    Mitochondrial DNA sequences recovered from eight Neandertal specimens cannot be detected in either early fossil Europeans or in modern populations. This indicates that, if Neandertals made any genetic contribution at all to modern humans, it must have been limited, though the extent of the contri...

  14. Mitochondrial genomes of parasitic flatworms.

    Science.gov (United States)

    Le, Thanh H; Blair, David; McManus, Donald P

    2002-05-01

    Complete or near-complete mitochondrial genomes are now available for 11 species or strains of parasitic flatworms belonging to the Trematoda and the Cestoda. The organization of these genomes is not strikingly different from those of other eumetazoans, although one gene (atp8) commonly found in other phyla is absent from flatworms. The gene order in most flatworms has similarities to those seen in higher protostomes such as annelids. However, the gene order has been drastically altered in Schistosoma mansoni, which obscures this possible relationship. Among the sequenced taxa, base composition varies considerably, creating potential difficulties for phylogeny reconstruction. Long non-coding regions are present in all taxa, but these vary in length from only a few hundred to approximately 10000 nucleotides. Among Schistosoma spp., the long non-coding regions are rich in repeats and length variation among individuals is known. Data from mitochondrial genomes are valuable for studies on species identification, phylogenies and biogeography.

  15. Twelve years of Neandertal genetic discoveries

    DEFF Research Database (Denmark)

    Orlando, Ludovic Antoine Alexandre; Hänni, Catherine

    2011-01-01

    specimens have delivered authentic mitochondrial sequences. This information has helped us to better understand the evolution of the Neandertal gene pool over space and time and to address the long-standing question of possible admixture with their modern human relatives. This chapter reviews current...

  16. Mitochondrial fusion and inheritance of the mitochondrial genome.

    Science.gov (United States)

    Takano, Hiroyoshi; Onoue, Kenta; Kawano, Shigeyuki

    2010-03-01

    Although maternal or uniparental inheritance of mitochondrial genomes is a general rule, biparental inheritance is sometimes observed in protists and fungi,including yeasts. In yeast, recombination occurs between the mitochondrial genomes inherited from both parents.Mitochondrial fusion observed in yeast zygotes is thought to set up a space for DNA recombination. In the last decade,a universal mitochondrial fusion mechanism has been uncovered, using yeast as a model. On the other hand, an alternative mitochondrial fusion mechanism has been identified in the true slime mold Physarum polycephalum.A specific mitochondrial plasmid, mF, has been detected as the genetic material that causes mitochondrial fusion in P. polycephalum. Without mF, fusion of the mitochondria is not observed throughout the life cycle, suggesting that Physarum has no constitutive mitochondrial fusion mechanism.Conversely, mitochondria fuse in zygotes and during sporulation with mF. The complete mF sequence suggests that one gene, ORF640, encodes a fusogen for Physarum mitochondria. Although in general, mitochondria are inherited uniparentally, biparental inheritance occurs with specific sexual crossing in P. polycephalum.An analysis of the transmission of mitochondrial genomes has shown that recombinations between two parental mitochondrial genomes require mitochondrial fusion,mediated by mF. Physarum is a unique organism for studying mitochondrial fusion.

  17. North African populations carry the signature of admixture with Neandertals.

    Directory of Open Access Journals (Sweden)

    Federico Sánchez-Quinto

    Full Text Available One of the main findings derived from the analysis of the Neandertal genome was the evidence for admixture between Neandertals and non-African modern humans. An alternative scenario is that the ancestral population of non-Africans was closer to Neandertals than to Africans because of ancient population substructure. Thus, the study of North African populations is crucial for testing both hypotheses. We analyzed a total of 780,000 SNPs in 125 individuals representing seven different North African locations and searched for their ancestral/derived state in comparison to different human populations and Neandertals. We found that North African populations have a significant excess of derived alleles shared with Neandertals, when compared to sub-Saharan Africans. This excess is similar to that found in non-African humans, a fact that can be interpreted as a sign of Neandertal admixture. Furthermore, the Neandertal's genetic signal is higher in populations with a local, pre-Neolithic North African ancestry. Therefore, the detected ancient admixture is not due to recent Near Eastern or European migrations. Sub-Saharan populations are the only ones not affected by the admixture event with Neandertals.

  18. Mitochondrial helicases and mitochondrial genome maintenance

    DEFF Research Database (Denmark)

    Aamann, Maria Diget; de Souza-Pinto, Nadja C; Kulikowicz, Tomasz

    2010-01-01

    Helicases are essential enzymes that utilize the energy of nucleotide hydrolysis to drive unwinding of nucleic acid duplexes. Helicases play roles in all aspects of DNA metabolism including DNA repair, DNA replication and transcription. The subcellular locations and functions of several helicases...... have been studied in detail; however, the roles of specific helicases in mitochondrial biology remain poorly characterized. This review presents important recent advances in identifying and characterizing mitochondrial helicases, some of which also operate in the nucleus....

  19. Mitochondrial genomes as living ‘fossils’

    OpenAIRE

    2013-01-01

    The huge variation between mitochondrial genomes makes untangling their evolutionary histories difficult. Richardson et al. report on the remarkably unaltered ‘fossil’ genome of the tulip tree, giving us many clues as to how the mitochondrial genomes of flowering plants have evolved over the last 150 million years, and raising questions about how such extraordinary sequence conservation can be maintained. See research article http://www.biomedcentral.com/1741-7007/11/29.

  20. Partial genetic turnover in Neandertals

    DEFF Research Database (Denmark)

    Dalén, Love; Orlando, Ludovic Antoine Alexandre; Shapiro, Beth

    2012-01-01

    Remarkably little is known about the population-level processes leading up to the extinction of the neandertal. To examine this, we use mtDNA sequences from 13 neandertal individuals, including a novel sequence from northern Spain, to examine neandertal demographic history. Our analyses indicate ...

  1. [The mitochondrial genome and aging].

    Science.gov (United States)

    Meissner, C; Mohamed, S A; von Wurmb, N; Oehmichen, M

    2001-12-01

    There is a lot of evidence that age-associated alterations of the mitochondrial genome occur, especially in postmitotic tissues such as brain, heart and skeletal muscle. These alterations are supposed to be a result of an attack of free radicals generated as normal byproducts of oxidative phosphorylation and lead to damage of proteins, lipids, and DNA. The alterations of mtDNA include oxidative damage of base pairs, point mutations, large-scale deletions or duplications. The 4977 bp deletion or "common deletion" reveals an age-dependent accumulation in postmitotic tissues, but not in fast-dividing tissues such as blood cells. In addition, it is observed that a tissue-specific accumulation occurs with the highest abundance in the basal ganglia, followed by skeletal muscle, heart, and lowest in cerebellar tissue. Third, pathological alterations of specific tissue, like ischemia/reperfusion events, display a pronounced accumulation of the deletion compared to age-matched controls. Because there are many mtDNA mutations, further analysis of all alterations of mtDNA will elucidate its role in the phenomenon of aging. Despite some criticisms of this free radical theory of aging, there is a lot of experimental evidence to support the important role of mitochondria in organismal aging.

  2. Dinoflagellates: a mitochondrial genome all at sea.

    Science.gov (United States)

    Nash, Edmund A; Nisbet, R Ellen R; Barbrook, Adrian C; Howe, Christopher J

    2008-07-01

    Dinoflagellate algae are notorious for their highly unusual organization of nuclear and chloroplast genomes. Early studies on the dinoflagellate mitochondrial genome indicated that it encodes the same three protein-coding genes found in Plasmodium spp., but with a complex organization and transcript editing. Recent work has extended this view, showing that the dinoflagellate mitochondrial genome contains a wide array of gene fragments and genes interspersed with noncoding inverted repeats. The genome seems to require noncanonical start and stop codons, as well as high levels of editing, trans-splicing and the addition of oligonucleotide caps at the 5' and 3' ends of transcripts. Despite its small coding content, the dinoflagellate mitochondrial genome is one of the most complex known.

  3. No evidence of Neandertal mtDNA contribution to early modern humans.

    Directory of Open Access Journals (Sweden)

    David Serre

    2004-03-01

    Full Text Available The retrieval of mitochondrial DNA (mtDNA sequences from four Neandertal fossils from Germany, Russia, and Croatia has demonstrated that these individuals carried closely related mtDNAs that are not found among current humans. However, these results do not definitively resolve the question of a possible Neandertal contribution to the gene pool of modern humans since such a contribution might have been erased by genetic drift or by the continuous influx of modern human DNA into the Neandertal gene pool. A further concern is that if some Neandertals carried mtDNA sequences similar to contemporaneous humans, such sequences may be erroneously regarded as modern contaminations when retrieved from fossils. Here we address these issues by the analysis of 24 Neandertal and 40 early modern human remains. The biomolecular preservation of four Neandertals and of five early modern humans was good enough to suggest the preservation of DNA. All four Neandertals yielded mtDNA sequences similar to those previously determined from Neandertal individuals, whereas none of the five early modern humans contained such mtDNA sequences. In combination with current mtDNA data, this excludes any large genetic contribution by Neandertals to early modern humans, but does not rule out the possibility of a smaller contribution.

  4. Evolution of gastropod mitochondrial genome arrangements

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    Zardoya Rafael

    2008-02-01

    Full Text Available Abstract Background Gastropod mitochondrial genomes exhibit an unusually great variety of gene orders compared to other metazoan mitochondrial genome such as e.g those of vertebrates. Hence, gastropod mitochondrial genomes constitute a good model system to study patterns, rates, and mechanisms of mitochondrial genome rearrangement. However, this kind of evolutionary comparative analysis requires a robust phylogenetic framework of the group under study, which has been elusive so far for gastropods in spite of the efforts carried out during the last two decades. Here, we report the complete nucleotide sequence of five mitochondrial genomes of gastropods (Pyramidella dolabrata, Ascobulla fragilis, Siphonaria pectinata, Onchidella celtica, and Myosotella myosotis, and we analyze them together with another ten complete mitochondrial genomes of gastropods currently available in molecular databases in order to reconstruct the phylogenetic relationships among the main lineages of gastropods. Results Comparative analyses with other mollusk mitochondrial genomes allowed us to describe molecular features and general trends in the evolution of mitochondrial genome organization in gastropods. Phylogenetic reconstruction with commonly used methods of phylogenetic inference (ME, MP, ML, BI arrived at a single topology, which was used to reconstruct the evolution of mitochondrial gene rearrangements in the group. Conclusion Four main lineages were identified within gastropods: Caenogastropoda, Vetigastropoda, Patellogastropoda, and Heterobranchia. Caenogastropoda and Vetigastropoda are sister taxa, as well as, Patellogastropoda and Heterobranchia. This result rejects the validity of the derived clade Apogastropoda (Caenogastropoda + Heterobranchia. The position of Patellogastropoda remains unclear likely due to long-branch attraction biases. Within Heterobranchia, the most heterogeneous group of gastropods, neither Euthyneura (because of the inclusion of P

  5. Complete mitochondrial genome of Ark shell Scapharca subcrenata.

    Science.gov (United States)

    Hou, Ya; Wu, Biao; Liu, Zhi-Hong; Yang, Ai-Guo; Ren, Jian-Feng; Zhou, Li-Qing; Dong, Chun-Guang; Tian, Ji-Teng

    2016-01-01

    Complete mitochondrial genome of Scapharca subcrenata was determined in this report. It is 48,161 bp in length, being the largest mitochondrial genome among reported shellfish at present. The entire mitochondrial genome consists of 57 genes including 12 protein-coding genes, 2 ribosomal RNAs and 41 transfer RNAs.

  6. The Divergence of Neandertal and Modern Human Y Chromosomes

    Science.gov (United States)

    Mendez, Fernando L.; Poznik, G. David; Castellano, Sergi; Bustamante, Carlos D.

    2016-01-01

    Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins. Here, we analyze ∼120 kb of exome-captured Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain. We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes—including A00, the highly divergent basal haplogroup. We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya) (95% confidence interval [CI]: 447–806 kya). This is ∼2.1 (95% CI: 1.7–2.9) times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages. This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes. The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct. We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y, TMSB4Y, USP9Y, and KDM5D. Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation. It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups. PMID:27058445

  7. The Divergence of Neandertal and Modern Human Y Chromosomes.

    Science.gov (United States)

    Mendez, Fernando L; Poznik, G David; Castellano, Sergi; Bustamante, Carlos D

    2016-04-07

    Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins. Here, we analyze ∼120 kb of exome-captured Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain. We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes-including A00, the highly divergent basal haplogroup. We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya) (95% confidence interval [CI]: 447-806 kya). This is ∼2.1 (95% CI: 1.7-2.9) times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages. This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes. The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct. We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y, TMSB4Y, USP9Y, and KDM5D. Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation. It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups.

  8. The Complete Mitochondrial Genome of Gossypium hirsutum and Evolutionary Analysis of Higher Plant Mitochondrial Genomes

    Science.gov (United States)

    Su, Aiguo; Geng, Jianing; Grover, Corrinne E.; Hu, Songnian; Hua, Jinping

    2013-01-01

    Background Mitochondria are the main manufacturers of cellular ATP in eukaryotes. The plant mitochondrial genome contains large number of foreign DNA and repeated sequences undergone frequently intramolecular recombination. Upland Cotton (Gossypium hirsutum L.) is one of the main natural fiber crops and also an important oil-producing plant in the world. Sequencing of the cotton mitochondrial (mt) genome could be helpful for the evolution research of plant mt genomes. Methodology/Principal Findings We utilized 454 technology for sequencing and combined with Fosmid library of the Gossypium hirsutum mt genome screening and positive clones sequencing and conducted a series of evolutionary analysis on Cycas taitungensis and 24 angiosperms mt genomes. After data assembling and contigs joining, the complete mitochondrial genome sequence of G. hirsutum was obtained. The completed G.hirsutum mt genome is 621,884 bp in length, and contained 68 genes, including 35 protein genes, four rRNA genes and 29 tRNA genes. Five gene clusters are found conserved in all plant mt genomes; one and four clusters are specifically conserved in monocots and dicots, respectively. Homologous sequences are distributed along the plant mt genomes and species closely related share the most homologous sequences. For species that have both mt and chloroplast genome sequences available, we checked the location of cp-like migration and found several fragments closely linked with mitochondrial genes. Conclusion The G. hirsutum mt genome possesses most of the common characters of higher plant mt genomes. The existence of syntenic gene clusters, as well as the conservation of some intergenic sequences and genic content among the plant mt genomes suggest that evolution of mt genomes is consistent with plant taxonomy but independent among different species. PMID:23940520

  9. The complete mitochondrial genome of Gossypium hirsutum and evolutionary analysis of higher plant mitochondrial genomes.

    Directory of Open Access Journals (Sweden)

    Guozheng Liu

    Full Text Available BACKGROUND: Mitochondria are the main manufacturers of cellular ATP in eukaryotes. The plant mitochondrial genome contains large number of foreign DNA and repeated sequences undergone frequently intramolecular recombination. Upland Cotton (Gossypium hirsutum L. is one of the main natural fiber crops and also an important oil-producing plant in the world. Sequencing of the cotton mitochondrial (mt genome could be helpful for the evolution research of plant mt genomes. METHODOLOGY/PRINCIPAL FINDINGS: We utilized 454 technology for sequencing and combined with Fosmid library of the Gossypium hirsutum mt genome screening and positive clones sequencing and conducted a series of evolutionary analysis on Cycas taitungensis and 24 angiosperms mt genomes. After data assembling and contigs joining, the complete mitochondrial genome sequence of G. hirsutum was obtained. The completed G.hirsutum mt genome is 621,884 bp in length, and contained 68 genes, including 35 protein genes, four rRNA genes and 29 tRNA genes. Five gene clusters are found conserved in all plant mt genomes; one and four clusters are specifically conserved in monocots and dicots, respectively. Homologous sequences are distributed along the plant mt genomes and species closely related share the most homologous sequences. For species that have both mt and chloroplast genome sequences available, we checked the location of cp-like migration and found several fragments closely linked with mitochondrial genes. CONCLUSION: The G. hirsutum mt genome possesses most of the common characters of higher plant mt genomes. The existence of syntenic gene clusters, as well as the conservation of some intergenic sequences and genic content among the plant mt genomes suggest that evolution of mt genomes is consistent with plant taxonomy but independent among different species.

  10. Mitochondrial genome organization and phylogeny of two vespid wasps.

    Science.gov (United States)

    Cameron, Stephen L; Dowton, Mark; Castro, Lyda R; Ruberu, Kalani; Whiting, Michael F; Austin, Andy D; Diement, Kieren; Stevens, Julia

    2008-10-01

    We sequenced the entire mitochondrial genome of Abispa ephippium (Hymenoptera: Vespoidea: Vespidae: Eumeninae) and most of the mitochondrial genome of Polistes humilis synoecus (Hymenoptera: Vespoidea: Vespidae: Polistinae). The arrangement of genes differed between the two genomes and also differed slightly from that inferred to be ancestral for the Hymenoptera. The genome organization for both vespids is different from that of all other mitochondrial genomes previously reported. A number of tRNA gene rearrangements were identified that represent potential synapomorphies for a subset of the Vespidae. Analysis of all available hymenopteran mitochondrial genome sequences recovered an uncontroversial phylogeny, one consistent with analyses of other types of data.

  11. Mitochondrial genome organization and vertebrate phylogenetics

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    Pereira Sérgio Luiz

    2000-01-01

    Full Text Available With the advent of DNA sequencing techniques the organization of the vertebrate mitochondrial genome shows variation between higher taxonomic levels. The most conserved gene order is found in placental mammals, turtles, fishes, some lizards and Xenopus. Birds, other species of lizards, crocodilians, marsupial mammals, snakes, tuatara, lamprey, and some other amphibians and one species of fish have gene orders that are less conserved. The most probable mechanism for new gene rearrangements seems to be tandem duplication and multiple deletion events, always associated with tRNA sequences. Some new rearrangements seem to be typical of monophyletic groups and the use of data from these groups may be useful for answering phylogenetic questions involving vertebrate higher taxonomic levels. Other features such as the secondary structure of tRNA, and the start and stop codons of protein-coding genes may also be useful in comparisons of vertebrate mitochondrial genomes.

  12. Complete mitochondrial genome of Paramisgurnus dabryanus.

    Science.gov (United States)

    Dai, Luyi; Guo, Baoying; Chu, Zhangjie; Wang, Yong; Wang, Xiaojun; Huang, Tao

    2016-01-01

    In this study, the complete mitochondrial genome of Paramisgurnus dabryanus was obtained by PCR base on 18 pairs of primers. Among the 18 primers, the 14 primers were from the previously published universal primers for Cyprinus carpio L. mitogenome amplification. The remaining 4 primers were designed on the basis of related species mtDNA sequences. The genome is 16,570 bp in length, including 2 ribosomal RNA genes. 13 proteins-coding genes, 22 transfer RNA genes, and a non-coding control region, the gene composition and order of which was similar to most reported from other vertebrates. Sequence analysis showed that the overall base composition of Paramisgurnus dabryanus is T 27.3%, C 26.9%, A 28.5%, and G 17.4%. The sequence is a slight A + T bias of 55.8%, which is similar to other fishes. Mitochondrial genome is widely used in phylogenetic analysis, evolutionary genomics, species identification and related research of fish.

  13. Sequencing and comparing whole mitochondrial genomes ofanimals

    Energy Technology Data Exchange (ETDEWEB)

    Boore, Jeffrey L.; Macey, J. Robert; Medina, Monica

    2005-04-22

    Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, that can be especially powerful. We describe here the protocols commonly used for physically isolating mtDNA, for amplifying these by PCR or RCA, for cloning,sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based on our experiences to date with determining and comparing complete mtDNA sequences.

  14. The pseudo-mitochondrial genome influences mistakes in heteroplasmy interpretation

    Directory of Open Access Journals (Sweden)

    Wittock Roy

    2006-07-01

    Full Text Available Abstract Background Nuclear mitochondrial pseudogenes (numts are a potential source of contamination during mitochondrial DNA PCR amplification. This possibility warrants careful experimental design and cautious interpretation of heteroplasmic results. Results Here we report the cloning and sequencing of numts loci, amplified from human tissue and rho-zero (ρ0 cells (control with primers known to amplify the mitochondrial genome. This paper is the first to fully sequence 46 paralogous nuclear DNA fragments that represent the entire mitochondrial genome. This is a surprisingly small number due primarily to the primer sets used in this study, because prior to this, BLAST searches have suggested that nuclear DNA harbors between 400 to 1,500 paralogous mitochondrial DNA fragments. Our results indicate that multiple numts were amplified simultaneously with the mitochondrial genome and increased the load of pseudogene signal in PCR reactions. Further, the entire mitochondrial genome was represented by multiple copies of paralogous nuclear sequences. Conclusion These findings suggest that mitochondrial genome disease-associated biomarkers must be rigorously authenticated to preclude any affiliation with paralogous nuclear pseudogenes. Importantly, the common perception that mitochondrial template "swamps" numts loci precluding detectable amplification, depends on the region of the mitochondrial genome targeted by the PCR reaction and the number of pseudogene loci that may co-amplify. Cloning and relevant sequencing data will facilitate the correct interpretation. This is the first complete, wet-lab characterization of numts that represent the entire mitochondrial genome.

  15. The mitochondrial genome encodes abundant small noncoding RNAs

    Institute of Scientific and Technical Information of China (English)

    Seungil Ro; Hsiu-Yen Ma; Chanjae Park; Nicole Ortogero; Rui Song; Grant W Hennig; Huili Zheng

    2013-01-01

    Small noncoding RNAs identified thus far are all encoded by the nuclear genome.Here,we report that the murine and human mitochondriai genomes encode thousands of small noncoding RNAs,which are predominantly derived from the sense transcripts of the mitochondrial genes (host genes),and we termed these small RNAs mitochondrial genome-encoded small RNAs (mitosRNAs).DICER inactivation affected,but did not completely abolish mitosRNA production.MitosRNAs appear to be products of currently unidentified mitochondrial ribonucleases.Overexpression of mitosRNAs enhanced expression levels of their host genes in vitro,and dysregulated mitosRNA expression was generally associated with aberrant mitochondrial gene expression in vivo.Our data demonstrate that in addition to 37 known mitochondrial genes,the mammalian mitochondrial genome also encodes abundant mitosRNAs,which may play an important regulatory role in the control of mitochondrial gene expression in the cell.

  16. The complete mitochondrial genome of Dugesia japonica (Platyhelminthes; order Tricladida).

    Science.gov (United States)

    Sakai, Masato; Sakaizumi, Mitsuru

    2012-10-01

    We used two sequencing methods, namely long polymerase chain reaction (PCR) and primer walking, to determine the complete mitochondrial DNA (mtDNA) sequence of Dugesia japonica and most of the mtDNA sequence of Dugesia ryukyuensis. The genome of D. japonica contained 36 genes including 12 of the 13 protein-coding genes characteristic of metazoan mitochondrial genomes, two ribosomal RNA genes, and 22 transfer RNA genes. The genome of D. ryukyuensis contained 33 genes, including 12 protein-coding genes, two ribosomal RNA genes, and 19 transfer RNA genes. The gene order of the mitochondrial genome from the Dugesia species showed no clear homology with either the Neodermata or other free-living Rhabditophora. This indicates that the platyhelminths exhibit great variability in mitochondrial gene order. This is the first complete sequence analysis of the mitochondrial genome of a free-living member of Rhabditophora, which will facilitate further studies on the population genetics and genomic evolution of the Platyhelminthes.

  17. Mitochondrial genome of Micrura bella (Nemertea: Heteronemertea), the largest mitochondrial genome known to phylum Nemertea.

    Science.gov (United States)

    Shen, Chunyang; Shi-Chun, Sun

    2016-07-01

    The complete mitochondrial genome (mitogenome) of Micrura bella was sequenced and analyzed. Being the largest mitogenome known to phylum Nemertea, the genome is 16 847 bp in length. It encodes 37 genes typical to metazoan mitogenomes and has the same gene arrangement with the other Heteronemertea mitogenomes sequenced to date. The genome has the maximal number of non-coding nucleotides (2037 bp at 25 sites) in Nemertea mitogenomes, among which two large non-coding regions were found (507 and 508 bp, respectively).

  18. Genome digging: insight into the mitochondrial genome of Homo.

    Directory of Open Access Journals (Sweden)

    Igor V Ovchinnikov

    Full Text Available BACKGROUND: A fraction of the Neanderthal mitochondrial genome sequence has a similarity with a 5,839-bp nuclear DNA sequence of mitochondrial origin (numt on the human chromosome 1. This fact has never been interpreted. Although this phenomenon may be attributed to contamination and mosaic assembly of Neanderthal mtDNA from short sequencing reads, we explain the mysterious similarity by integration of this numt (mtAncestor-1 into the nuclear genome of the common ancestor of Neanderthals and modern humans not long before their reproductive split. PRINCIPAL FINDINGS: Exploiting bioinformatics, we uncovered an additional numt (mtAncestor-2 with a high similarity to the Neanderthal mtDNA and indicated that both numts represent almost identical replicas of the mtDNA sequences ancestral to the mitochondrial genomes of Neanderthals and modern humans. In the proteins, encoded by mtDNA, the majority of amino acids distinguishing chimpanzees from humans and Neanderthals were acquired by the ancestral hominins. The overall rate of nonsynonymous evolution in Neanderthal mitochondrial protein-coding genes is not higher than in other lineages. The model incorporating the ancestral hominin mtDNA sequences estimates the average divergence age of the mtDNAs of Neanderthals and modern humans to be 450,000-485,000 years. The mtAncestor-1 and mtAncestor-2 sequences were incorporated into the nuclear genome approximately 620,000 years and 2,885,000 years ago, respectively. CONCLUSIONS: This study provides the first insight into the evolution of the mitochondrial DNA in hominins ancestral to Neanderthals and humans. We hypothesize that mtAncestor-1 and mtAncestor-2 are likely to be molecular fossils of the mtDNAs of Homo heidelbergensis and a stem Homo lineage. The d(N/d(S dynamics suggests that the effective population size of extinct hominins was low. However, the hominin lineage ancestral to humans, Neanderthals and H. heidelbergensis, had a larger effective

  19. The mitochondrial genome of the soybean cyst nematode, Heterodera glycines.

    Science.gov (United States)

    Gibson, Tracey; Farrugia, Daniel; Barrett, Jeff; Chitwood, David J; Rowe, Janet; Subbotin, Sergei; Dowton, Mark

    2011-07-01

    We sequenced the entire coding region of the mitochondrial genome of Heterodera glycines. The sequence obtained comprised 14.9 kb, with PCR evidence indicating that the entire genome comprised a single, circular molecule of approximately 21-22 kb. The genome is the most T-rich nematode mitochondrial genome reported to date, with T representing over half of all nucleotides on the coding strand. The genome also contains the highest number of poly(T) tracts so far reported (to our knowledge), with 60 poly(T) tracts ≥ 12 Ts. All genes are transcribed from the same mitochondrial strand. The organization of the mitochondrial genome of H. glycines shows a number of similarities compared with Radopholus similis, but fewer similarities when compared with Meloidogyne javanica. Very few gene boundaries are shared with Globodera pallida or Globodera rostochiensis. Partial mitochondrial genome sequences were also obtained for Heterodera cardiolata (5.3 kb) and Punctodera chalcoensis (6.8 kb), and these had identical organizations compared with H. glycines. We found PCR evidence of a minicircular mitochondrial genome in P. chalcoensis, but at low levels and lacking a noncoding region. Such circularised genome fragments may be present at low levels in a range of nematodes, with multipartite mitochondrial genomes representing a shift to a condition in which these subgenomic circles predominate.

  20. The complete mitochondrial genome sequence of Emperor Penguins (Aptenodytes forsteri).

    Science.gov (United States)

    Xu, Qiwu; Xia, Yan; Dang, Xiao; Chen, Xiaoli

    2016-09-01

    The emperor penguin (Aptenodytes forsteri) is the largest living species of penguin. Herein, we first reported the complete mitochondrial genome of emperor penguin. The mitochondrial genome is a circular molecule of 17 301 bp in length, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA, and one control region. To verify the accuracy and the utility of new determined mitogenome sequences, we constructed the species phylogenetic tree of emperor penguin together with 10 other closely species. This is the second complete mitochondrial genome of penguin, and this is going to be an important data to study mitochondrial evolution of birds.

  1. The Mitochondrial Genome of Raphanus sativus and Gene Evolution of Cruciferous Mitochondrial Types

    Institute of Scientific and Technical Information of China (English)

    Shengxin Chang; Jianmei Chen; Yankun Wang; Bingchao Gu; Jianbo He; Pu Chu; Rongzhan Guan

    2013-01-01

    To explore the mitochondrial genes of the Cruciferae family,the mitochondrial genome of Raphanus sativus (sat) was sequenced and annotated.The circular mitochondrial genome of sat is 239,723 bp and includes 33 protein-coding genes,three rRNA genes and 17 tRNA genes.The mitochondrial genome also contains a pair of large repeat sequences 5.9 kb in length,which may mediate genome reorganization into two sub-genomic circles,with predicted sizes of 124.8 kb and 115.0 kb,respectively.Furthermore,gene evolution of mitochondrial genomes within the Cruciferae family was analyzed using sat mitochondrial type (mitotype),together with six other reported mitotypes.The cruciferous mitochondrial genomes have maintained almost the same set of functional genes.Compared with Cycas taitungensis (a representative gymnosperm),the mitochondrial genomes of the Cruciferae have lost nine protein-coding genes and seven mitochondrial-like tRNA genes,but acquired six chloroplast-like tRNAs.Among the Cruciferae,to maintain the same set of genes that are necessary for mitochondrial function,the exons of the genes have changed at the lowest rates,as indicated by the numbers of single nucleotide polymorphisms.The open reading frames (ORFs) of unknown function in the cruciferous genomes are not conserved.Evolutionary events,such as mutations,genome reorganizations and sequence insertions or deletions (indels),have resulted in the nonconserved ORFs in the cruciferous mitochondrial genomes,which is becoming significantly different among mitotypes.This work represents the first phylogenic explanation of the evolution of genes of known function in the Cruciferae family.It revealed significant variation in ORFs and the causes of such variation.

  2. The mitochondrial genome of Raphanus sativus and gene evolution of cruciferous mitochondrial types.

    Science.gov (United States)

    Chang, Shengxin; Chen, Jianmei; Wang, Yankun; Gu, Bingchao; He, Jianbo; Chu, Pu; Guan, Rongzhan

    2013-03-20

    To explore the mitochondrial genes of the Cruciferae family, the mitochondrial genome of Raphanus sativus (sat) was sequenced and annotated. The circular mitochondrial genome of sat is 239,723 bp and includes 33 protein-coding genes, three rRNA genes and 17 tRNA genes. The mitochondrial genome also contains a pair of large repeat sequences 5.9 kb in length, which may mediate genome reorganization into two sub-genomic circles, with predicted sizes of 124.8 kb and 115.0 kb, respectively. Furthermore, gene evolution of mitochondrial genomes within the Cruciferae family was analyzed using sat mitochondrial type (mitotype), together with six other reported mitotypes. The cruciferous mitochondrial genomes have maintained almost the same set of functional genes. Compared with Cycas taitungensis (a representative gymnosperm), the mitochondrial genomes of the Cruciferae have lost nine protein-coding genes and seven mitochondrial-like tRNA genes, but acquired six chloroplast-like tRNAs. Among the Cruciferae, to maintain the same set of genes that are necessary for mitochondrial function, the exons of the genes have changed at the lowest rates, as indicated by the numbers of single nucleotide polymorphisms. The open reading frames (ORFs) of unknown function in the cruciferous genomes are not conserved. Evolutionary events, such as mutations, genome reorganizations and sequence insertions or deletions (indels), have resulted in the non-conserved ORFs in the cruciferous mitochondrial genomes, which is becoming significantly different among mitotypes. This work represents the first phylogenic explanation of the evolution of genes of known function in the Cruciferae family. It revealed significant variation in ORFs and the causes of such variation.

  3. Complete mitochondrial genome of a Asian lion (Panthera leo goojratensis).

    Science.gov (United States)

    Li, Yu-Fei; Wang, Qiang; Zhao, Jian-ning

    2016-01-01

    The entire mitochondrial genome of this Asian lion (Panthera leo goojratensis) was 17,183 bp in length, gene composition and arrangement conformed to other lions, which contained the typical structure of 22 tRNAs, 2 rRNAs, 13 protein-coding genes and a non-coding region. The characteristic of the mitochondrial genome was analyzed in detail.

  4. Assessing the relative rate of (mitochondrial) genomic change.

    OpenAIRE

    Dowton, Mark

    2004-01-01

    I report a framework for assessing whether one mitochondrial genome is significantly more rearranged than another. This relative rate of gene rearrangement test (RGR) behaves according to expectation, distinguishing between highly rearranged and mildly rearranged insect mitochondrial genomes. It may be more broadly applied to assess the relative rate of nuclear gene rearrangement.

  5. Assessing the relative rate of (mitochondrial) genomic change.

    Science.gov (United States)

    Dowton, Mark

    2004-06-01

    I report a framework for assessing whether one mitochondrial genome is significantly more rearranged than another. This relative rate of gene rearrangement test (RGR) behaves according to expectation, distinguishing between highly rearranged and mildly rearranged insect mitochondrial genomes. It may be more broadly applied to assess the relative rate of nuclear gene rearrangement.

  6. Selfish drive can trump function when animal mitochondrial genomes compete

    OpenAIRE

    Ma, H.; O'Farrell, PH

    2016-01-01

    Mitochondrial genomes compete for transmission from mother to progeny. We explored this competition by introducing a second genome into Drosophila melanogaster to follow transmission. Competitions between closely related genomes favored those functional in electron transport, resulting in a host-beneficial purifying selection. In contrast, matchups between distantly related genomes often favored those with negligible, negative or lethal consequences, indicating selfish selection. Exhibiting p...

  7. Complete mitochondrial genome of the guppy (Poecilia reticulata).

    Science.gov (United States)

    Kong, Xiang-Fei; Li, Jiong-Tang; Sun, Xiao-Wen

    2016-01-01

    The guppy (Poecilia reticulata), a member of the Poeciliidae family, is one of the most popular aquarium fish. Here, we reported the complete mitochondrial genome of P. reticulata. The genome is 16,570 bp in length, including 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The structure of non-coding control region was also analyzed. Comparing the mitochondrial genome of P. reticulata with its congener Xiphophorus maculatus revealed the high sequence similarity and the identical gene structure. The complete mitochondrial genome of the guppy would help study the evolution of Poeciliidae family.

  8. The mitochondrial genome of Baylisascaris procyonis.

    Directory of Open Access Journals (Sweden)

    Yue Xie

    Full Text Available BACKGROUND: Baylisascaris procyonis (Nematoda: Ascaridida, an intestinal nematode of raccoons, is emerging as an important helminthic zoonosis due to serious or fatal larval migrans in animals and humans. Despite its significant veterinary and public health impact, the epidemiology, molecular ecology and population genetics of this parasite remain largely unexplored. Mitochondrial (mt genomes can provide a foundation for investigations in these areas and assist in the diagnosis and control of B. procyonis. In this study, the first complete mt genome sequence of B. procyonis was determined using a polymerase chain reaction (PCR-based primer-walking strategy. METHODOLOGY/PRINCIPAL FINDINGS: The circular mt genome (14781 bp of B. procyonis contained 12 protein-coding, 22 transfer RNA and 2 ribosomal RNA genes congruent with other chromadorean nematodes. Interestingly, the B. procyonis mtDNA featured an extremely long AT-rich region (1375 bp and a high number of intergenic spacers (17, making it unique compared with other secernentean nematodes characterized to date. Additionally, the entire genome displayed notable levels of AT skew and GC skew. Based on pairwise comparisons and sliding window analysis of mt genes among the available 11 Ascaridida mtDNAs, new primer pairs were designed to amplify specific short fragments of the genes cytb (548 bp fragment and rrnL (200 bp fragment in the B. procyonis mtDNA, and tested as possible alternatives to existing mt molecular beacons for Ascaridida. Finally, phylogenetic analysis of mtDNAs provided novel estimates of the interrelationships of Baylisasaris and Ascaridida. CONCLUSIONS/SIGNIFICANCE: The complete mt genome sequence of B. procyonis sequenced here should contribute to molecular diagnostic methods, epidemiological investigations and ecological studies of B. procyonis and other related ascaridoids. The information will be important in refining the phylogenetic relationships within the order

  9. An X-linked haplotype of Neandertal origin is present among all non-African populations.

    Science.gov (United States)

    Yotova, Vania; Lefebvre, Jean-Francois; Moreau, Claudia; Gbeha, Elias; Hovhannesyan, Kristine; Bourgeois, Stephane; Bédarida, Sandra; Azevedo, Luisa; Amorim, Antonio; Sarkisian, Tamara; Avogbe, Patrice Hodonou; Chabi, Nicodeme; Dicko, Mamoudou Hama; Kou' Santa Amouzou, Emile Sabiba; Sanni, Ambaliou; Roberts-Thomson, June; Boettcher, Barry; Scott, Rodney J; Labuda, Damian

    2011-07-01

    Recent work on the Neandertal genome has raised the possibility of admixture between Neandertals and the expanding population of Homo sapiens who left Africa between 80 and 50 Kya (thousand years ago) to colonize the rest of the world. Here, we provide evidence of a notable presence (9% overall) of a Neandertal-derived X chromosome segment among all contemporary human populations outside Africa. Our analysis of 6,092 X-chromosomes from all inhabited continents supports earlier contentions that a mosaic of lineages of different time depths and different geographic provenance could have contributed to the genetic constitution of modern humans. It indicates a very early admixture between expanding African migrants and Neandertals prior to or very early on the route of the out-of-Africa expansion that led to the successful colonization of the planet.

  10. Complete mitochondrial genome of a wild Siberian tiger.

    Science.gov (United States)

    Sun, Yujiao; Lu, Taofeng; Sun, Zhaohui; Guan, Weijun; Liu, Zhensheng; Teng, Liwei; Wang, Shuo; Ma, Yuehui

    2015-01-01

    In this study, the complete mitochondrial genome of Siberian tiger (Panthera tigris altaica) was sequenced, using muscle tissue obtained from a male wild tiger. The total length of the mitochondrial genome is 16,996 bp. The genome structure of this tiger is in accordance with other Siberian tigers and it contains 12S rRNA gene, 16S rRNA gene, 22 tRNA genes, 13 protein-coding genes, and 1 control region.

  11. The complete mitochondrial genome of the Yorkshire pig (Sus scrofa).

    Science.gov (United States)

    Xu, Dong; Yang, Hu; Ma, Haiming

    2016-01-01

    This study aims to identify the complete nucleotide sequence of mitochondrial genome in the Yorkshire pig. Sequence analysis indicates that the genome structure is in accordance with other pig breeds, and it contains 22 tRNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and 1 control region (D-loop region). The complete mitochondrial genome sequence of the Yorkshire pig provides an important record set for further study on genetic mechanism.

  12. The complete mitochondrial genome of Bufo raddei.

    Science.gov (United States)

    Zhang, Wenya; Zhang, Xingjie; Guo, Rui; Tang, Yue; Zhang, Yingmei

    2016-09-01

    The complete mitochondrial genome of Bufo raddei is carried out in the present research using Illumina Hiseq 2500. The mitogenome is 17 602 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a D-loop region. The overall base composition of the H-strand is 29.15% for A, 26.09% for C, 15.16% for G, and 29.60% for T. The G + C content is 41.25%. Phylogenetic analyses of B. raddei and other 12 amphibian were carried out using Bayesian phylogenetic methods. The sequences of B. raddei were clustered in genus Bufo.

  13. Interpopulation hybrid breakdown maps to the mitochondrial genome.

    Science.gov (United States)

    Ellison, Christopher K; Burton, Ronald S

    2008-03-01

    Hybrid breakdown, or outbreeding depression, is the loss of fitness observed in crosses between genetically divergent populations. The role of maternally inherited mitochondrial genomes in hybrid breakdown has not been widely examined. Using laboratory crosses of the marine copepod Tigriopus californicus, we report that the low fitness of F(3) hybrids is completely restored in the offspring of maternal backcrosses, where parental mitochondrial and nuclear genomic combinations are reassembled. Paternal backcrosses, which result in mismatched mitochondrial and nuclear genomes, fail to restore hybrid fitness. These results suggest that fitness loss in T. californicus hybrids is completely attributable to nuclear-mitochondrial genomic interactions. Analyses of ATP synthetic capacity in isolated mitochondria from hybrid and backcross animals found that reduced ATP synthesis in hybrids was also largely restored in backcrosses, again with maternal backcrosses outperforming paternal backcrosses. The strong fitness consequences of nuclear-mitochondrial interactions have important, and often overlooked, implications for evolutionary and conservation biology.

  14. Selfish drive can trump function when animal mitochondrial genomes compete.

    Science.gov (United States)

    Ma, Hansong; O'Farrell, Patrick H

    2016-07-01

    Mitochondrial genomes compete for transmission from mother to progeny. We explored this competition by introducing a second genome into Drosophila melanogaster to follow transmission. Competitions between closely related genomes favored those functional in electron transport, resulting in a host-beneficial purifying selection. In contrast, matchups between distantly related genomes often favored those with negligible, negative or lethal consequences, indicating selfish selection. Exhibiting powerful selfish selection, a genome carrying a detrimental mutation displaced a complementing genome, leading to population death after several generations. In a different pairing, opposing selfish and purifying selection counterbalanced to give stable transmission of two genomes. Sequencing of recombinant mitochondrial genomes showed that the noncoding region, containing origins of replication, governs selfish transmission. Uniparental inheritance prevents encounters between distantly related genomes. Nonetheless, in each maternal lineage, constant competition among sibling genomes selects for super-replicators. We suggest that this relentless competition drives positive selection, promoting change in the sequences influencing transmission.

  15. Complete mitochondrial genome of the medicinal mushroom Ganoderma lucidum.

    Directory of Open Access Journals (Sweden)

    Jianqin Li

    Full Text Available Ganoderma lucidum is one of the well-known medicinal basidiomycetes worldwide. The mitochondrion, referred to as the second genome, is an organelle found in most eukaryotic cells and participates in critical cellular functions. Elucidating the structure and function of this genome is important to understand completely the genetic contents of G. lucidum. In this study, we assembled the mitochondrial genome of G. lucidum and analyzed the differential expressions of its encoded genes across three developmental stages. The mitochondrial genome is a typical circular DNA molecule of 60,630 bp with a GC content of 26.67%. Genome annotation identified genes that encode 15 conserved proteins, 27 tRNAs, small and large rRNAs, four homing endonucleases, and two hypothetical proteins. Except for genes encoding trnW and two hypothetical proteins, all genes were located on the positive strand. For the repeat structure analysis, eight forward, two inverted, and three tandem repeats were detected. A pair of fragments with a total length around 5.5 kb was found in both the nuclear and mitochondrial genomes, which suggests the possible transfer of DNA sequences between two genomes. RNA-Seq data for samples derived from three stages, namely, mycelia, primordia, and fruiting bodies, were mapped to the mitochondrial genome and qualified. The protein-coding genes were expressed higher in mycelia or primordial stages compared with those in the fruiting bodies. The rRNA abundances were significantly higher in all three stages. Two regions were transcribed but did not contain any identified protein or tRNA genes. Furthermore, three RNA-editing sites were detected. Genome synteny analysis showed that significant genome rearrangements occurred in the mitochondrial genomes. This study provides valuable information on the gene contents of the mitochondrial genome and their differential expressions at various developmental stages of G. lucidum. The results contribute to the

  16. IMGD: an integrated platform supporting comparative genomics and phylogenetics of insect mitochondrial genomes

    Directory of Open Access Journals (Sweden)

    Jung Kyongyong

    2009-04-01

    Full Text Available Abstract Background Sequences and organization of the mitochondrial genome have been used as markers to investigate evolutionary history and relationships in many taxonomic groups. The rapidly increasing mitochondrial genome sequences from diverse insects provide ample opportunities to explore various global evolutionary questions in the superclass Hexapoda. To adequately support such questions, it is imperative to establish an informatics platform that facilitates the retrieval and utilization of available mitochondrial genome sequence data. Results The Insect Mitochondrial Genome Database (IMGD is a new integrated platform that archives the mitochondrial genome sequences from 25,747 hexapod species, including 112 completely sequenced and 20 nearly completed genomes and 113,985 partially sequenced mitochondrial genomes. The Species-driven User Interface (SUI of IMGD supports data retrieval and diverse analyses at multi-taxon levels. The Phyloviewer implemented in IMGD provides three methods for drawing phylogenetic trees and displays the resulting trees on the web. The SNP database incorporated to IMGD presents the distribution of SNPs and INDELs in the mitochondrial genomes of multiple isolates within eight species. A newly developed comparative SNU Genome Browser supports the graphical presentation and interactive interface for the identified SNPs/INDELs. Conclusion The IMGD provides a solid foundation for the comparative mitochondrial genomics and phylogenetics of insects. All data and functions described here are available at the web site http://www.imgd.org/.

  17. The complete mitochondrial genome of the geophilomorph centipede Strigamia maritima.

    Directory of Open Access Journals (Sweden)

    Helen E Robertson

    Full Text Available Strigamia maritima (Myriapoda; Chilopoda is a species from the soil-living order of geophilomorph centipedes. The Geophilomorpha is the most speciose order of centipedes with over a 1000 species described. They are notable for their large number of appendage bearing segments and are being used as a laboratory model to study the embryological process of segmentation within the myriapods. Using a scaffold derived from the recently published genome of Strigamia maritima that contained multiple mitochondrial protein-coding genes, here we report the complete mitochondrial genome of Strigamia, the first from any geophilomorph centipede. The mitochondrial genome of S. maritima is a circular molecule of 14,938 base pairs, within which we could identify the typical mitochondrial genome complement of 13 protein-coding genes and 2 ribosomal RNA genes. Sequences resembling 16 of the 22 transfer RNA genes typical of metazoan mitochondrial genomes could be identified, many of which have clear deviations from the standard 'cloverleaf' secondary structures of tRNA. Phylogenetic trees derived from the concatenated alignment of protein-coding genes of S. maritima and >50 other metazoans were unable to resolve the Myriapoda as monophyletic, but did support a monophyletic group of chilopods: Strigamia was resolved as the sister group of the scolopendromorph Scolopocryptos sp. and these two (Geophilomorpha and Scolopendromorpha, along with the Lithobiomorpha, formed a monophyletic group the Pleurostigmomorpha. Gene order within the S. maritima mitochondrial genome is unique compared to any other arthropod or metazoan mitochondrial genome to which it has been compared. The highly unusual organisation of the mitochondrial genome of Strigamia maritima is in striking contrast with the conservatively evolving nuclear genome: sampling of more members of this order of centipedes will be required to see whether this unusual organization is typical of the Geophilomorpha or

  18. Complete mitochondrial genome and phylogeny of Pleistocene mammoth Mammuthus primigenius.

    Directory of Open Access Journals (Sweden)

    Evgeny I Rogaev

    2006-03-01

    Full Text Available Phylogenetic relationships between the extinct woolly mammoth (Mammuthus primigenius, and the Asian (Elephas maximus and African savanna (Loxodonta africana elephants remain unresolved. Here, we report the sequence of the complete mitochondrial genome (16,842 base pairs of a woolly mammoth extracted from permafrost-preserved remains from the Pleistocene epoch--the oldest mitochondrial genome sequence determined to date. We demonstrate that well-preserved mitochondrial genome fragments, as long as approximately 1,600-1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests that M. primigenius and E. maximus are sister species that diverged soon after their common ancestor split from the L. africana lineage. Low nucleotide diversity found between independently determined mitochondrial genomic sequences of woolly mammoths separated geographically and in time suggests that north-eastern Siberia was occupied by a relatively homogeneous population of M. primigenius throughout the late Pleistocene.

  19. Ethics of modifying the mitochondrial genome

    NARCIS (Netherlands)

    Bredenoord, A. L.; Dondorp, W.; Pennings, G.; De Wert, G.

    Recent preclinical studies have shown the feasibility of specific variants of nuclear transfer to prevent mitochondrial DNA disorders. Nuclear transfer could be a valuable reproductive option for carriers of mitochondrial mutations. A clinical application of nuclear transfer, however, would entail

  20. Taenia hydatigena: isolation of mitochondrial DNA, molecular cloning, and physical mitochondrial genome mapping.

    Science.gov (United States)

    Yap, K W; Thompson, R C; Rood, J I; Pawlowski, I D

    1987-06-01

    Mitochondrial DNA was isolated from Taenia hydatigena, T. crassiceps, and Echinococcus granulosus using a cetyltrimethylammonium bromide precipitation technique. The technique is simple, rapid, reproducible, and does not require extensive high speed ultracentrifugation. The advantage of using mitochondrial DNA from taeniid cestodes for comparative restriction analysis was demonstrated. Mitochondrial DNA of T. hydatigena was isolated as covalently closed circular molecules. These were linearized by single digestion with BamHI and the molecular weight was estimated from the linear form of 17.6 kb. The mitochondrial DNA of T. hydatigena is therefore similar in size and structure to that of many other animal species. The entire mitochondrial genome was cloned into pBR322 in Escherichia coli and a restriction map of the recombinant molecule was constructed. The potential of using the cloned mitochondrial genome as a probe in speciation studies as well as for providing functional information on the role of the cestode mitochondrion is discussed.

  1. Whole mitochondrial genome genetic diversity in an Estonian population sample.

    Science.gov (United States)

    Stoljarova, Monika; King, Jonathan L; Takahashi, Maiko; Aaspõllu, Anu; Budowle, Bruce

    2016-01-01

    Mitochondrial DNA is a useful marker for population studies, human identification, and forensic analysis. Commonly used hypervariable regions I and II (HVI/HVII) were reported to contain as little as 25% of mitochondrial DNA variants and therefore the majority of power of discrimination of mitochondrial DNA resides in the coding region. Massively parallel sequencing technology enables entire mitochondrial genome sequencing. In this study, buccal swabs were collected from 114 unrelated Estonians and whole mitochondrial genome sequences were generated using the Illumina MiSeq system. The results are concordant with previous mtDNA control region reports of high haplogroup HV and U frequencies (47.4 and 23.7% in this study, respectively) in the Estonian population. One sample with the Northern Asian haplogroup D was detected. The genetic diversity of the Estonian population sample was estimated to be 99.67 and 95.85%, for mtGenome and HVI/HVII data, respectively. The random match probability for mtGenome data was 1.20 versus 4.99% for HVI/HVII. The nucleotide mean pairwise difference was 27 ± 11 for mtGenome and 7 ± 3 for HVI/HVII data. These data describe the genetic diversity of the Estonian population sample and emphasize the power of discrimination of the entire mitochondrial genome over the hypervariable regions.

  2. Timing of human protein evolution as revealed by massively parallel capture of Neandertal nuclear DNA sequences

    Science.gov (United States)

    Burbano, Hernán A.; Hodges, Emily; Green, Richard E.; Briggs, Adrian W.; Krause, Johannes; Meyer, Matthias; Good, Jeffrey M.; Maricic, Tomislav; Johnson, Philipp L.F.; Xuan, Zhenyu; Rooks, Michelle; Bhattacharjee, Arindam; Brizuela, Leonardo; Albert, Frank W.; de la Rasilla, Marco; Fortea, Javier; Rosas, Antonio; Lachmann, Michael; Hannon, Gregory J.; Pääbo, Svante

    2010-01-01

    Whole genome shotgun sequencing is now possible for extinct organisms, as well as the targeted capture of specific regions. However, targeted resequencing of megabase sized parts of nuclear genomes has yet to be demonstrated for ancient DNA. Here we show that hybridization capture on microarrays can be used to generate large scale targeted data from Neandertal DNA even in the presence of ~99.8% microbial DNA. It is thus now possible to generate high quality data from large regions of the nuclear genome from Neandertals and other extinct organisms. Using this approach we have sequenced ~14,000 protein coding positions that have been inferred to have changed on the human lineage since the last common ancestor shared with chimpanzees. We identify 88 amino acid substitutions that have become fixed in all humans since the divergence from the Neandertals. PMID:20448179

  3. The longest ultraconserved sequences and evolution of vertebrate mitochondrial genomes

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    We compared 753 genomes of bacteria, archaea, and mitochondria (more than 540 M data) and found four unique ultraconserved sequences in 352 vertebrate mitochondrial genomes which are the longest or second longest or third longest ultraconserved subsequences in the vertebrate mitochondrial genomes, their lengths are approximate to those of small RNA. Surprisingly, the classification and evolution relationship among some high-level categories of animals can be clearly reflected by their regularity of occurrence; moreover, these findings gave rise to some new ideas of evolution of mitochondria and living beings. For instance, the variations in mitochondrial genomes of animals may help clarify the evolution relationship between Aves and Reptile, and understand the fact that the origin of mitochondrion is at least not a simple copy of genomes of lower living things such as bacteria and archaea.

  4. Mitochondrial genome instability in colorectal adenoma and adenocarcinoma.

    Science.gov (United States)

    de Araujo, Luiza F; Fonseca, Aline S; Muys, Bruna R; Plaça, Jessica R; Bueno, Rafaela B L; Lorenzi, Julio C C; Santos, Anemari R D; Molfetta, Greice A; Zanette, Dalila L; Souza, Jorge E S; Valente, Valeria; Silva, Wilson A

    2015-11-01

    Mitochondrial dysfunction is regarded as a hallmark of cancer progression. In the current study, we evaluated mitochondrial genome instability and copy number in colorectal cancer using Next Generation Sequencing approach and qPCR, respectively. The results revealed higher levels of heteroplasmy and depletion of the relative mtDNA copy number in colorectal adenocarcinoma. Adenocarcinoma samples also presented an increased number of mutations in nuclear genes encoding proteins which functions are related with mitochondria fusion, fission and localization. Moreover, we found a set of mitochondrial and nuclear genes, which cooperate in the same mitochondrial function simultaneously mutated in adenocarcinoma. In summary, these results support an important role for mitochondrial function and genomic instability in colorectal tumorigenesis.

  5. Rolling circle amplification of complete nematode mitochondrial genomes.

    Science.gov (United States)

    Tang, Sha; Hyman, Bradley C

    2005-06-01

    To enable investigation of nematode mitochondrial DNA evolution, methodology has been developed to amplify intact nematode mitochondrial genomes in preparative yields using a rolling circle replication strategy. Successful reactions were generated from whole cell template DNA prepared by alkaline lysis of the rhabditid nematode Caenorhabditis elegans and a mermithid nematode, Thaumamermis cosgrovei. These taxa, representing the two major nematode classes Chromodorea and Enoplea, maintain mitochondrial genomes of 13.8 kb and 20.0 kb, respectively. Efficient amplifications were conducted on template DNA isolated from individual or pooled nematodes that were alive or stored at -80 degrees C. Unexpectedly, these experiments revealed that multiple T. cosgrovei mitochondrial DNA haplotypes are maintained in our local population. Rolling circle amplification products can be used as templates for standard PCR reactions with specific primers that target mitochondrial genes or for direct DNA sequencing.

  6. Complete mitochondrial genome of the Scorpaenopsis cirrhosa (Scorpaeniformes: Scorpaenidae).

    Science.gov (United States)

    Wu, Zhongjie; Wang, Daoru; Hu, Jing; Wang, Qian

    2016-09-01

    The complete mitochondrial genome of the Scorpaenopsis cirrhosa has been sequenced. The mitochondrial genome is 16 966 bp in length, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region. The gene order and composition of S. cirrhosa mitochondrial genome was similar to that of most other vertebrates. The overall nucleotides base composition of the heavy strand is A (27.91%), G (17.71%), C (28.02%), and T (26.35%). With the exception of the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. The tRNA-Ser2 gene lacked DHC arm and could not fold into a typical clover-leaf secondary structure. Seen from the phylogenetic tree, S. cirrhosa, a stonefish and four rockfishes from the same order (Scorpaeniformes) clustered into one branch.

  7. The complete mitochondrial genome of the Synanceia verrucosa (Scorpaeniformes: Synanceiidae).

    Science.gov (United States)

    Wang, Qian; Wang, Jun; Luo, Jian; Chen, Guohua

    2016-11-01

    The complete mitochondrial genome of the Synanceia verrucosa has been sequenced. The mitochondrial genome is 16,506 bp in length, containing 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region. The gene order and the composition of S. verrucosa mitochondrial genome were similar to that of most other vertebrates. The overall nucleotides base composition of the heavy strand is A (31.01%), G (15.06%), C (25.60%), and T (28.34%). With the exception of the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. The tRNA-Ser2 gene lacked DHC arm and could not fold into a typical clover-leaf secondary structure. Seen from the phylogenetic tree, a stonefish (S. verrucosa), two lionfishes, and eight rockfishes from the same order (Scorpaeniformes) clustered into one branch.

  8. The complete mitochondrial genome of the Piaractus brachypomus (Characiformes: Characidae).

    Science.gov (United States)

    Chen, Huanpu; Li, Shuisheng; Xie, Zhenzhen; Zhang, Yong; Zhu, Chunhua; Deng, Siping; Li, Guangli; Huang, Hai

    2016-01-01

    The complete mitochondrial genome of the Piaractus brachypomus is described in the present study. The mitochondrial genome is 16,561 bp long and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The P. brachypomus mitochondrial genome shows the similar gene order and composition with those of most other vertebrates. The nucleotide compositions of the light strand in descending order is 31.57% of A, 26.19% of C, 26.18% of T and 16.06% of G. With the exception of the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand.

  9. The complete mitochondrial genome of Cephalothrix simula (Iwata) (Nemertea: Palaeonemertea).

    Science.gov (United States)

    Chen, Hai-Xia; Sundberg, Per; Norenburg, Jon L; Sun, Shi-Chun

    2009-08-01

    The first complete mitochondrial genome sequence for a nemertean, Cephalothrix simula, was determined by conventional and long PCR and sequencing with primer walking methods. This circular genome is 16,296 bp in size and encodes 37 genes (13 protein-coding genes, 2 ribosomal RNAs, and 22 transfer RNAs) typically found in metazoans. All genes are encoded on H-strand except two tRNAs (trnT and trnP). It differs from those reported for other metazoans, but some gene junctions are shared with those of other protostomes. Structure of the mitochondrial genome of C. simula is mostly concordant with the partial mitochondrial genome known for Cephalothrix rufifrons, but notable differences include three large indel events and transposition of 2 tRNAs. Nucleotide composition of the mitochondrial genome of C. simula is highly A+T biased. The compositional skew is strongly reflected in the codon-usage patterns and the amino acid compositions of the mitochondrial proteins. An AT-rich noncoding region with potential to form stem-loop structures may be involved in the initiation of replication or transcription. Gene adjacencies and phylogenetic analysis based on the 12 concatenated amino acid sequences (except atp8) of mitochondrial protein-coding genes show that the nemertean is close to the coelomate lophotrochozoans, rather than the acoelomate platyhelminths.

  10. A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny.

    Science.gov (United States)

    Bernt, Matthias; Bleidorn, Christoph; Braband, Anke; Dambach, Johannes; Donath, Alexander; Fritzsch, Guido; Golombek, Anja; Hadrys, Heike; Jühling, Frank; Meusemann, Karen; Middendorf, Martin; Misof, Bernhard; Perseke, Marleen; Podsiadlowski, Lars; von Reumont, Björn; Schierwater, Bernd; Schlegel, Martin; Schrödl, Michael; Simon, Sabrina; Stadler, Peter F; Stöger, Isabella; Struck, Torsten H

    2013-11-01

    About 2800 mitochondrial genomes of Metazoa are present in NCBI RefSeq today, two thirds belonging to vertebrates. Metazoan phylogeny was recently challenged by large scale EST approaches (phylogenomics), stabilizing classical nodes while simultaneously supporting new sister group hypotheses. The use of mitochondrial data in deep phylogeny analyses was often criticized because of high substitution rates on nucleotides, large differences in amino acid substitution rate between taxa, and biases in nucleotide frequencies. Nevertheless, mitochondrial genome data might still be promising as it allows for a larger taxon sampling, while presenting a smaller amount of sequence information. We present the most comprehensive analysis of bilaterian relationships based on mitochondrial genome data. The analyzed data set comprises more than 650 mitochondrial genomes that have been chosen to represent a profound sample of the phylogenetic as well as sequence diversity. The results are based on high quality amino acid alignments obtained from a complete reannotation of the mitogenomic sequences from NCBI RefSeq database. However, the results failed to give support for many otherwise undisputed high-ranking taxa, like Mollusca, Hexapoda, Arthropoda, and suffer from extreme long branches of Nematoda, Platyhelminthes, and some other taxa. In order to identify the sources of misleading phylogenetic signals, we discuss several problems associated with mitochondrial genome data sets, e.g. the nucleotide and amino acid landscapes and a strong correlation of gene rearrangements with long branches.

  11. Archaeology. The makers of the Protoaurignacian and implications for Neandertal extinction.

    Science.gov (United States)

    Benazzi, S; Slon, V; Talamo, S; Negrino, F; Peresani, M; Bailey, S E; Sawyer, S; Panetta, D; Vicino, G; Starnini, E; Mannino, M A; Salvadori, P A; Meyer, M; Pääbo, S; Hublin, J-J

    2015-05-15

    The Protoaurignacian culture is pivotal to the debate about the timing of the arrival of modern humans in western Europe and the demise of Neandertals. However, which group is responsible for this culture remains uncertain. We investigated dental remains associated with the Protoaurignacian. The lower deciduous incisor from Riparo Bombrini is modern human, based on its morphology. The upper deciduous incisor from Grotta di Fumane contains ancient mitochondrial DNA of a modern human type. These teeth are the oldest human remains in an Aurignacian-related archaeological context, confirming that by 41,000 calendar years before the present, modern humans bearing Protoaurignacian culture spread into southern Europe. Because the last Neandertals date to 41,030 to 39,260 calendar years before the present, we suggest that the Protoaurignacian triggered the demise of Neandertals in this area.

  12. The mitochondrial genome of the lone star tick (Amblyomma americanum).

    Science.gov (United States)

    Williams-Newkirk, Amanda J; Burroughs, Mark; Changayil, Shankar S; Dasch, Gregory A

    2015-09-01

    Amblyomma americanum is an abundant tick in the southeastern, midwestern, and northeastern United States. It is a vector of multiple diseases, but limited genomic resources are available for it. We sequenced the complete mitochondrial genome of a single female A. americanum collected in Georgia using the Illumina platform. The consensus sequence was 14,709 bp long, and the mean coverage across the assembly was >12,000×. All expected tick genomic features were present, including two "Tick-Box" motifs, and in the expected order for the Metastriata. Heteroplasmy rates were low compared to the most closely related tick for which data are available, Amblyomma cajennense. The phylogeny derived from the concatenated protein coding and rRNA genes from the 33 available tick mitochondrial genomes was consistent with those previously proposed for the Acari. This is the first complete mitochondrial sequence for A. americanum, which provides a useful reference for future studies of A. americanum population genetics and tick phylogeny.

  13. Ethics of modifying the mitochondrial genome

    NARCIS (Netherlands)

    Bredenoord, A. L.; Dondorp, W.; Pennings, G.; De Wert, G.

    2011-01-01

    Recent preclinical studies have shown the feasibility of specific variants of nuclear transfer to prevent mitochondrial DNA disorders. Nuclear transfer could be a valuable reproductive option for carriers of mitochondrial mutations. A clinical application of nuclear transfer, however, would entail g

  14. Ethics of modifying the mitochondrial genome

    NARCIS (Netherlands)

    Bredenoord, A. L.; Dondorp, W.; Pennings, G.; De Wert, G.

    2011-01-01

    Recent preclinical studies have shown the feasibility of specific variants of nuclear transfer to prevent mitochondrial DNA disorders. Nuclear transfer could be a valuable reproductive option for carriers of mitochondrial mutations. A clinical application of nuclear transfer, however, would entail g

  15. The little brown bat nuclear genome contains an entire mitochondrial genome: Real or artifact?

    Science.gov (United States)

    Shi, Huizhen; Xing, Yutong; Mao, Xiuguang

    2017-09-20

    Nuclear mitochondrial DNA sequences (NUMTs) have been documented in almost all eukaryotic genomes studied. Recently, with the number of sequenced genomes increasing, extremely large NUMTs, even a nearly entire mitochondrial genome, have been reported in some plants and animals. However, few such studies provided strong experimental evidences for these important discoveries. In this study using a computer-based search method an entire mitochondrial genome (NUMT-1) was found in the nuclear genome of a bat species (Myotis lucifugus). This super-large NUMT shared a same scaffold with a 754bp nuclear genomic sequence and a second NUMT (NUMT-2, 3292bp). If NUMT-1 was real, it will be the largest NUMT found in animals and this finding will provide valuable insights into the mode of generation of NUMTs in the nuclear genome. Unfortunately, although the initial sequencing technology of the published M. lucifugus genome makes the possibility of artifact less likely, our results from both the PCR amplification followed by Sanger sequencing and mapping method based on the whole-genome resequencing datasets suggested that the scaffold containing the entire mitochondrial genome was artifact possibly due to a misassembly of mitochondrial and the nuclear DNA sequences. Our current study highlights the necessity to validate the authenticity of extremely large NUMTs identified in previous searches on whole-genome sequence assemblies. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. A mitochondrial genome sequence of the Tibetan antelope (Pantholops hodgsonii)

    DEFF Research Database (Denmark)

    Xu, Shu Qing; Yang, Ying Zhong; Zhou, Jun

    2005-01-01

    To investigate genetic mechanisms of high altitude adaptations of native mammals on the Tibetan Plateau, we compared mitochondrial sequences of the endangered Pantholops hodgsonii with its lowland distant relatives Ovis aries and Capra hircus, as well as other mammals. The complete mitochondrial...... genome of P. hodgsonii (16,498 bp) revealed a similar gene order as of other mammals. Because of tandem duplications, the control region of P. hodgsonii mitochondrial genome is shorter than those of O. aries and C. hircus, but longer than those of Bos species. Phylogenetic analysis based on alignments...... that the COXI (cytochrome c oxidase subunit I) gene was under positive selection in P. hodgsonii and Bos grunniens. Considering the same climates and environments shared by these two mammalian species, we proposed that the mitochondrial COXI gene is probably relevant for these native mammals to adapt the high...

  17. The mitochondrial genome of the venomous cone snail Conus consors.

    Directory of Open Access Journals (Sweden)

    Age Brauer

    Full Text Available Cone snails are venomous predatory marine neogastropods that belong to the species-rich superfamily of the Conoidea. So far, the mitochondrial genomes of two cone snail species (Conus textile and Conus borgesi have been described, and these feed on snails and worms, respectively. Here, we report the mitochondrial genome sequence of the fish-hunting cone snail Conus consors and describe a novel putative control region (CR which seems to be absent in the mitochondrial DNA (mtDNA of other cone snail species. This possible CR spans about 700 base pairs (bp and is located between the genes encoding the transfer RNA for phenylalanine (tRNA-Phe, trnF and cytochrome c oxidase subunit III (cox3. The novel putative CR contains several sequence motifs that suggest a role in mitochondrial replication and transcription.

  18. Complete mitochondrial genome of Esox reichertii (Amur pike).

    Science.gov (United States)

    Liu, Yu; Yang, Jun

    2015-01-01

    The whole mitochondrial genome of Esox reichertii (fish) was first sequenced and characterized. It was determined to be 16,909 bp long, which contains the control region (CR), the origin of light-strand replication (OL), 22 transfer RNA genes, 2 ribosomal genes and 13 protein-coding genes. Overall base composition of the complete mitochondrial DNA was 28.65% A, 28.67% T, 27.28% C and 15.41% G, with 57.32%AT.

  19. Neandertal cannibalism and Neandertal bones used as tools in Northern Europe.

    Science.gov (United States)

    Rougier, Hélène; Crevecoeur, Isabelle; Beauval, Cédric; Posth, Cosimo; Flas, Damien; Wißing, Christoph; Furtwängler, Anja; Germonpré, Mietje; Gómez-Olivencia, Asier; Semal, Patrick; van der Plicht, Johannes; Bocherens, Hervé; Krause, Johannes

    2016-07-06

    Almost 150 years after the first identification of Neandertal skeletal material, the cognitive and symbolic abilities of these populations remain a subject of intense debate. We present 99 new Neandertal remains from the Troisième caverne of Goyet (Belgium) dated to 40,500-45,500 calBP. The remains were identified through a multidisciplinary study that combines morphometrics, taphonomy, stable isotopes, radiocarbon dating and genetic analyses. The Goyet Neandertal bones show distinctive anthropogenic modifications, which provides clear evidence for butchery activities as well as four bones having been used for retouching stone tools. In addition to being the first site to have yielded multiple Neandertal bones used as retouchers, Goyet not only provides the first unambiguous evidence of Neandertal cannibalism in Northern Europe, but also highlights considerable diversity in mortuary behaviour among the region's late Neandertal population in the period immediately preceding their disappearance.

  20. Re-engineering the mitochondrial genomes in mammalian cells

    Science.gov (United States)

    Koob, Michael D; Yoo, Young Hyun

    2010-01-01

    Mitochondria are subcellular organelles composed of two discrete membranes in the cytoplasm of eukaryotic cells. They have long been recognized as the generators of energy for the cell and also have been known to associate with several metabolic pathways that are crucial for cellular function. Mitochondria have their own genome, mitochondrial DNA (mtDNA), that is completely separated and independent from the much larger nuclear genome, and even have their own system for making proteins from the genes in this mtDNA genome. The human mtDNA is a small (~16.5 kb) circular DNA and defects in this genome can cause a wide range of inherited human diseases. Despite of the significant advances in discovering the mtDNA defects, however, there are currently no effective therapies for these clinically devastating diseases due to the lack of technology for introducing specific modifications into the mitochondrial genomes and for generating accurate mtDNA disease models. The ability to engineer the mitochondrial genomes would provide a powerful tool to create mutants with which many crucial experiments can be performed in the basic mammalian mitochondrial genetic studies as well as in the treatment of human mtDNA diseases. In this review we summarize the current approaches associated with the correction of mtDNA mutations in cells and describe our own efforts for introducing engineered mtDNA constructs into the mitochondria of living cells through bacterial conjugation. PMID:21189990

  1. The complete mitochondrial genome sequence of the Daweishan Mini chicken.

    Science.gov (United States)

    Yan, Ming-Li; Ding, Su-Ping; Ye, Shao-Hui; Wang, Chun-Guang; He, Bao-Li; Yuan, Zhi-Dong; Liu, Li-Li

    2016-01-01

    Daweishan Mini chicken is a valuable chicken breed in China. In this study, the complete mitochondrial genome sequence of Daweishan Mini chicken using PCR amplification, sequencing and assembling has been obtained for the first time. The total length of the mitochondrial genome was 16,785 bp, with the base composition of 30.26% A, 23.73% T, 32.51% C, 13.51% G. It contained 37 genes (2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes) and a major non-coding control region (D-loop region). The protein start codons are ATG, except for COX1 that begins with GTG. The complete mitochondrial genome sequence of Daweishan Mini chicken provides an important data set for further investigation on the phylogenetic relationships within Gallus gallus.

  2. Complete mitochondrial genome of Nanjiang Yellow goat (Capra hircus).

    Science.gov (United States)

    Li, Haijun; Meng, Xiangren; Zhang, Hao; Duan, Xiaoyue; Niu, Lili; Wang, Linjie; Li, Li; Zhang, Hongping; Wu, Hongda; Zhong, Tao

    2016-01-01

    Nanjiang Yellow goat (Capra hircus) is the first cultured mutton breed in China. In this study, the complete mitochondrial genome sequence of Nanjiang Yellow goat has been identified for the first time. The total length of the mitochondrial genome was 16,639 bp, with the base composition of 33.54% A, 26.05% C, 13.11% G and 27.30% T. It contained 37 genes (22 transfer RNA genes, 2 ribosomal RNA genes, and 13 protein-coding genes) and a major non-coding control region (D-loop). Most of the genes have ATG initiation codons, whereas ND2, ND3 and ND5 start with ATA. The complete mitochondrial genome sequence of Nanjiang Yellow goat provides an important data set for further estimation on the phylogeographic structure of domestic goats.

  3. Expression of a transferred nuclear gene in a mitochondrial genome

    Directory of Open Access Journals (Sweden)

    Yichun Qiu

    2014-08-01

    Full Text Available Transfer of mitochondrial genes to the nucleus, and subsequent gain of regulatory elements for expression, is an ongoing evolutionary process in plants. Many examples have been characterized, which in some cases have revealed sources of mitochondrial targeting sequences and cis-regulatory elements. In contrast, there have been no reports of a nuclear gene that has undergone intracellular transfer to the mitochondrial genome and become expressed. Here we show that the orf164 gene in the mitochondrial genome of several Brassicaceae species, including Arabidopsis, is derived from the nuclear ARF17 gene that codes for an auxin responsive protein and is present across flowering plants. Orf164 corresponds to a portion of ARF17, and the nucleotide and amino acid sequences are 79% and 81% identical, respectively. Orf164 is transcribed in several organ types of Arabidopsis thaliana, as detected by RT-PCR. In addition, orf164 is transcribed in five other Brassicaceae within the tribes Camelineae, Erysimeae and Cardamineae, but the gene is not present in Brassica or Raphanus. This study shows that nuclear genes can be transferred to the mitochondrial genome and become expressed, providing a new perspective on the movement of genes between the genomes of subcellular compartments.

  4. The complete mitochondrial genome of the stomatopod crustacean Squilla mantis

    Directory of Open Access Journals (Sweden)

    Cook Charles E

    2005-08-01

    Full Text Available Abstract Background Animal mitochondrial genomes are physically separate from the much larger nuclear genomes and have proven useful both for phylogenetic studies and for understanding genome evolution. Within the phylum Arthropoda the subphylum Crustacea includes over 50,000 named species with immense variation in body plans and habitats, yet only 23 complete mitochondrial genomes are available from this subphylum. Results I describe here the complete mitochondrial genome of the crustacean Squilla mantis (Crustacea: Malacostraca: Stomatopoda. This 15994-nucleotide genome, the first described from a hoplocarid, contains the standard complement of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding AT-rich region that is found in most other metazoans. The gene order is identical to that considered ancestral for hexapods and crustaceans. The 70% AT base composition is within the range described for other arthropods. A single unusual feature of the genome is a 230 nucleotide non-coding region between a serine transfer RNA and the nad1 gene, which has no apparent function. I also compare gene order, nucleotide composition, and codon usage of the S. mantis genome and eight other malacostracan crustaceans. A translocation of the histidine transfer RNA gene is shared by three taxa in the order Decapoda, infraorder Brachyura; Callinectes sapidus, Portunus trituberculatus and Pseudocarcinus gigas. This translocation may be diagnostic for the Brachyura. For all nine taxa nucleotide composition is biased towards AT-richness, as expected for arthropods, and is within the range reported for other arthropods. Codon usage is biased, and much of this bias is probably due to the skew in nucleotide composition towards AT-richness. Conclusion The mitochondrial genome of Squilla mantis contains one unusual feature, a 230 base pair non-coding region has so far not been described in any other malacostracan. Comparisons with other

  5. Complete Mitochondrial Genome of Eruca sativa Mill. (Garden Rocket)

    OpenAIRE

    Yankun Wang; Pu Chu; Qing Yang; Shengxin Chang; Jianmei Chen; Maolong Hu; Rongzhan Guan

    2014-01-01

    Eruca sativa (Cruciferae family) is an ancient crop of great economic and agronomic importance. Here, the complete mitochondrial genome of Eruca sativa was sequenced and annotated. The circular molecule is 247,696 bp long, with a G+C content of 45.07%, containing 33 protein-coding genes, three rRNA genes, and 18 tRNA genes. The Eruca sativa mitochondrial genome may be divided into six master circles and four subgenomic molecules via three pairwise large repeats, resulting in a more dynamic st...

  6. Complete mitochondrial genome of Sicyopterus japonicus (Perciformes, Gobiidae).

    Science.gov (United States)

    Chiang, Tzen-Yuh; Chen, I-Shiung; Lin, Hung-Du; Chang, Wen-Been; Ju, Yu-Min

    2013-06-01

    In this study, we sequenced the complete mitochondrial genome of Sicyopterus japonicus (Perciformes, Gobiidae). This mitochondrial genome consists of 16,514 base pairs (bp), with 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 non-coding control region (CR), also with the gene synteny identical to that of typical vertebrates. CR, of 843 bp in length, is located between tRNA(Pro) and tRNA(Phe). The overall base composition of the heavy strand shows T 26.1%, C 28.7%, A 28.3%, and G 16.91%, with a slight AT bias of 54.4%.

  7. The mitochondrial genome of the entomoparasitic green alga helicosporidium.

    Directory of Open Access Journals (Sweden)

    Jean-François Pombert

    Full Text Available BACKGROUND: Helicosporidia are achlorophyllous, non-photosynthetic protists that are obligate parasites of invertebrates. Highly specialized, these pathogens feature an unusual cyst stage that dehisces inside the infected organism and releases a filamentous cell displaying surface projections, which will penetrate the host gut wall and eventually reproduce in the hemolymph. Long classified as incertae sedis or as relatives of other parasites such as Apicomplexa or Microsporidia, the Helicosporidia were surprisingly identified through molecular phylogeny as belonging to the Chlorophyta, a phylum of green algae. Most phylogenetic analyses involving Helicosporidia have placed them within the subgroup Trebouxiophyceae and further suggested a close affiliation between the Helicosporidia and the genus Prototheca. Prototheca species are also achlorophyllous and pathogenic, but they infect vertebrate hosts, inducing protothecosis in humans. The complete plastid genome of an Helicosporidium species was recently described and is a model of compaction and reduction. Here we describe the complete mitochondrial genome sequence of the same strain, Helicosporidium sp. ATCC 50920 isolated from the black fly Simulium jonesi. METHODOLOGY/PRINCIPAL FINDINGS: The circular mapping 49343 bp mitochondrial genome of Helicosporidium closely resembles that of the vertebrate parasite Prototheca wickerhamii. The two genomes share an almost identical gene complement and display a level of synteny that is higher than any other sequenced chlorophyte mitochondrial DNAs. Interestingly, the Helicosporidium mtDNA feature a trans-spliced group I intron, and a second group I intron that contains two open reading frames that appear to be degenerate maturase/endonuclease genes, both rare characteristics for this type of intron. CONCLUSIONS/SIGNIFICANCE: The architecture, genome content, and phylogeny of the Helicosporidium mitochondrial genome are all congruent with its close

  8. Mitochondrial DNA insertions in the nuclear Capra hircus genome.

    Science.gov (United States)

    Ning, F Y; Fu, J; Du, Z H

    2017-01-23

    Nuclear mitochondrial pseudogenes (numts), originating from mtDNA insertions into the nuclear genome, have been detected in many species. However, the distribution of numts in the newly published nuclear genome of domestic goat (Capra hircus) has not yet been explored. We used the entire goat mtDNA sequence and nuclear genome, to identify 118 numts using BLAST. Of these, 79 were able to map sequences to the genome. Further analysis showed that the size of the numts ranged from 318 to 9608 bp, and the homologous identity between numts and their respective corresponding mtDNA fragments varied between 65 and 99%. The identified Yunnan black goat numts covered nearly all the mitochondrial genes including mtDNA control region, and were distributed over all chromosomes with the exception of chromosomes 18, 21, and 25. The Y chromosome was excluded from our analysis, as sequence data are currently not available. Among the discovered 79 numts that we were able to map to the genome, 26 relatively complete mitochondrial genes were detected. Our results constitute valuable information for subsequent studies related to mitochondrial genes and goat evolution.

  9. Mitochondrial DNA insertions in the nuclear horse genome.

    Science.gov (United States)

    Nergadze, S G; Lupotto, M; Pellanda, P; Santagostino, M; Vitelli, V; Giulotto, E

    2010-12-01

    The insertion of mitochondrial DNA in the nuclear genome generates numts, nuclear sequences of mitochondrial origin. In the horse reference genome, we identified 82 numts and showed that the entire horse mitochondrial DNA is represented as numts without gross bias. Numts were inserted in the horse nuclear genome at random sites and were probably generated during the repair of DNA double-strand breaks. We then analysed 12 numt loci in 20 unrelated horses and found that null alleles, lacking the mitochondrial DNA insertion, were present at six of these loci. At some loci, the null allele is prevalent in the sample analysed, suggesting that, in the horse population, the number of numt loci may be higher than 82 present in the reference genome. Contrary to humans, the insertion polymorphism of numts is extremely frequent in the horse population, supporting the hypothesis that the genome of this species is in a rapidly evolving state. © 2010 The Authors, Journal compilation © 2010 Stichting International Foundation for Animal Genetics.

  10. Conflict between translation initiation and elongation in vertebrate mitochondrial genomes.

    Directory of Open Access Journals (Sweden)

    Xuhua Xia

    Full Text Available The strand-biased mutation spectrum in vertebrate mitochondrial genomes results in an AC-rich L-strand and a GT-rich H-strand. Because the L-strand is the sense strand of 12 protein-coding genes out of the 13, the third codon position is overall strongly AC-biased. The wobble site of the anticodon of the 22 mitochondrial tRNAs is either U or G to pair with the most abundant synonymous codon, with only one exception. The wobble site of Met-tRNA is C instead of U, forming the Watson-Crick match with AUG instead of AUA, the latter being much more frequent than the former. This has been attributed to a compromise between translation initiation and elongation; i.e., AUG is not only a methionine codon, but also an initiation codon, and an anticodon matching AUG will increase the initiation rate. However, such an anticodon would impose selection against the use of AUA codons because AUA needs to be wobble-translated. According to this translation conflict hypothesis, AUA should be used relatively less frequently compared to UUA in the UUR codon family. A comprehensive analysis of mitochondrial genomes from a variety of vertebrate species revealed a general deficiency of AUA codons relative to UUA codons. In contrast, urochordate mitochondrial genomes with two tRNA(Met genes with CAU and UAU anticodons exhibit increased AUA codon usage. Furthermore, six bivalve mitochondrial genomes with both of their tRNA-Met genes with a CAU anticodon have reduced AUA usage relative to three other bivalve mitochondrial genomes with one of their two tRNA-Met genes having a CAU anticodon and the other having a UAU anticodon. We conclude that the translation conflict hypothesis is empirically supported, and our results highlight the fine details of selection in shaping molecular evolution.

  11. Virtual ancestor reconstruction: Revealing the ancestor of modern humans and Neandertals.

    Science.gov (United States)

    Mounier, Aurélien; Mirazón Lahr, Marta

    2016-02-01

    The timing and geographic origin of the common ancestor of modern humans and Neandertals remain controversial. A poor Pleistocene hominin fossil record and the evolutionary complexities introduced by dispersals and regionalisation of lineages have fuelled taxonomic uncertainty, while new ancient genomic data have raised completely new questions. Here, we use maximum likelihood and 3D geometric morphometric methods to predict possible morphologies of the last common ancestor of modern humans and Neandertals from a simplified, fully resolved phylogeny. We describe the fully rendered 3D shapes of the predicted ancestors of humans and Neandertals, and assess their similarity to individual fossils or populations of fossils of Pleistocene age. Our results support models of an Afro-European ancestral population in the Middle Pleistocene (Homo heidelbergensis sensu lato) and further predict an African origin for this ancestral population. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. The complete mitochondrial genome of Dixella aestivalis (Diptera: Nematocera: Dixidae).

    Science.gov (United States)

    Briscoe, Andrew G; Sivell, Duncan; Harbach, Ralph E

    2017-01-01

    Dixidae, meniscus midges, belong to the suborder Nematocera of the order Diptera. The family includes 197 known species classified in nine genera. The complete mitochondrial genome of the Dixella aestivalis (Meigen) from the United Kingdom is reported here, along with its annotation and comparison with the genome of an unidentified species of Dixella from China. The circular genome consists of 16 465 bp and has a gene content consisting of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a non-coding, A + T-rich, control region. The mitochondrial genome of D. aestivalis can be used to identify genetic markers for species identification, and will be valuable for resolving phylogenetic relationships within the genus, family Dixidae and suborder Nematocera.

  13. The complete mitochondrial genome of Iwatanemertes piperata (Nemertea: Heteronemertea).

    Science.gov (United States)

    Shen, Chun-Yang; Sun, Wen-Yan; Sun, Shi-Chun

    2015-01-01

    The complete mitochondrial genome of Iwatanemertes piperata (Nemertea: Heteronemertea) was determined. The genome, which contains 13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes, is 16,382 bp in length and has a base composition of G (25.87%), A (21.53%), T (40.64%) and C (11.95%). The gene order is identical to other Heteronemertea mitogenomes published to date.

  14. The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)

    DEFF Research Database (Denmark)

    Miller, Webb; Drautz, Daniela I; Janecka, Jan E

    2009-01-01

    We report the first two complete mitochondrial genome sequences of the thylacine (Thylacinus cynocephalus), or so-called Tasmanian tiger, extinct since 1936. The thylacine's phylogenetic position within australidelphian marsupials has long been debated, and here we provide strong support for the ......We report the first two complete mitochondrial genome sequences of the thylacine (Thylacinus cynocephalus), or so-called Tasmanian tiger, extinct since 1936. The thylacine's phylogenetic position within australidelphian marsupials has long been debated, and here we provide strong support...... for the thylacine's basal position in Dasyuromorphia, aided by mitochondrial genome sequence that we generated from the extant numbat (Myrmecobius fasciatus). Surprisingly, both of our thylacine sequences differ by 11%-15% from putative thylacine mitochondrial genes in GenBank, with one of our samples originating...... from a direct offspring of the previously sequenced individual. Our data sample each mitochondrial nucleotide an average of 50 times, thereby providing the first high-fidelity reference sequence for thylacine population genetics. Our two sequences differ in only five nucleotides out of 15,452, hinting...

  15. Complete mitochondrial genome of Empoasca vitis (Hemiptera: Cicadellidae).

    Science.gov (United States)

    Zhou, Ningning; Wang, Mengxin; Cui, Lin; Chen, Xuexin; Han, Baoyu

    2016-01-01

    The complete mitochondrial genome of Empoasca vitis was sequenced. The length of the mitogenome is 15,154 bp with 78.35% AT content (GenBank accession No. KJ815009). The genome encode 37 typical mitochondrial genes including 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNA genes and an A+T-rich region. The gene arrangement is similar to that of Drosophila yakuba, the presumed ancestral insect mitochondrial gene arrangement. Except for cox2 using GTG as start codon, other protein-coding genes (PCGs) share the start codons ATN. Usual termination codon TAA and incomplete stop codon T are using by 13 protein-coding genes. The A+T-rich region has a length of 977 bp with the AT content high to 88.95%.

  16. Mutations of mitochondrial genome in patients with carotid atherosclerosis

    Directory of Open Access Journals (Sweden)

    Margarita A Sazonova

    2015-03-01

    Full Text Available With aim of detection the spectrum of mitochondrial DNA mutations in patients with carotid atherosclerosis from Moscow Region, we used a Roche 454 high-throughput sequencing of the whole mitochondrial genome. We have found that the presence of a number of homoplasmic mitochondrial DNA mutations in genes of 16S ribosomal RNA, subunits 2, 4 and 5 NADH dehydrogenase, subunits 1 and 2 cytochrome C oxidase, subunit 6 ATP-synthase, tRNA- Leu 2 and cytochrome B differed between conventionally healthy participants of the study and patients with carotid atherosclerosis. We also found heteroplasmic mutations, including insertions one or several nucleotides, that occurred more frequently in mitochondrial DNA of conventionally healthy participants of the study or patients with atherosclerotic lesions.

  17. The complete mitochondrial genome sequence of Diaphorina citri (Hemiptera: Psyllidae)

    Science.gov (United States)

    The first complete mitochondrial genome (mitogenome) sequence of Asian citrus psyllid, Diaphorina citri (Hemiptera: Psyllidae), from Guangzhou, China is presented. The circular mitogenome is 14,996 bp in length with an A+T content of 74.5%, and contains 13 protein-coding genes (PCGs), 22 tRNA genes ...

  18. Mitochondrial genome function and maternal inheritance.

    Science.gov (United States)

    Allen, John F; de Paula, Wilson B M

    2013-10-01

    The persistence of mtDNA to encode a small subset of mitochondrial proteins reflects the selective advantage of co-location of key respiratory chain subunit genes with their gene products. The disadvantage of this co-location is exposure of mtDNA to mutagenic ROS (reactive oxygen species), which are by-products of aerobic respiration. The resulting 'vicious circle' of mitochondrial mutation has been proposed to underlie aging and its associated degenerative diseases. Recent evidence is consistent with the hypothesis that oocyte mitochondria escape the aging process by acting as quiescent genetic templates, transcriptionally and bioenergetically repressed. Transmission of unexpressed mtDNA in the female germline is considered as a reason for the existence of separate sexes, i.e. male and female. Maternal inheritance then circumvents incremental accumulation of age-related disease in each new generation.

  19. Complete mitochondrial DNA genome of tetraploid Carassius auratus gibelio.

    Science.gov (United States)

    Li, Zhong; Liang, Hong-Wei; Zou, Gui-Wei

    2016-01-01

    The complete mitochondrial genome was sequenced from the tetraploid Carassius auratus gibelio in this study. The genome sequence was 16,576 bp in length. The mitochondrial genome contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and 2 non-coding regions (control region and origin of light-strand replication). All genes were encoded on the heavy strain except for ND6 and eight tRNA genes. The overall base composition is 31.61% A, 25.81% T, 26.62% G, 15.96% C, with an A+T bias of 57.42%. The complete mitogenome data provides useful genetic markers for the studies on the molecular identification, population genetics, phylogenetic analysis and conservation genetics.

  20. The complete mitochondrial genome of Lophiogobius ocellicauda (Perciformes, Gobiidae).

    Science.gov (United States)

    Quan, Xianqing; Jin, Xiaoxiao; Sun, Yuena

    2014-04-01

    Lophiogobius ocellicauda, which is a small demersal fish and inhabited brackish and freshwater environment of estuary, is a kind of forage fish of some predaceous economic fish. In this paper, the complete mitochondrial genome of L. ocellicauda was firstly determined. The genome is 16,663 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 main non-coding regions (the control region and the origin of the light strand replication). The complete mitochondrial genome base composition is 26.4% for T, 28.4% for C, 29.2% for A and 16.0% for G, with a slight A + T bias of 55.6%. Within the control region, the termination associated sequence, central and conserved sequence block domains were found.

  1. Phylogeny and evolution of Cervidae based on complete mitochondrial genomes.

    Science.gov (United States)

    Zhang, W-Q; Zhang, M-H

    2012-03-14

    Mitochondrial DNA sequences can be used to estimate phylogenetic relationships among animal taxa and for molecular phylogenetic evolution analysis. With the development of sequencing technology, more and more mitochondrial sequences have been made available in public databases, including whole mitochondrial DNA sequences. These data have been used for phylogenetic analysis of animal species, and for studies of evolutionary processes. We made phylogenetic analyses of 19 species of Cervidae, with Bos taurus as the outgroup. We used neighbor joining, maximum likelihood, maximum parsimony, and Bayesian inference methods on whole mitochondrial genome sequences. The consensus phylogenetic trees supported monophyly of the family Cervidae; it was divided into two subfamilies, Plesiometacarpalia and Telemetacarpalia, and four tribes, Cervinae, Muntiacinae, Hydropotinae, and Odocoileinae. The divergence times in these families were estimated by phylogenetic analysis using the Bayesian method with a relaxed molecular clock method; the results were consistent with those of previous studies. We concluded that the evolutionary structure of the family Cervidae can be reconstructed by phylogenetic analysis based on whole mitochondrial genomes; this method could be used broadly in phylogenetic evolutionary analysis of animal taxa.

  2. The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus).

    Science.gov (United States)

    Miller, Webb; Drautz, Daniela I; Janecka, Jan E; Lesk, Arthur M; Ratan, Aakrosh; Tomsho, Lynn P; Packard, Mike; Zhang, Yeting; McClellan, Lindsay R; Qi, Ji; Zhao, Fangqing; Gilbert, M Thomas P; Dalén, Love; Arsuaga, Juan Luis; Ericson, Per G P; Huson, Daniel H; Helgen, Kristofer M; Murphy, William J; Götherström, Anders; Schuster, Stephan C

    2009-02-01

    We report the first two complete mitochondrial genome sequences of the thylacine (Thylacinus cynocephalus), or so-called Tasmanian tiger, extinct since 1936. The thylacine's phylogenetic position within australidelphian marsupials has long been debated, and here we provide strong support for the thylacine's basal position in Dasyuromorphia, aided by mitochondrial genome sequence that we generated from the extant numbat (Myrmecobius fasciatus). Surprisingly, both of our thylacine sequences differ by 11%-15% from putative thylacine mitochondrial genes in GenBank, with one of our samples originating from a direct offspring of the previously sequenced individual. Our data sample each mitochondrial nucleotide an average of 50 times, thereby providing the first high-fidelity reference sequence for thylacine population genetics. Our two sequences differ in only five nucleotides out of 15,452, hinting at a very low genetic diversity shortly before extinction. Despite the samples' heavy contamination with bacterial and human DNA and their temperate storage history, we estimate that as much as one-third of the total DNA in each sample is from the thylacine. The microbial content of the two thylacine samples was subjected to metagenomic analysis, and showed striking differences between a wild-captured individual and a born-in-captivity one. This study therefore adds to the growing evidence that extensive sequencing of museum collections is both feasible and desirable, and can yield complete genomes.

  3. Complete mitochondrial genome of Nanorana pleskei (Amphibia: Anura: Dicroglossidae and evolutionary characteristics of the amphibian mitochondrial genomes

    Directory of Open Access Journals (Sweden)

    Guiying CHEN, Bin WANG, Jiongyu LIU, Feng XIE, Jianping JIANG

    2011-12-01

    Full Text Available The complete mitochondrial genome of Nanorana pleskei from the Qinghai-Tibet Plateau was sequenced. It includes 17,660 base pairs, containing 13 protein-coding genes, two rRNAs and 23 tRNAs. A tandem duplication of tRNAMet gene was found in this mitochondrial genome, and the similarity between the two tRNAMet genes is 85.8%, being the highest in amphibian mitochondrial genomes sequenced thus far. Based on gene organization, 24 types were found from 145 amphibian mitochondrial genomes. Type 1 was present in 108 species, type 11 in 11 species, types 5, 16, 17, and 20 each in two species, and the others each present in one species. Fifteen types were found in Anura, being the most diversity in three orders of the Lissamphibia. Our phylogenetic results using 11 protein-coding gene sequences of 145 amphibian mitochondrial genomes strongly support the monophyly of the Lissamphibia, as well as its three orders, the Gymnophiona, Caudata, and Anura, among which the relationships were ((Gymnophiona (Caudata, Anura. Based on the phylogenetic trees, type 1 was recognized as the ancestral type for amphibians, and type 11 was the synapomorphic type for the Neobatrachia. Gene rearrangements among lineages provide meaningful phylogenetic information. The rearrangement of the LTPF tRNA gene cluster and the translocation of the ND5 gene only found in the Neobatrachia support the monophyly of this group; similarly, the tandem duplication of the tRNAMet genes only found in the Dicroglossidae support the monophyly of this family [Current Zoology 57 (6: 785–805, 2011].

  4. Complete mitochondrial genome of the Siamese fighting fish (Betta splendens).

    Science.gov (United States)

    Song, Ying-Nan; Xiao, Gui-Bao; Li, Jiong-Tang

    2016-11-01

    The Siamese fighting fish (Betta splendens) is one of the popular aquarium fish. Serious attentions have been paid to the biodiversity of the fish. The mitochondrial genome of the Siamese fighting fish is reported to be 17 099 bp and includes 37 genes. The gene organization is similar to other fish mitogenomes. The control region is AT-rich and includes three tandem repeats. Phylogenetic analysis reveals that the fish is close to fish in the Macropodus genus. This mitogenome will assist in studying the mitochondrial variations and population structure in this fish and examine the evolutionary relationship among fish in the Osphronemidae family.

  5. Mitochondrial genome of the African lion Panthera leo leo.

    Science.gov (United States)

    Ma, Yue-ping; Wang, Shuo

    2015-01-01

    In this study, the complete mitochondrial genome sequence of the African lion P. leo leo was reported. The total length of the mitogenome was 17,054 bp. It contained the typical mitochondrial structure, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region; 21 of the tRNA genes folded into typical cloverleaf secondary structure except for tRNASe. The overall composition of the mitogenome was A (32.0%), G (14.5%), C (26.5%) and T (27.0%). The new sequence will provide molecular genetic information for conservation genetics study of this important large carnivore.

  6. Mitochondrial genome variability within the Candida parapsilosis species complex.

    Science.gov (United States)

    Valach, Matus; Pryszcz, Leszek P; Tomaska, Lubomir; Gacser, Attila; Gabaldón, Toni; Nosek, Jozef

    2012-09-01

    Candida parapsilosis species complex includes three closely related species, namely C. parapsilosis (sensu stricto), C. orthopsilosis, and C. metapsilosis. Unlike most other yeast lineages, members of this species complex possess a linear mitochondrial genome. Yet, its circularized mutant form was identified in strains of C. orthopsilosis and C. metapsilosis. To investigate the underlying variability, we performed comparative analyses of the complete mitochondrial DNA sequences in a collection of strains. Our results demonstrate that in contrast to C. parapsilosis and C. metapsilosis, C. orthopsilosis exhibits remarkably high nucleotide diversity whose pattern is consistent with intraspecific genetic exchange.

  7. Complete mitochondrial genome of Rhinogobius giurinus (Perciformes: Gobiidae: Gobionellinae).

    Science.gov (United States)

    Xie, Lingpeng; Yang, Xuefen; Ma, Zhihong; Yang, Ruibin

    2015-04-01

    In this study, we present the complete mitochondrial gene for the freshwater goby Rhinogobius giurinus. The genome is a circular molecule of 16,520 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and 2 main non-coding regions (the control region and the origin of the light strand replication). The overall base composition of R. giurinus is 26.08% for T, 29.56% for C, 27.73% for A and 16.63% for G, with a slight A + T bias of 53.81%. It has the typical vertebrate mitochondrial gene arrangement.

  8. Complete sequence of the mitochondrial genome of a diatom alga Synedra acus and comparative analysis of diatom mitochondrial genomes.

    Science.gov (United States)

    Ravin, Nikolai V; Galachyants, Yuri P; Mardanov, Andrey V; Beletsky, Alexey V; Petrova, Darya P; Sherbakova, Tatyana A; Zakharova, Yuliya R; Likhoshway, Yelena V; Skryabin, Konstantin G; Grachev, Mikhail A

    2010-06-01

    The first two mitochondrial genomes of marine diatoms were previously reported for the centric Thalassiosira pseudonana and the raphid pennate Phaeodactylum tricornutum. As part of a genomic project, we sequenced the complete mitochondrial genome of the freshwater araphid pennate diatom Synedra acus. This 46,657 bp mtDNA encodes 2 rRNAs, 24 tRNAs, and 33 proteins. The mtDNA of S. acus contains three group II introns, two inserted into the cox1 gene and containing ORFs, and one inserted into the rnl gene and lacking an ORF. The compact gene organization contrasts with the presence of a 4.9-kb-long intergenic region, which contains repeat sequences. Comparison of the three sequenced mtDNAs showed that these three genomes carry similar gene pools, but the positions of some genes are rearranged. Phylogenetic analysis performed with a fragment of the cox1 gene of diatoms and other heterokonts produced a tree that is similar to that derived from 18S RNA genes. The introns of mtDNA in the diatoms seem to be polyphyletic. This study demonstrates that pyrosequencing is an efficient method for complete sequencing of mitochondrial genomes from diatoms, and may soon give valuable information about the molecular phylogeny of this outstanding group of unicellular organisms.

  9. The complete mitochondrial genome of eastern lowland gorilla, Gorilla beringei graueri, and comparative mitochondrial genomics of Gorilla species.

    Science.gov (United States)

    Hu, Xiao-di; Gao, Li-zhi

    2016-01-01

    In this study, we determined the complete mitochondrial (mt) genome of eastern lowland gorilla, Gorilla beringei graueri for the first time. The total genome was 16,416 bp in length. It contained a total of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region (D-loop region). The base composition was A (30.88%), G (13.10%), C (30.89%) and T (25.13%), indicating that the percentage of A+T (56.01%) was higher than G+C (43.99%). Comparisons with the other publicly available Gorilla mitogenome showed the conservation of gene order and base compositions but a bunch of nucleotide diversity. This complete mitochondrial genome sequence will provide valuable genetic information for further studies on conservation genetics of eastern lowland gorilla.

  10. Genome-Wide Analysis Reveals Coating of the Mitochondrial Genome by TFAM

    OpenAIRE

    Wang, Yun E.; Marinov, Georgi K.; Wold, Barbara J.; Chan, David C.

    2013-01-01

    Mitochondria contain a 16.6 kb circular genome encoding 13 proteins as well as mitochondrial tRNAs and rRNAs. Copies of the genome are organized into nucleoids containing both DNA and proteins, including the machinery required for mtDNA replication and transcription. The transcription factor TFAM is critical for initiation of transcription and replication of the genome, and is also thought to perform a packaging function. Although specific binding sites required for initiation of transcriptio...

  11. Unexpectedly Streamlined Mitochondrial Genome of the Euglenozoan Euglena gracilis.

    Science.gov (United States)

    Dobáková, Eva; Flegontov, Pavel; Skalický, Tomáš; Lukeš, Julius

    2015-11-20

    In this study, we describe the mitochondrial genome of the excavate flagellate Euglena gracilis. Its gene complement is reduced as compared with the well-studied sister groups Diplonemea and Kinetoplastea. We have identified seven protein-coding genes: Three subunits of respiratory complex I (nad1, nad4, and nad5), one subunit of complex III (cob), and three subunits of complex IV (cox1, cox2, and a highly divergent cox3). Moreover, fragments of ribosomal RNA genes have also been identified. Genes encoding subunits of complex V, ribosomal proteins and tRNAs were missing, and are likely located in the nuclear genome. Although mitochondrial genomes of diplonemids and kinetoplastids possess the most complex RNA processing machineries known, including trans-splicing and editing of the uridine insertion/deletion type, respectively, our transcriptomic data suggest their total absence in E. gracilis. This finding supports a scenario in which the complex mitochondrial processing machineries of both sister groups evolved relatively late in evolution from a streamlined genome and transcriptome of their common predecessor.

  12. Mitochondrial genome evolution in fire ants (Hymenoptera: Formicidae).

    Science.gov (United States)

    Gotzek, Dietrich; Clarke, Jessica; Shoemaker, DeWayne

    2010-10-07

    Complete mitochondrial genome sequences have become important tools for the study of genome architecture, phylogeny, and molecular evolution. Despite the rapid increase in available mitogenomes, the taxonomic sampling often poorly reflects phylogenetic diversity and is often also biased to represent deeper (family-level) evolutionary relationships. We present the first fully sequenced ant (Hymenoptera: Formicidae) mitochondrial genomes. We sampled four mitogenomes from three species of fire ants, genus Solenopsis, which represent various evolutionary depths. Overall, ant mitogenomes appear to be typical of hymenopteran mitogenomes, displaying a general A+T-bias. The Solenopsis mitogenomes are slightly more compact than other hymentoperan mitogenomes (~15.5 kb), retaining all protein coding genes, ribosomal, and transfer RNAs. We also present evidence of recombination between the mitogenomes of the two conspecific Solenopsis mitogenomes. Finally, we discuss potential ways to improve the estimation of phylogenies using complete mitochondrial genome sequences. The ant mitogenome presents an important addition to the continued efforts in studying hymenopteran mitogenome architecture, evolution, and phylogenetics. We provide further evidence that the sampling across many taxonomic levels (including conspecifics and congeners) is useful and important to gain detailed insights into mitogenome evolution. We also discuss ways that may help improve the use of mitogenomes in phylogenetic analyses by accounting for non-stationary and non-homogeneous evolution among branches.

  13. Complete mitochondrial genome of Hirudo nipponia (Annelida, Hirudinea).

    Science.gov (United States)

    Xu, Yunling; Nie, Jing; Hou, Junjie; Xiao, Ling; Lv, Pan

    2016-01-01

    The complete mitochondrial genome (14,414 bp) of the blood-feeding leech Hirudo nipponia, which was an important natural medicinal resource, was sequenced and characterized. The genome encodes 13 protein-coding genes, 2 rRNAs and 22 tRNAs. The content of A + T was 72.60% for H. nipponia (31.69% A, 40.91% T, 15.45% G and 11.95% C). All protein-coding genes started with ATN except for nad3 and nad5, which used GTG as start codon. Eight protein-coding genes stopped with termination codon TAA. Five protein-coding genes used incomplete stop codon TA or T. The A + T-rich region was located between tRNA-Arg and tRNA-His with a length of 83 bp. This is the first report about completely sequenced mitochondrial genome from the family Hirudinidae. The complete mitochondrial genomes of H. nipponia would be useful for the exploration of Hirudinea polygenetic relationships.

  14. Complete DNA sequences of the mitochondrial genomes of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis: insight into the evolution of linear DNA genomes from mitochondrial telomere mutants.

    Science.gov (United States)

    Kosa, Peter; Valach, Matus; Tomaska, Lubomir; Wolfe, Kenneth H; Nosek, Jozef

    2006-01-01

    We determined complete mitochondrial DNA sequences of the two yeast species, Candida orthopsilosis and Candida metapsilosis, and compared them with the linear mitochondrial genome of their close relative, C.parapsilosis. Mitochondria of all the three species harbor compact genomes encoding the same set of genes arranged in the identical order. Differences in the length of these genomes result mainly from the presence/absence of introns. Multiple alterations were identified also in the sequences of the ribosomal and transfer RNAs, and proteins. However, the most striking feature of C.orthopsilosis and C.metapsilosis is the existence of strains differing in the molecular form of the mitochondrial genome (circular-mapping versus linear). Their analysis opens a unique window for understanding the role of mitochondrial telomeres in the stability and evolution of molecular architecture of the genome. Our results indicate that the circular-mapping mitochondrial genome derived from the linear form by intramolecular end-to-end fusions. Moreover, we suggest that the linear mitochondrial genome evolved from a circular-mapping form present in a common ancestor of the three species and, at the same time, the emergence of mitochondrial telomeres enabled the formation of linear monomeric DNA forms. In addition, comparison of isogenic C.metapsilosis strains differing in the form of the organellar genome suggests a possibility that, under some circumstances, the linearity and/or the presence of telomeres provide a competitive advantage over a circular-mapping mitochondrial genome.

  15. Complete mitochondrial genome of Naumann's thrush Turdus naumanni (Passeriformes: Turdidae).

    Science.gov (United States)

    Li, Bo; Zhou, Lizhi; Liu, Gang; Gu, Changming

    2016-01-01

    The mitochondrial DNA of Naumann's thrush Turdus naumanni (Passeriformes: Turdidae) is 16,750 bp long with A + T contents of 52.79%. It has typical circular mitochondrial genomes that encode the complete set of 37 genes which are usually found in birds. All protein-coding genes use the standard mitochondrial initiation codon ATG, except for ND2 and COI start with GTG. TAN is the most frequent stop codon, and AGN and T- - are also occurred very common. All tRNAs possess the classic clover leaf secondary structure except for tRNA(Ser(AGN)) and tRNA(Lys(CUN)), which lack the "DHU" stem, only forming a simple loop.

  16. Rearrangement and evolution of mitochondrial genomes in parrots.

    Science.gov (United States)

    Eberhard, Jessica R; Wright, Timothy F

    2016-01-01

    Mitochondrial genome rearrangements that result in control region duplication have been described for a variety of birds, but the mechanisms leading to their appearance and maintenance remain unclear, and their effect on sequence evolution has not been explored. A recent survey of mitochondrial genomes in the Psittaciformes (parrots) found that control region duplications have arisen independently at least six times across the order. We analyzed complete mitochondrial genome sequences from 20 parrot species, including representatives of each lineage with control region duplications, to document the gene order changes and to examine effects of genome rearrangements on patterns of sequence evolution. The gene order previously reported for Amazona parrots was found for four of the six independently derived genome rearrangements, and a previously undescribed gene order was found in Prioniturus luconensis, representing a fifth clade with rearranged genomes; the gene order resulting from the remaining rearrangement event could not be confirmed. In all rearranged genomes, two copies of the control region are present and are very similar at the sequence level, while duplicates of the other genes involved in the rearrangement show signs of degeneration or have been lost altogether. We compared rates of sequence evolution in genomes with and without control region duplications and did not find a consistent acceleration or deceleration associated with the duplications. This could be due to the fact that most of the genome rearrangement events in parrots are ancient, and additionally, to an effect of body size on evolutionary rate that we found for mitochondrial but not nuclear sequences. Base composition analyses found that relative to other birds, parrots have unusually strong compositional asymmetry (AT- and GC-skew) in their coding sequences, especially at fourfold degenerate sites. Furthermore, we found higher AT skew in species with control region duplications. One

  17. Mitochondrial genome analysis of the predatory mite Phytoseiulus persimilis and a revisit of the Metaseiulus occidentalis mitochondrial genome.

    Science.gov (United States)

    Dermauw, Wannes; Vanholme, Bartel; Tirry, Luc; Van Leeuwen, Thomas

    2010-04-01

    In this study we sequenced and analysed the complete mitochondrial (mt) genome of the Chilean predatory mite Phytoseiulus persimilis Athias-Henriot (Chelicerata: Acari: Mesostigmata: Phytoseiidae: Amblyseiinae). The 16 199 bp genome (79.8% AT) contains the standard set of 13 protein-coding and 24 RNA genes. Compared with the ancestral arthropod mtDNA pattern, the gene order is extremely reshuffled (35 genes changed position) and represents a novel arrangement within the arthropods. This is probably related to the presence of several large noncoding regions in the genome. In contrast with the mt genome of the closely related species Metaseiulus occidentalis (Phytoseiidae: Typhlodrominae) - which was reported to be unusually large (24 961 bp), to lack nad6 and nad3 protein-coding genes, and to contain 22 tRNAs without T-arms - the genome of P. persimilis has all the features of a standard metazoan mt genome. Consequently, we performed additional experiments on the M. occidentalis mt genome. Our preliminary restriction digests and Southern hybridization data revealed that this genome is smaller than previously reported. In addition, we cloned nad3 in M. occidentalis and positioned this gene between nad4L and 12S-rRNA on the mt genome. Finally, we report that at least 15 of the 22 tRNAs in the M. occidentalis mt genome can be folded into canonical cloverleaf structures similar to their counterparts in P. persimilis.

  18. Efficient Mitochondrial Genome Editing by CRISPR/Cas9

    Directory of Open Access Journals (Sweden)

    Areum Jo

    2015-01-01

    Full Text Available The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9 system has been widely used for nuclear DNA editing to generate mutations or correct specific disease alleles. Despite its flexible application, it has not been determined if CRISPR/Cas9, originally identified as a bacterial defense system against virus, can be targeted to mitochondria for mtDNA editing. Here, we show that regular FLAG-Cas9 can localize to mitochondria to edit mitochondrial DNA with sgRNAs targeting specific loci of the mitochondrial genome. Expression of FLAG-Cas9 together with gRNA targeting Cox1 and Cox3 leads to cleavage of the specific mtDNA loci. In addition, we observed disruption of mitochondrial protein homeostasis following mtDNA truncation or cleavage by CRISPR/Cas9. To overcome nonspecific distribution of FLAG-Cas9, we also created a mitochondria-targeted Cas9 (mitoCas9. This new version of Cas9 localizes only to mitochondria; together with expression of gRNA targeting mtDNA, there is specific cleavage of mtDNA. MitoCas9-induced reduction of mtDNA and its transcription leads to mitochondrial membrane potential disruption and cell growth inhibition. This mitoCas9 could be applied to edit mtDNA together with gRNA expression vectors without affecting genomic DNA. In this brief study, we demonstrate that mtDNA editing is possible using CRISPR/Cas9. Moreover, our development of mitoCas9 with specific localization to the mitochondria should facilitate its application for mitochondrial genome editing.

  19. Accelerated evolution of the mitochondrial genome in an alloplasmic line of durum wheat

    Science.gov (United States)

    Wheat is not only an important crop but also an excellent plant species for nuclear mitochondrial interaction studies. To investigate the level of sequence changes introduced into the mitochondrial genome under the alloplasmic conditions, three mitochondrial genomes of Triticum-Aegilops species w...

  20. Mitochondrial genome interrogation for forensic casework and research studies.

    Science.gov (United States)

    Roby, Rhonda K; Sprouse, Marc; Phillips, Nicole; Alicea-Centeno, Alessandra; Shewale, Shantanu; Shore, Sabrina; Paul, Natasha

    2014-04-24

    This unit describes methods used in the analysis of mitochondrial DNA (mtDNA) for forensic and research applications. UNIT describes procedures specifically for forensic casework where the DNA from evidentiary material is often degraded or inhibited. In this unit, protocols are described for quantification of mtDNA before amplification; amplification of the entire control region from high-quality samples as well as procedures for interrogating the whole mitochondrial genome (mtGenome); quantification of mtDNA post-amplification; and, post-PCR cleanup and sequencing. The protocols for amplification were developed for high-throughput databasing applications for forensic DNA testing such as reference samples and population studies. However, these same protocols can be applied to biomedical research such as age-related disease and health disparities research.

  1. The complete mitochondrial genome of Liobagrus kingi (Teleostei, Siluriformes: Amblycipitidae).

    Science.gov (United States)

    Jia, Xiang-Yang; Li, Ying-Wen; Wang, Deng-Qiang; Tian, Hui-Wu; Xiong, Xing; Li, Shu-Hua; Chen, Da-Qing

    2013-08-01

    Liobagrus kingi is endemic to southwest China and listed as endangered species (IUCN 2012). Genetic diversity is necessary for conservation issue. In studying this, the complete mitochondrial genome sequence of L. kingi has been obtained with PCR, which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region with the total length of 16,483 bp. The gene arrangement and composition are similar to that of other vertebrates. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. Just like most other vertebrates, the against bias of G has a universality in different statistical results. The complete mitochondrial genome sequence of L. kingi would contribute to better understand population genetics and protect its genetic diversity.

  2. Complete mitochondrial DNA genome of Zacco platypus (Cypriniformes: Cyprinidae).

    Science.gov (United States)

    Ueng, Yih-Tsong; Chen, Kun-Neng; Han, Chiao-Chuan; Cheng, Chung-Yao; Li, Yi-Min

    2015-04-01

    The complete mitochondrial genome of Zacco platypus (Cypriniformes, Cyprinidae), which has broader distribution range and diverse genetic structure than other species under the genus Zacco, was first determined in this study. The mitochondrial genome is 16,612 base pairs (bp) in length, encoding 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and 1 non-coding control region. Its gene arrangement and translation direction were identical to those of other typical vertebrate. Control region (D-Loop), of 929 bp lengths long, is located between tRNA(Pro) and tRNA(Phe). The overall base composition of the heavy strand shows T 27.02%, C 26.23%, A 28.94% and G 17.82%, with a slight AT bias of 55.95%.

  3. Complete mitochondrial DNA genome of Microphysogobio brevirostris (Cypriniformes: Cyprinidae).

    Science.gov (United States)

    Cheng, Chung-Yao; Wang, Jiang-Ping; Ho, Chuan-Wen; Cheng, Ju-Wen; Ueng, Yih-Tsong

    2015-04-01

    In this study, we sequenced the complete mitochondrial genome of Microphysogobio brevirostris (Cypriniformes, Cyprinidae), an endemic primary freshwater fish in Taiwan. This mitochondrial genome, consisting of 16,608 base pairs (bp), encoded 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a non-coding control region as those found in other vertebrates, with the gene synteny identical to that of typical vertebrates. Control region (D-Loop), of 929 bp lengths long, is located between tRNA(Pro) and tRNA(Phe). The overall base composition of the heavy strand shows T 26.28%, C 26.62%, A 30.26%, and G 16.85%, with a slight AT bias of 56.53%.

  4. The complete mitochondrial genome of Lista haraldusalis (Lepidoptera: Pyralidae).

    Science.gov (United States)

    Ye, Fei; Yu, Hai-Li; Li, Peng-Fei; You, Ping

    2015-01-01

    We have determined the complete mitochondrial genome of Lista haraldusalis Walker, 1859. The mitochondrial genome of L. haraldusalis is 15,213 bp in size with 81.5% A+T content. It consists of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), 2 ribosomal RNA (rRNA) genes and an A+T-rich region. All PCGs start with ATN codon, except for COI, which begins with TTAG. Eleven PCGs stop with typical stop codon TAA and TAG. But ND6 and COII use incomplete stop codon T. All of the 22 tRNAs have the typical cloverleaf structure except for tRNASer(AGN) lacking of the dihydrouridine (DHU) stem. The conserved motif ATACTA, poly-T stretch, ATAGA, ATTTA and microsatellite-like (AT)11 were found in the intergenic region between tRNASer(UCN) and ND1 and the A+T-rich region of L. haraldusalis, respectively.

  5. The complete mitochondrial genome of Paracymoriza distinctalis (Lepidoptera: Crambidae).

    Science.gov (United States)

    Ye, Fei; You, Ping

    2016-01-01

    The complete mitochondrial genome of Paracymoriza distinctalis (Leech, 1889) has been determined in this article. The mitochondrial genome of P. distinctalis was 15,354 bp in length, containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and an A + T-rich region. All PCGs start with ATN codon, except for COI, which begins with CGA. Eleven PCGs stop with typical stop codon TAA. But ND5 and COII use incomplete stop codon T. All the 22 tRNAs have the typical clover-leaf structure except for tRNA(Ser)(AGN) lacking the dihydrouridine (DHU) stem. There were several conserved motifs in the intergenic region between tRNA(Ser)(UCN) and ND1 and the A + T-rich region of P. distinctalis.

  6. Complete mitochondrial genome organization of Tor tor (Hamilton, 1822).

    Science.gov (United States)

    Kumar, Rohit; Goel, Chirag; Kumari Sahoo, Prabhati; Singh, Atul K; Barat, Ashoktaru

    2016-07-01

    The complete mitochondrial genome of Tor tor, a threatened "Mahseer" was sequenced for the first time. The mitochondrial genome size determined to be 16,554 bp in length and consisted of 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNA genes and a control region or displacement loop (D-Loop) region, resembling the typical organizational pattern of most of the teleost. The overall base composition found was A: 31.8%, T: 25%, G: 15.7% and C: 27.4%; A + T: 56.9% and G + C: 43.1%. The phylogenetic tree constructed using 11 other cyprinids' total mtDNA datasets confirmed the location of present species among mahseers. The total sequence data could support further study in molecular systematics, species identification, evolutionary and conservation genetics.

  7. Complete mitochondrial genome of the mudskipper Boleophthalmus boddarti (Perciformes, Gobiidae).

    Science.gov (United States)

    Zhang, Yu Ting; Ghaffar, Mazlan Abd; Li, Zhe; Chen, Wei; Chen, Shi Xi; Hong, Wan Shu

    2016-01-01

    The Boddart's goggle-eyed mudskipper, Boleophthalmus boddarti (Perciformes, Gobiidae) is an amphibious fish, inhabiting brackish waters of estuaries and builds burrows in soft mud along the intertidal zone. In this paper, the complete mitochondrial genome sequence of B. boddarti was firstly determined. The circle genome (16,727 bp) comprises 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. The overall base composition of B. boddarti is 29.1% for C, 28.9% for A, 25.9% for T, and 16.0% for G, with a slight A + T bias of 54.8%. The termination-associated sequence, conserved sequence block domains, and a 131-bp tandem repeat were found in the control region. It has the typical vertebrate mitochondrial gene arrangement.

  8. The complete mitochondrial genome of Sus cebifrons (Sus, Suidae).

    Science.gov (United States)

    Liu, Fang; Tang, Hong-Xia; Liu, Yong-Gang; Bai, Ming-Jie; Tang, Yan-Xia

    2015-06-01

    In this work, we report the complete mitochondrial genome sequence of Sus cebifrons (Visayan warty pig). The total length of the mitogenome was 16,475 bp, and its overall base composition was estimated to be 35.0% for A, 25.8% for T, 26.2% for C and 13.0% for G, indicating an A-T (60.8%)-rich feature in Sus cebifrons mitogenome. It contained the typical structure of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a noncoding control region (D-loop region). The arrangement of these genes was the same as that found in other pigs. The complete mitochondrial genome sequence of the Sus cebifrons would provide new genetic resources for pig domestication study.

  9. A Mitochondrial Genome Sequence of the Tibetan Antelope( Pantholops hodgsonii )

    Institute of Scientific and Technical Information of China (English)

    Shu-Qing Xu; Xiao-Guang Zheng; Ri-Li Ge; Ying-Zhong Yang; Jun Zhou; Guo-En Jing; Yun-Tian Chen; Jun Wang; Huan-Ming Yang; Jian Wang; Jun Yu

    2005-01-01

    To investigate genetic mechanisms of high altitude adaptations of native mammals on the Tibetan Plateau, we compared mitochondrial sequences of the endangered Pantholops hodgsonii with its lowland distant relatives Ovis aries and Capra hircus, as well as other mammals. The complete mitochondrial genome of P. hodgsonii (16,498 bp) revealed a similar gene order as of other mammals. Because of tandem duplications, the control region of P. hodgsonii mitochondrial genome is shorter than those of O. aries and C. hircus, but longer than those of Bos species. Phylogenetic analysis based on alignments of the entire cytochrome b genes suggested that P. hodgsonii is more closely related to O. aries and C. hircus, rather than to species of the Antilopinae subfamily. The estimated divergence time between P.hodgsonii and O. aries is about 2.25 million years ago. Further analysis on natural selection indicated that the COXI (cytochrome c oxidase subunit I) gene was under positive selection in P. hodgsonii and Bos grunniens. Considering the same climates and environments shared by these two mammalian species, we proposed that the mitochondrial COXI gene is probably relevant for these native mammals to adapt the high altitude environment unique to the Tibetan Plateau.

  10. Systematically fragmented genes in a multipartite mitochondrial genome

    Science.gov (United States)

    Vlcek, Cestmir; Marande, William; Teijeiro, Shona; Lukeš, Julius; Burger, Gertraud

    2011-01-01

    Arguably, the most bizarre mitochondrial DNA (mtDNA) is that of the euglenozoan eukaryote Diplonema papillatum. The genome consists of numerous small circular chromosomes none of which appears to encode a complete gene. For instance, the cox1 coding sequence is spread out over nine different chromosomes in non-overlapping pieces (modules), which are transcribed separately and joined to a contiguous mRNA by trans-splicing. Here, we examine how many genes are encoded by Diplonema mtDNA and whether all are fragmented and their transcripts trans-spliced. Module identification is challenging due to the sequence divergence of Diplonema mitochondrial genes. By employing most sensitive protein profile search algorithms and comparing genomic with cDNA sequence, we recognize a total of 11 typical mitochondrial genes. The 10 protein-coding genes are systematically chopped up into three to 12 modules of 60–350 bp length. The corresponding mRNAs are all trans-spliced. Identification of ribosomal RNAs is most difficult. So far, we only detect the 3′-module of the large subunit ribosomal RNA (rRNA); it does not trans-splice with other pieces. The small subunit rRNA gene remains elusive. Our results open new intriguing questions about the biochemistry and evolution of mitochondrial trans-splicing in Diplonema. PMID:20935050

  11. The mitochondrial genome of Malus domestica and the import-driven hypothesis of mitochondrial genome expansion in seed plants.

    Science.gov (United States)

    Goremykin, Vadim V; Lockhart, Peter J; Viola, Roberto; Velasco, Riccardo

    2012-08-01

    Mitochondrial genomes of spermatophytes are the largest of all organellar genomes. Their large size has been attributed to various factors; however, the relative contribution of these factors to mitochondrial DNA (mtDNA) expansion remains undetermined. We estimated their relative contribution in Malus domestica (apple). The mitochondrial genome of apple has a size of 396 947 bp and a one to nine ratio of coding to non-coding DNA, close to the corresponding average values for angiosperms. We determined that 71.5% of the apple mtDNA sequence was highly similar to sequences of its nuclear DNA. Using nuclear gene exons, nuclear transposable elements and chloroplast DNA as markers of promiscuous DNA content in mtDNA, we estimated that approximately 20% of the apple mtDNA consisted of DNA sequences imported from other cell compartments, mostly from the nucleus. Similar marker-based estimates of promiscuous DNA content in the mitochondrial genomes of other species ranged between 21.2 and 25.3% of the total mtDNA length for grape, between 23.1 and 38.6% for rice, and between 47.1 and 78.4% for maize. All these estimates are conservative, because they underestimate the import of non-functional DNA. We propose that the import of promiscuous DNA is a core mechanism for mtDNA size expansion in seed plants. In apple, maize and grape this mechanism contributed far more to genome expansion than did homologous recombination. In rice the estimated contribution of both mechanisms was found to be similar.

  12. The complete mitochondrial genome of Tetrastemma olgarum (Nemertea: Hoplonemertea).

    Science.gov (United States)

    Sun, Wen-Yan; Shen, Chun-Yang; Sun, Shi-Chun

    2016-01-01

    The complete mitochondrial genome (mitogenome) of Tetrastemma olgarum is sequenced. It is 14,580 bp in length and contains 37 genes typical for metazoan mitogenomes. The gene order is identical to that of the previously published Hoplonemertea mitogenomes. All genes are encoded on the heavy strand except for trnT and trnP. The coding strand is AT-rich, accounting for 69.2% of overall nucleotide composition.

  13. Complete mitochondrial genome of the ocellate river stingray (Potamotrygon motoro).

    Science.gov (United States)

    Song, Hong-Mei; Mu, Xi-Dong; Wei, Min-Xia; Wang, Xue-Jie; Luo, Jian-Ren; Hu, Yin-Chang

    2015-01-01

    We determined the first complete mitochondrial genome sequence of Potamotrygon motoro from South American freshwater stingrays. The total length of P. motoro mitogenome is 17,448 bp, which consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region, with the genome organization and gene order being identical to that of the typical vertebrate. The overall nucleotide composition is 32.3% A, 24.4% T, 30.5% C and 12.8% G. These data will provide useful molecular information for phylogenetic relationships within the family Potamotrygonidae species.

  14. The complete mitochondrial genome of Elaphe bimaculata (Reptilia, Serpentes, Colubridae).

    Science.gov (United States)

    Yan, Long; Geng, Zhang-Zhen; Yan, Peng; Wu, Xiao-Bing

    2016-01-01

    The Chinese leopard snake (Elaphe bimaculata) is an endemic species to China. The complete nucleotide sequence of the mitochondrial (mt) genome of E. bimaculata is determined in this study. The circle genome was 17,183 bp in length and consisted of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 duplicate control regions. Several peculiar features were observed in mitogenome of E. bimaculata, such as the translocation of tRNA(Leu(UUR)) gene and an incomplete copy for tRNA(Pro).

  15. The complete mitochondrial genome of the Metriaclima zebra.

    Science.gov (United States)

    Chen, Xi; Song, Xiao-Lei; Chen, Ling-Yun; Li, Yong

    2016-09-01

    Cichlid fish from East Africa are remarkable for phenotypic and behavioral diversity on a backdrop of genomic similarity. Metriaclima zebra is a member of the Cichlidae family. Here, we reported the complete mitogenome sequence of M. zebra, which was 16 582 bp and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 non-coding control region. A phylogenetic tree was constructed based on complete mitogenomes of M. zebra and 11 closely related Cichlidae species to approve the accuracy. The complete mitochondrial genome of the M. zebra would provide more information for the research of M. zebra and the evolution of Cichlidae family.

  16. How rapidly does the human mitochondrial genome evolve?

    Energy Technology Data Exchange (ETDEWEB)

    Howell, N.; Kubacka, I. [Univ. of Texas Medical Branch, Galveston, TX (United States); Mackey, D.A. [Univ. of Melbourne (Australia)]|[Univ. of Tasmania, Launceston (Australia)

    1996-09-01

    The results of an empirical nucleotide-sequencing approach indicate that the evolution of the human mitochondrial noncoding D-loop is both more rapid and more complex than is revealed by standard phylogenetic approaches. The nucleotide sequence of the D-loop region of the mitochondrial genome was determined for 45 members of a large matrilineal Leber hereditary optic neuropathy pedigree. Two germ-line mutations have arisen in members of one branch of the family, thereby leading to triplasmic descendants with three mitochondrial genotypes. Segregation toward the homoplasmic state can occur within a single generation in some of these descendants, a result that suggests rapid fixation of mitochondrial mutations as a result of developmental bottlenecking. However, slow segregation was observed in other offspring, and therefore no single or simple pattern of segregation can be generalized from the available data. Evidence for rare mtDNA recombination within the D-loop was obtained for one family member. In addition to these germ-line mutations, a somatic mutation was found in the D-loop of one family member. When this genealogical approach was applied to the nucleotide sequences of mitochondrial coding regions, the results again indicated a very rapid rate of evolution. 44 refs., 2 figs., 2 tabs.

  17. The complete mitochondrial genome of Dixella sp. (Diptera: Nematocera, Dixidae).

    Science.gov (United States)

    Kang, Zehui; Li, Xuankun; Yang, Ding

    2016-01-01

    In the present paper, the first complete mitochondrial genome of the family Dixidae is reported. The complete mitochondrial genome of Dixella sp. is a circular molecule of 15,574 bp in length, containing all 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (srRNA and lrRNA), and a long control region. Its gene arrangement is conserved with the ancestral gene order of Drosophila yakuba, which is considered to exhibit the ground pattern of Hexapoda mitochondrial genome. Most PCGs start with standard ATN codons, while COI uses CCG, ND1 uses TTG and ND5 uses GTG as start codons. All PCGs terminate in the common stop codons TAA, except for COII and ND5 which end with a single thymine stop codon. There is a 703 bp of the control region, located between srRNA and tRNA(lle)-tRNA(Gln)-tRNA(Met) (IQM) cluster, without conserved blocks or long tandem repeats.

  18. Complete mitochondrial genome of Oxya chinensis (Orthoptera, Acridoidea)

    Institute of Scientific and Technical Information of China (English)

    Chenyan Zhang; Yuan Huang

    2008-01-01

    The complete sequence of Oxya chinensis (O.chinensis) mitochondrial genome is reported here.It is 15,443 bp in length and contains 75.9% A+T.The protein-coding genes have a similar A+T content (75.2%).The initiation codon of the cytochrome oxidase subunit I gene in the mitochondrial genome of O.chinensis appears to be ATC,instead of the tetranucleotides that have been reported in Locusta migratoria (L.migratoria) mitochondrial genome.The sizes of the large and small ribosomal RNA genes are 1319 and 850 bp,respectively.The transfer RNA genes have been modeled and showed strong resemblance to the dipteran transfer RNAs,and all anticodons are identical to those of dipteran.The A+T-rich region is 562 bp,shorter than that of other known Orthoptera insects.The six conserved domains were identified within the A+T-rich region by comparing its sequence with those of other grasshoppers.The result of phylogenetic analysis based on the dataset containing 12 concatenated protein sequences confirms the close relationship of O.chinensis with L.migratoria.

  19. Extensive Mitochondrial mRNA Editing and Unusual Mitochondrial Genome Organization in Calcaronean Sponges.

    Science.gov (United States)

    Lavrov, Dennis V; Adamski, Marcin; Chevaldonné, Pierre; Adamska, Maja

    2016-01-11

    One of the unusual features of DNA-containing organelles in general and mitochondria in particular is the frequent occurrence of RNA editing [1]. The term "RNA editing" refers to a variety of mechanistically unrelated biochemical processes that alter RNA sequence during or after transcription [2]. The editing can be insertional, deletional, or substitutional and has been found in all major types of RNAs [3, 4]. Although mitochondrial mRNA editing is widespread in some eukaryotic lineages [5-7], it is rare in animals, with reported cases limited both in their scope and in phylogenetic distribution [8-11] (see also [12]). While analyzing genomic data from calcaronean sponges Sycon ciliatum and Leucosolenia complicata, we were perplexed by the lack of recognizable mitochondrial coding sequences. Comparison of genomic and transcriptomic data from these species revealed the presence of mitochondrial cryptogenes whose transcripts undergo extensive editing. This editing consisted of single or double uridylate (U) insertions in pre-existing short poly(U) tracts. Subsequent analysis revealed the presence of similar editing in Sycon coactum and the loss of editing in Petrobiona massiliana, a hypercalcified calcaronean sponge. In addition, mitochondrial genomes of at least some calcaronean sponges were found to have a highly unusual architecture, with nearly all genes located on individual and likely linear chromosomes. Phylogenetic analysis of mitochondrial coding sequences revealed accelerated rates of sequence evolution in this group. The latter observation presents a challenge for the mutational-hazard hypothesis [13], which posits that mRNA editing should not occur in lineages with an elevated mutation rate.

  20. The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus

    Directory of Open Access Journals (Sweden)

    Huynh Minh

    2009-11-01

    Full Text Available Abstract Background There are thousands of very diverse ciliate species from which only a handful mitochondrial genomes have been studied so far. These genomes are rather similar because the ciliates analysed (Tetrahymena spp. and Paramecium aurelia are closely related. Here we study the mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus. These ciliates are only distantly related to Tetrahymena spp. and Paramecium aurelia, but more closely related to Nyctotherus ovalis, which possesses a hydrogenosomal (mitochondrial genome. Results The linear mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus were sequenced and compared with the mitochondrial genomes of several Tetrahymena species, Paramecium aurelia and the partially sequenced mitochondrial genome of the anaerobic ciliate Nyctotherus ovalis. This study reports new features such as long 5'gene extensions of several mitochondrial genes, extremely long cox1 and cox2 open reading frames and a large repeat in the middle of the linear mitochondrial genome. The repeat separates the open reading frames into two blocks, each having a single direction of transcription, from the repeat towards the ends of the chromosome. Although the Euplotes mitochondrial gene content is almost identical to that of Paramecium and Tetrahymena, the order of the genes is completely different. In contrast, the 33273 bp (excluding the repeat region piece of the mitochondrial genome that has been sequenced in both Euplotes species exhibits no difference in gene order. Unexpectedly, many of the mitochondrial genes of E. minuta encoding ribosomal proteins possess N-terminal extensions that are similar to mitochondrial targeting signals. Conclusion The mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus are rather different from the previously studied genomes. Many genes are extended in size compared to mitochondrial

  1. Mitochondrial genome of Silurus asotus (Teleostei: Siluriformes).

    Science.gov (United States)

    Zeng, Qing; Wang, Zhijian; Peng, Zuogang

    2011-10-01

    The complete mitogenome sequence of the Amur catfish Silurus asotus was determined using long PCRs. The genome was 16,528 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region; the gene composition and order of which was similar to most other vertebrates. The overall base composition of the heavy strand is 30.5% A, 25.8% T, 28.0% C, and 15.8% G, with an AT content of 56.3%. The mtDNA sequence of S. asotus shared 93.6% and 90.6% sequence identity with that of Silurus meridionalis and Silurus glanis. This mitogenome sequence data would play an important role in silurid catfish phylogenetics and siluriform catfish systematics in general.

  2. Detouring of cisplatin to access mitochondrial genome for overcoming resistance.

    Science.gov (United States)

    Marrache, Sean; Pathak, Rakesh K; Dhar, Shanta

    2014-07-22

    Chemoresistance of cisplatin therapy is related to extensive repair of cisplatin-modified DNA in the nucleus by the nucleotide excision repair (NER). Delivering cisplatin to the mitochondria to attack mitochondrial genome lacking NER machinery can lead to a rationally designed therapy for metastatic, chemoresistant cancers and might overcome the problems associated with conventional cisplatin treatment. An engineered hydrophobic mitochondria-targeted cisplatin prodrug, Platin-M, was constructed using a strain-promoted alkyne-azide cycloaddition chemistry. Efficient delivery of Platin-M using a biocompatible polymeric nanoparticle (NP) based on biodegradable poly(lactic-co-glycolic acid)-block-polyethyleneglycol functionalized with a terminal triphenylphosphonium cation, which has remarkable activity to target mitochondria of cells, resulted in controlled release of cisplatin from Platin-M locally inside the mitochondrial matrix to attack mtDNA and exhibited otherwise-resistant advanced cancer sensitive to cisplatin-based chemotherapy. Identification of an optimized targeted-NP formulation with brain-penetrating properties allowed for delivery of Platin-M inside the mitochondria of neuroblastoma cells resulting in ∼17 times more activity than cisplatin. The remarkable activity of Platin-M and its targeted-NP in cisplatin-resistant cells was correlated with the hyperpolarization of mitochondria in these cells and mitochondrial bioenergetics studies in the resistance cells further supported this hypothesis. This unique dual-targeting approach to controlled mitochondrial delivery of cisplatin in the form of a prodrug to attack the mitochondrial genome lacking NER machinery and in vivo distribution of the delivery vehicle in the brain suggested previously undescribed routes for cisplatin-based therapy.

  3. Mitochondrial genome diversity in dagger and needle nematodes (Nematoda: Longidoridae)

    Science.gov (United States)

    Palomares-Rius, J. E.; Cantalapiedra-Navarrete, C.; Archidona-Yuste, A.; Blok, V. C.; Castillo, P.

    2017-01-01

    Dagger and needle nematodes included in the family Longidoridae (viz. Longidorus, Paralongidorus, and Xiphinema) are highly polyphagous plant-parasitic nematodes in wild and cultivated plants and some of them are plant-virus vectors (nepovirus). The mitochondrial (mt) genomes of the dagger and needle nematodes, Xiphinema rivesi, Xiphinema pachtaicum, Longidorus vineacola and Paralongidorus litoralis were sequenced in this study. The four circular mt genomes have an estimated size of 12.6, 12.5, 13.5 and 12.7 kb, respectively. Up to date, the mt genome of X. pachtaicum is the smallest genome found in Nematoda. The four mt genomes contain 12 protein-coding genes (viz. cox1-3, nad1-6, nad4L, atp6 and cob) and two ribosomal RNA genes (rrnL and rrnS), but the atp8 gene was not detected. These mt genomes showed a gene arrangement very different within the Longidoridae species sequenced, with the exception of very closely related species (X. americanum and X. rivesi). The sizes of non-coding regions in the Longidoridae nematodes were very small and were present in a few places in the mt genome. Phylogenetic analysis of all coding genes showed a closer relationship between Longidorus and Paralongidorus and different phylogenetic possibilities for the three Xiphinema species. PMID:28150734

  4. Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera.

    Science.gov (United States)

    Meganathan, P R; Pagan, Heidi J T; McCulloch, Eve S; Stevens, Richard D; Ray, David A

    2012-01-15

    Order Chiroptera is a unique group of mammals whose members have attained self-powered flight as their main mode of locomotion. Much speculation persists regarding bat evolution; however, lack of sufficient molecular data hampers evolutionary and conservation studies. Of ~1200 species, complete mitochondrial genome sequences are available for only eleven. Additional sequences should be generated if we are to resolve many questions concerning these fascinating mammals. Herein, we describe the complete mitochondrial genomes of three bats: Corynorhinus rafinesquii, Lasiurus borealis and Artibeus lituratus. We also compare the currently available mitochondrial genomes and analyze codon usage in Chiroptera. C. rafinesquii, L. borealis and A. lituratus mitochondrial genomes are 16438 bp, 17048 bp and 16709 bp, respectively. Genome organization and gene arrangements are similar to other bats. Phylogenetic analyses using complete mitochondrial genome sequences support previously established phylogenetic relationships and suggest utility in future studies focusing on the evolutionary aspects of these species. Comprehensive analyses of available bat mitochondrial genomes reveal distinct nucleotide patterns and synonymous codon preferences corresponding to different chiropteran families. These patterns suggest that mutational and selection forces are acting to different extents within Chiroptera and shape their mitochondrial genomes.

  5. The complete mitochondrial genome of the Hoffmann's two-toed sloth (Choloepus hoffmanni).

    Science.gov (United States)

    Song, Xiaolei; Chen, Lingyun; Chen, Xi; Jia, Huijue

    2016-09-01

    The Hoffmann's two-toed sloth (Choloepus hoffmanni), a member of Folivora suborder, is found in the rainforest canopy of South America. Both the Hoffmann's two-toed sloth and human belong to Eutheria subclass. In this study, the complete mitochondrial genome of C. hoffmanni is reported . The whole mitochondrial genome is 16 466 bp in length, including 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. Comparison between the mitochondrial genome of the C. hoffmanni and that of its congener Choloepus didactylus revealed a high similarity in their gene sequences. We also constructed a phylogenetic tree on the complete mitochondrial genomes of these two species and other 14 closely related species to show their phylogenic relationship. To conclude, we analyzed the complete mitochondrial genome of C. hoffmanni and its phylogenic relationship with other related species, which would facilitate our understanding of the evolution of eutherian mitochondrial genome.

  6. POSSIBLE ROLE OF MITOCHONDRIAL GENOME MUTATIONS IN CORONARY HEART DISEASE

    Directory of Open Access Journals (Sweden)

    L. A. Egorova

    2014-07-01

    Full Text Available Mitochondria are not only the major producers of adenosine triphosphate, but also an endogenous source of reactive oxygen species. Mitochondrialdysfunction plays a key role in the trigger and progression of atherosclerotic lesion. Impaired function in the mitochondria due to their elevated level of oxidized oxygen species, the accumulation of mitochondrial DNA damages, and the exhaustion of respiratory chains induces dysfunction and apoptosis in the endothelial cells; activation of matrix metalloproteinases; growth of vascular smooth muscle cells and their migration into the intima; expression of adhesion molecules, and oxidation of low-density lipoproteins. Mitochondrial dysfunction may be an important unifying mechanism that accounts for the atherogenic effect of major cardiovascular risk factors. Small clinical pilot studies have shown an association of different mitochondrial genome mutations with atherosclerotic lesion in the artery. Taking into account the available data on the possible role of mitochondria in atherogenesis, novel drugs are now being designed to affect mitochondrial function.

  7. The Complete DNA Sequence of the Mitochondrial Genome of a ``living Fossil,'' the Coelacanth (Latimeria Chalumnae)

    OpenAIRE

    Zardoya, Rafael; Meyer, Axel

    1997-01-01

    The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latirneria chalumnae) was determined. Thec oelacanth mitochondrial genome orderi s identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous reg...

  8. Complete mitochondrial genome of the gray mouse lemur, Microcebus murinus (Primates, Cheirogaleidae).

    Science.gov (United States)

    Lecompte, Emilie; Crouau-Roy, Brigitte; Aujard, Fabienne; Holota, Hélène; Murienne, Jérôme

    2016-09-01

    We report the high-coverage complete mitochondrial genome sequence of the gray mouse lemur Microcebus murinus. The sequencing has been performed on an Illumina Hiseq 2500 platform, with a genome skimming strategy. The total length of this mitogenome is 16 963 bp, containing 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 non-coding region (D-loop region). The genome organization, nucleotide composition and codon usage are similar to those reported from other primate's mitochondrial genomes. The complete mitochondrial genome sequence reported here will be useful for comparative genomics studies in primates.

  9. The complete mitochondrial genome of the armored catfish, Hypostomus plecostomus (Siluriformes: Loricariidae).

    Science.gov (United States)

    Liu, Shikai; Zhang, Jiaren; Yao, Jun; Liu, Zhanjiang

    2016-05-01

    The complete mitochondrial genome of the armored catfish, Hypostomus plecostomus, was determined by next generation sequencing of genomic DNA without prior sample processing or primer design. Bioinformatics analysis resulted in the entire mitochondrial genome sequence with length of 16,523 bp. The H. plecostomus mitochondrial genome is consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region, showing typical circular molecule structure of mitochondrial genome as in other vertebrates. The whole genome base composition was estimated to be 31.8% A, 27.0% T, 14.6% G, and 26.6% C, with A/T bias of 58.8%. This work provided the H. plecostomus mitochondrial genome sequence which should be valuable for species identification, phylogenetic analysis and conservation genetics studies in catfishes.

  10. Complete mitochondrial DNA genome of Pseudobagrus brevicaudatus (Siluriformes: Bagridae).

    Science.gov (United States)

    Liang, Hong-Wei; Meng, Yan; Li, Zhong; Zhang, Yan; Zou, Gui-wei

    2014-06-01

    The complete mitochondrial genome of Pseudobagrus brevicaudatus (Siluriformes: Bagridae) was sequenced in this study. The total length of the mitogenome is 16,533 bp, with the base composition of 31.6% A, 26.8% T, 15.0%G, 26.6% C. The gene order and genes were the same as that found in other previously reported catfishes, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 non-coding control region. Except for ND6 gene and 8 tRNA genes, all other mitochondrial genes were encoded on the heavy strand. This complete mitogenome data provides the basis for taxonomic and conservation research of this and closely related species.

  11. The evolutionary processes of mitochondrial and chloroplast genomes differ from those of nuclear genomes

    Science.gov (United States)

    Korpelainen, Helena

    2004-11-01

    This paper first introduces our present knowledge of the origin of mitochondria and chloroplasts, and the organization and inheritance patterns of their genomes, and then carries on to review the evolutionary processes influencing mitochondrial and chloroplast genomes. The differences in evolutionary phenomena between the nuclear and cytoplasmic genomes are highlighted. It is emphasized that varying inheritance patterns and copy numbers among different types of genomes, and the potential advantage achieved through the transfer of many cytoplasmic genes to the nucleus, have important implications for the evolution of nuclear, mitochondrial and chloroplast genomes. Cytoplasmic genes transferred to the nucleus have joined the more strictly controlled genetic system of the nuclear genome, including also sexual recombination, while genes retained within the cytoplasmic organelles can be involved in selection and drift processes both within and among individuals. Within-individual processes can be either intra- or intercellular. In the case of heteroplasmy, which is attributed to mutations or biparental inheritance, within-individual selection on cytoplasmic DNA may provide a mechanism by which the organism can adapt rapidly. The inheritance of cytoplasmic genomes is not universally maternal. The presence of a range of inheritance patterns indicates that different strategies have been adopted by different organisms. On the other hand, the variability occasionally observed in the inheritance mechanisms of cytoplasmic genomes reduces heritability and increases environmental components in phenotypic features and, consequently, decreases the potential for adaptive evolution.

  12. Preliminary analysis of the mitochondrial genome evolutionary pattern in primates

    Institute of Scientific and Technical Information of China (English)

    Liang ZHAO; Xingtao ZHANG; Xingkui TAO; Weiwei WANG; Ming LI

    2012-01-01

    Since the birth of molecular evolutionary analysis,primates have been a central focus of study and mitochondrial DNA is well suited to these endeavors because of its unique features.Surprisingly,to date no comprehensive evaluation of the nucleotide substitution patterns has been conducted on the mitochondrial genome of primates.Here,we analyzed the evolutionary patterns and evaluated selection and recombination in the mitochondrial genomes of 44 Primates species downloaded from GenBank.The results revealed that a strong rate heterogeneity occurred among sites and genes in all comparisons.Likewise,an obvious decline in primate nucleotide diversity was noted in the subunit rRNAs and tRNAs as compared to the protein-coding genes.Within 13 protein-coding genes,the pattern of nonsynonymous divergence was similar to that of overall nucleotide divergence,while synonymous changes differed only for individual genes,indicating that the rate heterogeneity may result from the rate of change at nonsynonymous sites.Codon usage analysis revealed that there was intermediate codon usage bias in primate protein-coding genes,and supported the idea that GC mutation pressure might determine codon usage and that positive selection is not the driving force for the codon usage bias.Neutrality tests using site-specific positive selection from a Bayesian framework indicated no sites were under positive selection for any gene,consistent with near neutrality.Recombination tests based on the pairwise homoplasy test statistic supported complete linkage even for much older divergent primate species.Thus,with the exception of rate heterogeneity among mitochondrial genes,evaluating the validity assumed complete linkage and selective neutrality in primates prior to phylogenetic or phylogeographic analysis seems unnecessary.

  13. Preliminary analysis of the mitochondrial genome evolutionary pattern in primates.

    Science.gov (United States)

    Zhao, Liang; Zhang, Xingtao; Tao, Xingkui; Wang, Weiwei; Li, Ming

    2012-08-01

    Since the birth of molecular evolutionary analysis, primates have been a central focus of study and mitochondrial DNA is well suited to these endeavors because of its unique features. Surprisingly, to date no comprehensive evaluation of the nucleotide substitution patterns has been conducted on the mitochondrial genome of primates. Here, we analyzed the evolutionary patterns and evaluated selection and recombination in the mitochondrial genomes of 44 Primates species downloaded from GenBank. The results revealed that a strong rate heterogeneity occurred among sites and genes in all comparisons. Likewise, an obvious decline in primate nucleotide diversity was noted in the subunit rRNAs and tRNAs as compared to the protein-coding genes. Within 13 protein-coding genes, the pattern of nonsynonymous divergence was similar to that of overall nucleotide divergence, while synonymous changes differed only for individual genes, indicating that the rate heterogeneity may result from the rate of change at nonsynonymous sites. Codon usage analysis revealed that there was intermediate codon usage bias in primate protein-coding genes, and supported the idea that GC mutation pressure might determine codon usage and that positive selection is not the driving force for the codon usage bias. Neutrality tests using site-specific positive selection from a Bayesian framework indicated no sites were under positive selection for any gene, consistent with near neutrality. Recombination tests based on the pairwise homoplasy test statistic supported complete linkage even for much older divergent primate species. Thus, with the exception of rate heterogeneity among mitochondrial genes, evaluating the validity assumed complete linkage and selective neutrality in primates prior to phylogenetic or phylogeographic analysis seems unnecessary.

  14. Evolution of linear mitochondrial genomes in medusozoan cnidarians.

    Science.gov (United States)

    Kayal, Ehsan; Bentlage, Bastian; Collins, Allen G; Kayal, Mohsen; Pirro, Stacy; Lavrov, Dennis V

    2012-01-01

    In nearly all animals, mitochondrial DNA (mtDNA) consists of a single circular molecule that encodes several subunits of the protein complexes involved in oxidative phosphorylation as well as part of the machinery for their expression. By contrast, mtDNA in species belonging to Medusozoa (one of the two major lineages in the phylum Cnidaria) comprises one to several linear molecules. Many questions remain on the ubiquity of linear mtDNA in medusozoans and the mechanisms responsible for its evolution, replication, and transcription. To address some of these questions, we determined the sequences of nearly complete linear mtDNA from 24 species representing all four medusozoan classes: Cubozoa, Hydrozoa, Scyphozoa, and Staurozoa. All newly determined medusozoan mitochondrial genomes harbor the 17 genes typical for cnidarians and map as linear molecules with a high degree of gene order conservation relative to the anthozoans. In addition, two open reading frames (ORFs), polB and ORF314, are identified in cubozoan, schyphozoan, staurozoan, and trachyline hydrozoan mtDNA. polB belongs to the B-type DNA polymerase gene family, while the product of ORF314 may act as a terminal protein that binds telomeres. We posit that these two ORFs are remnants of a linear plasmid that invaded the mitochondrial genomes of the last common ancestor of Medusozoa and are responsible for its linearity. Hydroidolinan hydrozoans have lost the two ORFs and instead have duplicated cox1 at each end of their mitochondrial chromosome(s). Fragmentation of mtDNA occurred independently in Cubozoa and Hydridae (Hydrozoa, Hydroidolina). Our broad sampling allows us to reconstruct the evolutionary history of linear mtDNA in medusozoans.

  15. The mitochondrial genome, a growing interest inside an organelle

    Directory of Open Access Journals (Sweden)

    Marco Crimi

    2008-03-01

    Full Text Available Marco Crimi1, Roberta Rigolio21National Institute of Molecular Genetics (INGM, Functional Genomics Unit, Milan, Italy; 2Department of Neurosciences and Biomedical Technologies, University of Milan Bicocca, Monza, ItalyAbstract: Mitochondria are semi-autonomously reproductive organelles within eukaryotic cells carrying their own genetic material, called the mitochondrial genome (mtDNA. Until some years ago, mtDNA had primarily been used as a tool in population genetics. As scientists began associating mtDNA mutations with dozens of mysterious disorders, as well as the aging process and a variety of chronic degenerative diseases, it became increasingly evident that the information contained in this genome had substantial potential applications to improve human health. Today, mitochondria research covers a wide range of disciplines, including clinical medicine, biochemistry, genetics, molecular cell biology, bioinformatics, plant sciences and physiology. The present review intends to present a summary of the most exiting fields of the mitochondrial research bringing together several contributes in terms of original prospective and future applications.Keywords: mtDNA, heteroplasmy, molecular diagnostics, mitochondriopathies, nanogenomics

  16. The complete mitochondrial genome of Pseudo-nitzschia multiseries (Baciuariophyta).

    Science.gov (United States)

    Yuan, Xiao-Long; Cao, Min; Bi, Gui-Qi

    2016-07-01

    Pseudo-nitzschia multiseries belongs to Baciuariophyta, which can produce the neurotoxin known as domoic acid, a toxin that can cause amnesic shellfish poisoning in human beings. The research aspects mainly focus on its toxicity and diversity. However, there is no mitochondrial genome information about P. multiseries. The complete mitochondrial genome of P. multiseries was obtained through amplifying. The mitogenome is 46 283 bp in length with 31.04% GC content. It has a typical cyclic structure. The genome contains 37 protein-coding genes, including unidentified open reading frames, 23 tRNAs and 2rRNAs. Four group II introns were found in rps5, cob, cox1 and cox2. The co-linear analysis result exhibited existence of gene modules re-arrangements and inversions among P. multiseries, Synedra acus and Thalassiosira pseudonana. The gene contents comparison showed they have high similarities. Phylogeny results suggest P. multiseries has a close evolutionary relationship with T. pseudonana.

  17. Complete sequence of the mitochondrial genome of Tetrahymena pyriformis and comparison with Paramecium aurelia mitochondrial DNA.

    Science.gov (United States)

    Burger, G; Zhu, Y; Littlejohn, T G; Greenwood, S J; Schnare, M N; Lang, B F; Gray, M W

    2000-03-24

    We report the complete nucleotide sequence of the Tetrahymena pyriformis mitochondrial genome and a comparison of its gene content and organization with that of Paramecium aurelia mtDNA. T. pyriformis mtDNA is a linear molecule of 47,172 bp (78.7 % A+T) excluding telomeric sequences (identical tandem repeats of 31 bp at each end of the genome). In addition to genes encoding the previously described bipartite small and large subunit rRNAs, the T. pyriformis mitochondrial genome contains 21 protein-coding genes that are clearly homologous to genes of defined function in other mtDNAs, including one (yejR) that specifies a component of a cytochrome c biogenesis pathway. As well, T. pyriformis mtDNA contains 22 open reading frames of unknown function larger than 60 codons, potentially specifying proteins ranging in size from 74 to 1386 amino acid residues. A total of 13 of these open reading frames ("ciliate-specific") are found in P. aurelia mtDNA, whereas the remaining nine appear to be unique to T. pyriformis; however, of the latter, five are positionally equivalent and of similar size in the two ciliate mitochondrial genomes, suggesting they may also be homologous, even though this is not evident from sequence comparisons. Only eight tRNA genes encoding seven distinct tRNAs are found in T. pyriformis mtDNA, formally confirming a long-standing proposal that most T. pyriformis mitochondrial tRNAs are nucleus-encoded species imported from the cytosol. Atypical features of mitochondrial gene organization and expression in T. pyriformis mtDNA include split and rearranged large subunit rRNA genes, as well as a split nad1 gene (encoding subunit 1 of NADH dehydrogenase of respiratory complex I) whose two segments are located on and transcribed from opposite strands, as is also the case in P. aurelia. Gene content and arrangement are very similar in T. pyriformis and P. aurelia mtDNAs, the two differing by a limited number of duplication, inversion and rearrangement events

  18. Use of red ochre by early Neandertals

    NARCIS (Netherlands)

    Roebroeks, W.; Sier, M.J.; Kellberg Nielsen, T.; De Loecker, D.; Parés, J.; Arps, C.E.S.; Mücher, H.J.

    2012-01-01

    The use of manganese and iron oxides by late Neandertals is well documented in Europe, especially for the period 60–40 kya. Such finds often have been interpreted as pigments even though their exact function is largely unknown. Here we report significantly older iron oxide finds that constitute

  19. Complete mitochondrial genome of yellow meal worm(Tenebrio molitor)

    OpenAIRE

    Liu, Li-Na; Wang, Cheng-Ye

    2014-01-01

    The yellow meal worm(Tenebrio molitor L.) is an important resource insect typically used as animal feed additive. It is also widely used for biological research. The first complete mitochondrial genome of T. molitor was determined for the first time by long PCR and conserved primer walking approaches. The results showed that the entire mitogenome of T. molitor was 15 785 bp long, with 72.35% A+T content [deposited in GenBank with accession number KF418153]. The gene order and orientation were...

  20. Characterization of complete mitochondrial genomes of indigenous Mayans in Mexico.

    Science.gov (United States)

    Mizuno, Fuzuki; Wang, Li; Sugiyama, Saburo; Kurosaki, Kunihiko; Granados, Julio; Gomez-Trejo, Celta; Acuña-Alonzo, Víctor; Ueda, Shintaroh

    2017-08-22

    The authors have previously published the complete mitochondrial genome (mitogenome) sequences of two indigenous Mesoamerican populations, Mazahua (n = 25) and Zapotec (n = 88). This study determined the complete mitogenome sequences of nine unrelated individuals from the indigenous Maya population living in Mexico. Their mitogenome sequences could be classified into either of the haplogroups A2 and C1. Surprisingly, there were no mitogenome sequences (haplotypes) that the Maya, Mazahua, and Zapotec people share in common. This indicates that no genetic exchange, at least matrilineally, has occurred among them.

  1. Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin

    Science.gov (United States)

    2011-01-01

    Background The melon belongs to the Cucurbitaceae family, whose economic importance among vegetable crops is second only to Solanaceae. The melon has a small genome size (454 Mb), which makes it suitable for molecular and genetic studies. Despite similar nuclear and chloroplast genome sizes, cucurbits show great variation when their mitochondrial genomes are compared. The melon possesses the largest plant mitochondrial genome, as much as eight times larger than that of other cucurbits. Results The nucleotide sequences of the melon chloroplast and mitochondrial genomes were determined. The chloroplast genome (156,017 bp) included 132 genes, with 98 single-copy genes dispersed between the small (SSC) and large (LSC) single-copy regions and 17 duplicated genes in the inverted repeat regions (IRa and IRb). A comparison of the cucumber and melon chloroplast genomes showed differences in only approximately 5% of nucleotides, mainly due to short indels and SNPs. Additionally, 2.74 Mb of mitochondrial sequence, accounting for 95% of the estimated mitochondrial genome size, were assembled into five scaffolds and four additional unscaffolded contigs. An 84% of the mitochondrial genome is contained in a single scaffold. The gene-coding region accounted for 1.7% (45,926 bp) of the total sequence, including 51 protein-coding genes, 4 conserved ORFs, 3 rRNA genes and 24 tRNA genes. Despite the differences observed in the mitochondrial genome sizes of cucurbit species, Citrullus lanatus (379 kb), Cucurbita pepo (983 kb) and Cucumis melo (2,740 kb) share 120 kb of sequence, including the predicted protein-coding regions. Nevertheless, melon contained a high number of repetitive sequences and a high content of DNA of nuclear origin, which represented 42% and 47% of the total sequence, respectively. Conclusions Whereas the size and gene organisation of chloroplast genomes are similar among the cucurbit species, mitochondrial genomes show a wide variety of sizes, with a non

  2. Complete mitochondrial genome of Drabescoides nuchalis (Hemiptera: Cicadellidae).

    Science.gov (United States)

    Wu, Yunfei; Dai, Renhuai; Zhan, Hongping; Qu, Ling

    2016-09-01

    The complete mitochondrial genome (mitogenome) of Drabescoides nuchalis (Hemiptera: Cicadellidae) was sequenced. It is 15 309 bp in length with 75.62% (A + T) content and comprises 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNA genes, and a non-coding region (GenBank accession no. KR349344). Gene order is identical to that of the inferred ancestral insect genome. All PCGs start with an ATN codon and terminate with TAA except ND4, which has an incomplete stop codon (T). The anticodons are identical to those of Drosophila yakuba. The phylogenetic tree confirms D. nuchalis and two Cicadellidae species are clustered into a clade, and Cicadellidae is a monophyletic group and provides support for the sister relationship of leafhopper and treehopper.

  3. The Neandertal vertebral column 1: the cervical spine.

    Science.gov (United States)

    Gómez-Olivencia, Asier; Been, Ella; Arsuaga, Juan Luis; Stock, Jay T

    2013-06-01

    This paper provides a metric analysis of the Neandertal cervical spine in relation to modern human variation. All seven cervical vertebrae have been analysed. Metric data from eight Neandertal individuals are compared with a large sample of modern humans. The significance of morphometric differences is tested using both z-scores and two-tailed Wilcoxon signed rank tests. The results identify significant metric and morphological differences between Neandertals and modern humans in all seven cervical vertebrae. Neandertal vertebrae are mediolaterally wider and dorsoventrally longer than modern humans, due in part to longer and more horizontally oriented spinous processes. This suggests that Neandertal cervical morphology was more stable in both mid-sagittal and coronal planes. It is hypothesized that the differences in cranial size and shape in the Neandertal and modern human lineages from their Middle Pleistocene ancestors could account for some of the differences in the neck anatomy between these species.

  4. The mitochondrial genome of the legume Vigna radiata and the analysis of recombination across short mitochondrial repeats.

    Directory of Open Access Journals (Sweden)

    Andrew J Alverson

    Full Text Available The mitochondrial genomes of seed plants are exceptionally fluid in size, structure, and sequence content, with the accumulation and activity of repetitive sequences underlying much of this variation. We report the first fully sequenced mitochondrial genome of a legume, Vigna radiata (mung bean, and show that despite its unexceptional size (401,262 nt, the genome is unusually depauperate in repetitive DNA and "promiscuous" sequences from the chloroplast and nuclear genomes. Although Vigna lacks the large, recombinationally active repeats typical of most other seed plants, a PCR survey of its modest repertoire of short (38-297 nt repeats nevertheless revealed evidence for recombination across all of them. A set of novel control assays showed, however, that these results could instead reflect, in part or entirely, artifacts of PCR-mediated recombination. Consequently, we recommend that other methods, especially high-depth genome sequencing, be used instead of PCR to infer patterns of plant mitochondrial recombination. The average-sized but repeat- and feature-poor mitochondrial genome of Vigna makes it ever more difficult to generalize about the factors shaping the size and sequence content of plant mitochondrial genomes.

  5. Evaluating Neandertal genetics and phylogeny

    DEFF Research Database (Denmark)

    Hebsgaard, MB; Wiuf, Carsten; Gilbert, MTP

    2007-01-01

    The retrieval of Neanderthal (Homo neanderthalsensis) mitochondrial DNA is thought to be among the most significant ancient DNA contributions to date, allowing conflicting hypotheses on modern human (Homo sapiens) evolution to be tested directly. Recently, however, both the authenticity of the Ne......The retrieval of Neanderthal (Homo neanderthalsensis) mitochondrial DNA is thought to be among the most significant ancient DNA contributions to date, allowing conflicting hypotheses on modern human (Homo sapiens) evolution to be tested directly. Recently, however, both the authenticity...

  6. The complete mitochondrial genome of the Atylotus miser (Diptera: Tabanomorpha: Tabanidae), with mitochondrial genome phylogeny of lower Brachycera (Orthorrhapha).

    Science.gov (United States)

    Wang, Kai; Li, Xuankun; Ding, Shuangmei; Wang, Ning; Mao, Meng; Wang, Mengqing; Yang, Ding

    2016-07-15

    Brachycera is a clade with over 80,000 described species and originated from the Mesozoic, and its larvae employ comprehensive feeding strategies. The phylogeny of the lower Brachycera has been studied intensively over the past decades. In order to supplement the lack of genetic data in this important group, we sequenced the complete mitochondrial (mt) genome of Atylotus miser as well as the nearly complete mt genomes of another 11 orthorrhaphous flies. The mt genome of A. miser is 15,858bp, which is typical of Diptera, with 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a 993bp control region. The rest of the orthorrhaphous mt genomes in our study have the similar structure with A. miser. Additionally, we conducted a phylogenetic analysis of 20 mt genomes using Maximum-likelihood and Bayesian methods in order to reconstruct the evolutionary relationship of Orthorrhapha. The results show that all infraorders of Brachycera are monophyletic, and a relationship of Tabanomorpha+((Xylophagomorpha+Stratiomyomorpha)+Muscomorpha) has been proposed. Within Xylophagomorpha, Nemestrinoidae forms the sister group of Xylophagidae.

  7. The Large Mitochondrial Genome of Symbiodinium minutum Reveals Conserved Noncoding Sequences between Dinoflagellates and Apicomplexans.

    Science.gov (United States)

    Shoguchi, Eiichi; Shinzato, Chuya; Hisata, Kanako; Satoh, Nori; Mungpakdee, Sutada

    2015-07-20

    Even though mitochondrial genomes, which characterize eukaryotic cells, were first discovered more than 50 years ago, mitochondrial genomics remains an important topic in molecular biology and genome sciences. The Phylum Alveolata comprises three major groups (ciliates, apicomplexans, and dinoflagellates), the mitochondrial genomes of which have diverged widely. Even though the gene content of dinoflagellate mitochondrial genomes is reportedly comparable to that of apicomplexans, the highly fragmented and rearranged genome structures of dinoflagellates have frustrated whole genomic analysis. Consequently, noncoding sequences and gene arrangements of dinoflagellate mitochondrial genomes have not been well characterized. Here we report that the continuous assembled genome (∼326 kb) of the dinoflagellate, Symbiodinium minutum, is AT-rich (∼64.3%) and that it contains three protein-coding genes. Based upon in silico analysis, the remaining 99% of the genome comprises transcriptomic noncoding sequences. RNA edited sites and unique, possible start and stop codons clarify conserved regions among dinoflagellates. Our massive transcriptome analysis shows that almost all regions of the genome are transcribed, including 27 possible fragmented ribosomal RNA genes and 12 uncharacterized small RNAs that are similar to mitochondrial RNA genes of the malarial parasite, Plasmodium falciparum. Gene map comparisons show that gene order is only slightly conserved between S. minutum and P. falciparum. However, small RNAs and intergenic sequences share sequence similarities with P. falciparum, suggesting that the function of noncoding sequences has been preserved despite development of very different genome structures.

  8. The complete mitochondrial genome of Callerebia suroia (Lepidoptera: Nymphalidae: Satyrinae).

    Science.gov (United States)

    Shi, Qinghui; Zhang, Wei; Hao, Jiasheng

    2016-01-01

    The complete mitochondrial genome (mitogenome) of Callerebia suroia (Lepidoptera: Nymphalidae: Satyrinae) was determined and analyzed in this paper. The circular genome is 15,208 bp long, including 37 typical mitochondrial genes and one non-coding AT-rich region. All protein-coding genes (PCGs) started with ATN, except for COI gene with CGA(R), which is often found in other butterflies; nine PCGs harbor the typical stop codon TAA, whereas COI, COII, ND5 and ND4 end with a single T. All tRNA genes display typical secondary clover-leaf structures, except for tRNA(Ser)(AGN), whose dihydrouridine (DHU) arm is replaced by a simple loop. The lrRNA and srRNA genes are 1,347 bp and 753 bp in length, with their AT contents of 84.4% and 85.4%, respectively. The 417 bp AT-rich region contains non repetitive sequences, but harbor several features common to the lepidopterans, including the motif ATAGA followed by a 19-bp poly-T stretch and a microsatellite-like (TA)8 element preceded by the ATTTA motif.

  9. Complete mitochondrial genome of Eruca sativa Mill. (Garden rocket.

    Directory of Open Access Journals (Sweden)

    Yankun Wang

    Full Text Available Eruca sativa (Cruciferae family is an ancient crop of great economic and agronomic importance. Here, the complete mitochondrial genome of Eruca sativa was sequenced and annotated. The circular molecule is 247,696 bp long, with a G+C content of 45.07%, containing 33 protein-coding genes, three rRNA genes, and 18 tRNA genes. The Eruca sativa mitochondrial genome may be divided into six master circles and four subgenomic molecules via three pairwise large repeats, resulting in a more dynamic structure of the Eruca sativa mtDNA compared with other cruciferous mitotypes. Comparison with the Brassica napus MtDNA revealed that most of the genes with known function are conserved between these two mitotypes except for the ccmFN2 and rrn18 genes, and 27 point mutations were scattered in the 14 protein-coding genes. Evolutionary relationships analysis suggested that Eruca sativa is more closely related to the Brassica species and to Raphanus sativus than to Arabidopsis thaliana.

  10. Complete mitochondrial genome of Eruca sativa Mill. (Garden rocket).

    Science.gov (United States)

    Wang, Yankun; Chu, Pu; Yang, Qing; Chang, Shengxin; Chen, Jianmei; Hu, Maolong; Guan, Rongzhan

    2014-01-01

    Eruca sativa (Cruciferae family) is an ancient crop of great economic and agronomic importance. Here, the complete mitochondrial genome of Eruca sativa was sequenced and annotated. The circular molecule is 247,696 bp long, with a G+C content of 45.07%, containing 33 protein-coding genes, three rRNA genes, and 18 tRNA genes. The Eruca sativa mitochondrial genome may be divided into six master circles and four subgenomic molecules via three pairwise large repeats, resulting in a more dynamic structure of the Eruca sativa mtDNA compared with other cruciferous mitotypes. Comparison with the Brassica napus MtDNA revealed that most of the genes with known function are conserved between these two mitotypes except for the ccmFN2 and rrn18 genes, and 27 point mutations were scattered in the 14 protein-coding genes. Evolutionary relationships analysis suggested that Eruca sativa is more closely related to the Brassica species and to Raphanus sativus than to Arabidopsis thaliana.

  11. Genome-wide analysis reveals coating of the mitochondrial genome by TFAM.

    Directory of Open Access Journals (Sweden)

    Yun E Wang

    Full Text Available Mitochondria contain a 16.6 kb circular genome encoding 13 proteins as well as mitochondrial tRNAs and rRNAs. Copies of the genome are organized into nucleoids containing both DNA and proteins, including the machinery required for mtDNA replication and transcription. The transcription factor TFAM is critical for initiation of transcription and replication of the genome, and is also thought to perform a packaging function. Although specific binding sites required for initiation of transcription have been identified in the D-loop, little is known about the characteristics of TFAM binding in its nonspecific packaging state. In addition, it is unclear whether TFAM also plays a role in the regulation of nuclear gene expression. Here we investigate these questions by using ChIP-seq to directly localize TFAM binding to DNA in human cells. Our results demonstrate that TFAM uniformly coats the whole mitochondrial genome, with no evidence of robust TFAM binding to the nuclear genome. Our study represents the first high-resolution assessment of TFAM binding on a genome-wide scale in human cells.

  12. Complete mitochondrial genome of the rabbitfish Siganus fuscescens (Perciformes, Siganidae).

    Science.gov (United States)

    Oh, Dae-Ju; Kim, Ji-Young; Lee, Jung-A; Yoon, Weon-Jong; Park, Soo-Yeong; Jung, Yong-Hwan

    2007-08-01

    We determined the complete nucleotide sequence of the mitochondrial genome for the rabbitfish Siganus fuscescens (Perciformes, Siganidae). This mitochondrial genome, consisting of 16,491 base pairs (bp), included 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a noncoding control region similar those found in other vertebrates; the gene order was identical to that of typical vertebrates. Most of the genes of S. fuscescens were encoded on the H-strand, while the ND6 and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser [UCN], Glu, and Pro) genes were encoded on the L-strand. The reading frames of ATPase 8 and 6 and those of ND4L and ND4 overlapped by ten and seven nucleotides, respectively. All mitochondrial protein-coding genes began with an ATG start codon, except for CO1, which started with GTG. Open reading frames of S. fuscescens ended with TAA (ND1, CO1, ATPase 8, ND4L, ND5 and ND6), and the remainder had incomplete stop codons, either TA (ATPase 6 and CO3) or T (ND2, CO2, ND3, ND4, and Cytb). The origin of L-strand replication in S. fuscescens was located in a cluster of five tRNA genes (WANCY) and was 34 nucleotides in length. A major noncoding region between the tRNA-Pro and tRNA-Phe genes (828 bp) was considered to be the control region (D-loop). Within this sequence, we identified a conserved sequence block characteristic of this region. The rabbitfish was grouped with Siganus canaliculatus in most parsimony analyses, which showed 100% bootstrap support for their divergence. These findings are useful for inferring phylogenetic relationships and identification within the suborder Acanthuroidei.

  13. The complete mitochondrial genome sequence of Eimeria magna (Apicomplexa: Coccidia).

    Science.gov (United States)

    Tian, Si-Qin; Cui, Ping; Fang, Su-Fang; Liu, Guo-Hua; Wang, Chun-Ren; Zhu, Xing-Quan

    2015-01-01

    In the present study, we determined the complete mitochondrial DNA (mtDNA) sequence of Eimeria magna from rabbits for the first time, and compared its gene contents and genome organizations with that of seven Eimeria spp. from domestic chickens. The size of the complete mt genome sequence of E. magna is 6249 bp, which consists of 3 protein-coding genes (cytb, cox1 and cox3), 12 gene fragments for the large subunit (LSU) rRNA, and 7 gene fragments for the small subunit (SSU) rRNA, without transfer RNA genes, in accordance with that of Eimeria spp. from chickens. The putative direction of translation for three genes (cytb, cox1 and cox3) was the same as those of Eimeria species from domestic chickens. The content of A + T is 65.16% for E. magna mt genome (29.73% A, 35.43% T, 17.09 G and 17.75% C). The E. magna mt genome sequence provides novel mtDNA markers for studying the molecular epidemiology and population genetics of Eimeria spp. and has implications for the molecular diagnosis and control of rabbit coccidiosis.

  14. The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus.

    NARCIS (Netherlands)

    Graaf, R.M. de; Alen, T.A. van; Dutilh, B.E.; Kuiper, J.W.P.; Zoggel, H.J. van; Huynh, M.B.; Gortz, H.D.; Huynen, M.A.; Hackstein, J.H.P.

    2009-01-01

    BACKGROUND: There are thousands of very diverse ciliate species from which only a handful mitochondrial genomes have been studied so far. These genomes are rather similar because the ciliates analysed (Tetrahymena spp. and Paramecium aurelia) are closely related. Here we study the mitochondrial geno

  15. Complete mitochondrial genome of the Moltrecht's minnow, Aphyocypris moltrechti (Teleostei, Cyprinidae), in comparison with A. kikuchii.

    Science.gov (United States)

    Jang-Liaw, Nian-Hong; Tsai, Chi-Li; Chang, Chia-Hao; Watanabe, Katsutoshi

    2013-04-01

    We sequenced the complete mitochondrial genome of the Moltrecht's minnow, Aphyocypris moltrechti, which is known as an endemic species to Taiwan. The complete mitochondrial genome is 16,617 bp in size, consisting of 37 genes coding for 13 proteins, 2 rRNAs, 22 tRNAs, and 1 control region. Its gene arrangement pattern was identical with most vertebrates. We compared the mitochondrial genome of A. moltrechti with that of the Kikuchi's minnow, Aphyocypris kikuchii, which had been considered closely related to A. moltrechti within a same genus. Nucleotide sequence divergence (K2P distance) between the two whole mitochondrial genomes was 11.62%. The detailed comparison between the mitochondrial genomes of two species was done.

  16. Comparative mitochondrial genomics toward exploring molecular markers in the medicinal fungus Cordyceps militaris.

    Science.gov (United States)

    Zhang, Shu; Hao, Ai-Jing; Zhao, Yu-Xiang; Zhang, Xiao-Yu; Zhang, Yong-Jie

    2017-01-10

    Cordyceps militaris is a fungus used for developing health food, but knowledge about its intraspecific differentiation is limited due to lack of efficient markers. Herein, we assembled the mitochondrial genomes of eight C. militaris strains and performed a comparative mitochondrial genomic analysis together with three previously reported mitochondrial genomes of the fungus. Sizes of the 11 mitochondrial genomes varied from 26.5 to 33.9 kb mainly due to variable intron contents (from two to eight introns per strain). Nucleotide variability varied according to different regions with non-coding regions showing higher variation frequency than coding regions. Recombination events were identified between some locus pairs but seemed not to contribute greatly to genetic variations of the fungus. Based on nucleotide diversity fluctuations across the alignment of all mitochondrial genomes, molecular markers with the potential to be used for future typing studies were determined.

  17. De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome

    Directory of Open Access Journals (Sweden)

    Iorizzo Massimo

    2012-05-01

    Full Text Available Abstract Background Sequence analysis of organelle genomes has revealed important aspects of plant cell evolution. The scope of this study was to develop an approach for de novo assembly of the carrot mitochondrial genome using next generation sequence data from total genomic DNA. Results Sequencing data from a carrot 454 whole genome library were used to develop a de novo assembly of the mitochondrial genome. Development of a new bioinformatic tool allowed visualizing contig connections and elucidation of the de novo assembly. Southern hybridization demonstrated recombination across two large repeats. Genome annotation allowed identification of 44 protein coding genes, three rRNA and 17 tRNA. Identification of the plastid genome sequence allowed organelle genome comparison. Mitochondrial intergenic sequence analysis allowed detection of a fragment of DNA specific to the carrot plastid genome. PCR amplification and sequence analysis across different Apiaceae species revealed consistent conservation of this fragment in the mitochondrial genomes and an insertion in Daucus plastid genomes, giving evidence of a mitochondrial to plastid transfer of DNA. Sequence similarity with a retrotransposon element suggests a possibility that a transposon-like event transferred this sequence into the plastid genome. Conclusions This study confirmed that whole genome sequencing is a practical approach for de novo assembly of higher plant mitochondrial genomes. In addition, a new aspect of intercompartmental genome interaction was reported providing the first evidence for DNA transfer into an angiosperm plastid genome. The approach used here could be used more broadly to sequence and assemble mitochondrial genomes of diverse species. This information will allow us to better understand intercompartmental interactions and cell evolution.

  18. The complete mitochondrial genome of the Huang Lang chicken.

    Science.gov (United States)

    Yu, Qi-Fang; Liu, Li-Li; Fu, Chen-Xing; He, Shao-Ping; Li, Si; He, Jian-Hua

    2016-01-01

    Huang Lang chicken is the native breed of Hunan province in China. The complete mitochondrial (mt) genome sequence plays an important role in the accurate determination of phylogenetic relationships among metazoans. It is the first time that the complete mt genome sequence of the Huang Lang chicken was reported in this work, which was determined through the polymerase chain reaction-based method. The total length of the mitogenome is 16,786 bp, with the base composition of 30.25% for A, 23.71% for T, 32.53% for C and 13.51% for G, in the order C > A > T > G feature occurs in the Huang Lang chicken. It contains the typical structure, including two ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). The complete mt genome sequence of the Huang Lang chicken provided an important data for further study on the genetic mechanism.

  19. Analysis of the complete Fischoederius elongatus (Paramphistomidae, Trematoda) mitochondrial genome.

    Science.gov (United States)

    Yang, Xin; Zhao, Yunyang; Wang, Lixia; Feng, Hanli; Tan, Li; Lei, Weiqiang; Zhao, Pengfei; Hu, Min; Fang, Rui

    2015-05-20

    Fischoederius elongates is an important trematode of Paramphistomes in ruminants. Animals infected with F. elongates often don't show obvious symptoms, so it is easy to be ignored. However it can cause severe economic losses to the breeding industry. Knowledge of the mitochondrial genome of F. elongates can be used for phylogenetic and epidemiological studies. The complete mt genome sequence of F. elongates is 14,120 bp in length and contains 12 protein-coding genes, 22 tRNA genes, two rRNA genes and two non-coding regions (LNR and SNR). The gene arrangement of F. elongates is the same as other trematodes, such as Fasciola hepatica and Paramphistomum cervi. Phylogenetic analyses using concatenated amino acid sequences of the 12 protein-coding genes by Maximum-likelihood and Neighbor-joining analysis method showed that F. elongates was closely related to P. cervi. The complete mt genome sequence of F. elongates should provide information for phylogenetic and epidemiological studies for F. elongates and the family Paramphistomidae.

  20. Codon usage and bias in mitochondrial genomes of parasitic platyhelminthes

    Science.gov (United States)

    McManus, Donald Peter; Blair, David

    2004-01-01

    Sequences of the complete protein-coding portions of the mitochondrial (mt) genome were analysed for 6 species of cestodes (including hydatid tapeworms and the pork tapeworm) and 5 species of trematodes (blood flukes and liver- and lung-flukes). A near-complete sequence was also available for an additional trematode (the blood flukeSchistosoma malayensis). All of these parasites belong to a large flatworm taxon named the Neodermata. Considerable variation was found in the base composition of the protein-coding genes among these neodermatans. This variation was reflected in statistically-significant differences in numbers of each inferred amino acid between many pairs of species. Both convergence and divergence in nucleotide, and hence amino acid, composition was noted among groups within the Neodermata. Considerable variation in skew (unequal representation of complementary bases on the same strand) was found among the species studied. A pattern is thus emerging of diversity in the mt genome in neodermatans that may cast light on evolution of mt genomes generally. PMID:15591833

  1. Mitochondrial genome sequences of Nematocera (lower Diptera): evidence of rearrangement following a complete genome duplication in a winter crane fly.

    Science.gov (United States)

    Beckenbach, Andrew T

    2012-01-01

    The complete mitochondrial DNA sequences of eight representatives of lower Diptera, suborder Nematocera, along with nearly complete sequences from two other species, are presented. These taxa represent eight families not previously represented by complete mitochondrial DNA sequences. Most of the sequences retain the ancestral dipteran mitochondrial gene arrangement, while one sequence, that of the midge Arachnocampa flava (family Keroplatidae), has an inversion of the trnE gene. The most unusual result is the extensive rearrangement of the mitochondrial genome of a winter crane fly, Paracladura trichoptera (family Trichocera). The pattern of rearrangement indicates that the mechanism of rearrangement involved a tandem duplication of the entire mitochondrial genome, followed by random and nonrandom loss of one copy of each gene. Another winter crane fly retains the ancestral diperan gene arrangement. A preliminary mitochondrial phylogeny of the Diptera is also presented.

  2. Complete mitochondrial genome of a Wild Amur Moose (Alces alces cameloides).

    Science.gov (United States)

    Yu, Yanze; Feng, Yuan; Wang, Hongcheng; Yang, Yong; Duan, Yubao; Zhou, Zhengyan; Zhang, Minghai

    2016-11-01

    In this study, the complete mitochondrial genome (mt DNA) of Amur Moose (Alces alces cameloides) was sequenced, using muscle tissue obtained from a male Amur moose. The total length of the mitochondrial genome is 16,305 bp. The genome structure of Amur moose is similar to other moose and it contains 12S rRNA gene, 16S rRNA gene, 22 tRNA genes, 13 protein-coding genes, and 1 control region.

  3. Complete mitochondrial genome of the Greek marsh frog Pelophylax cretensis (Anura, Ranidae).

    Science.gov (United States)

    Hofman, Sebastian; Pabijan, Maciej; Osikowski, Artur; Szymura, Jacek M

    2016-05-01

    We sequenced the complete mitochondrial genome of the Greek marsh frog Pelophylax cretensis, a water frog species endemic to the island of Crete. The genome sequence was 17,829 bp in size, and the gene order and contents were identical to those of previously reported mitochondrial genomes of other water frog species. This is the first complete mitogenome (i.e. including control region) described for western Palaearctic water frogs.

  4. Mitochondrial genome regulates mitotic fidelity by maintaining centrosomal homeostasis.

    Science.gov (United States)

    Donthamsetty, Shashikiran; Brahmbhatt, Meera; Pannu, Vaishali; Rida, Padmashree C G; Ramarathinam, Sujatha; Ogden, Angela; Cheng, Alice; Singh, Keshav K; Aneja, Ritu

    2014-01-01

    Centrosomes direct spindle morphogenesis to assemble a bipolar mitotic apparatus to enable error-free chromosome segregation and preclude chromosomal instability (CIN). Amplified centrosomes, a hallmark of cancer cells, set the stage for CIN, which underlies malignant transformation and evolution of aggressive phenotypes. Several studies report CIN and a tumorigenic and/or aggressive transformation in mitochondrial DNA (mtDNA)-depleted cells. Although several nuclear-encoded proteins are implicated in centrosome duplication and spindle organization, the involvement of mtDNA encoded proteins in centrosome amplification (CA) remains elusive. Here we show that disruption of mitochondrial function by depletion of mtDNA induces robust CA and mitotic aberrations in osteosarcoma cells. We found that overexpression of Aurora A, Polo-like kinase 4 (PLK4), and Cyclin E was associated with emergence of amplified centrosomes. Supernumerary centrosomes in rho0 (mtDNA-depleted) cells resulted in multipolar mitoses bearing "real" centrosomes with paired centrioles at the multiple poles. This abnormal phenotype was recapitulated by inhibition of respiratory complex I in parental cells, suggesting a role for electron transport chain (ETC) in maintaining numeral centrosomal homeostasis. Furthermore, rho0 cells displayed a decreased proliferative capacity owing to a G 2/M arrest. Downregulation of nuclear-encoded p53 in rho0 cells underscores the importance of mitochondrial and nuclear genome crosstalk and may perhaps underlie the observed mitotic aberrations. By contrast, repletion of wild-type mtDNA in rho0 cells (cybrid) demonstrated a much lesser extent of CA and spindle multipolarity, suggesting partial restoration of centrosomal homeostasis. Our study provides compelling evidence to implicate the role of mitochondria in regulation of centrosome duplication, spindle architecture, and spindle pole integrity.

  5. Complete mitochondrial DNA genome of Pseudobagrus truncatus (Siluriformes: Bagridae).

    Science.gov (United States)

    Liang, Hong-wei; Meng, Yan; Li, Zhong; Zhang, Yan; Zou, Gui-wei

    2014-06-01

    In this study, the complete mitochondrial DNA (mtDNA) sequence of Pseudobagrus truncatus (Siluriformes: Bagridae) was determined. The complete mtDNA genome sequence of P. truncatus is 16,533 bp in size. It consists of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and one non-coding control region. The gene order and genes were the same as that found in other previously reported catfishes. The overall-based composition was 31.6% A, 26.7% T, 14.9% G and 26.8% C, with a high A + T content (58.3%). This complete mitogenome of P. truncatus provides a basic data for studies on species identification, molecular systematics and conservation genetics.

  6. The complete mitochondrial genome of Gonepteryx mahaguru (Lepidoptera: Pieridae).

    Science.gov (United States)

    Yang, Jianing; Xu, Chang; Li, Jialian; Lei, Ying; Fan, Cheng; Gao, Yuan; Xu, Chongren; Wang, Rongjiang

    2016-01-01

    The complete mitochondrial genome of Gonepteryx mahaguru (Lepidoptera: Pieridae) is 15,221 bp in length, containing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (LrRNA and SrRNA) and 1 non-coding A + T-rich region. The nucleotide composition is significantly biased toward A + T (80.9%). All PCGs are initiated by classical ATN codon, with the exception of COI, which begins with TTA codon. Nine PCGs harbor the complete stop codon TAA, whereas COI, COII, ND4 and ND5 stop with incomplete codons, single T or TA. All tRNAs can be folded into the typical cloverleaf secondary structure, except for tRNA(Ser)(AGN). The A + T content of AT-rich region is 95.2%, same to the highest one in the known species in Pieridae.

  7. The complete mitochondrial genome of Bemisia afer (Hemiptera: Aleyrodidae).

    Science.gov (United States)

    Wang, Hua-Ling; Xiao, Na; Yang, Jiao; Wang, Xiao-Wei; Colvin, John; Liu, Shu-Sheng

    2016-01-01

    The length of the Bemisia afer (Priesner & Hosny) (Hemiptera: Aleyrodidae) mitochondrial genome (mitogenome) is 14,968 bp and consists of 13 protein coding genes (PCGs), 21 transfer RNAs (tRNA), 2 ribosomal RNAs and 1 control region. Apart from one serine transfer RNA gene (tRNA-Ser) which is absent, the synteny is consistent with the mitogenomes of other whitefly species. The overall base composition of the heavy strand for A, G, T and C is 28.96, 18.97, 36.7 and 15.37%, respectively, with a slight AT bias. Two rare codons (GTG and TTG) are employed as start codons by some PCGs. B. afer is a group of cryptic species. This first mitogenome cloned from African cassava B. afer, therefore, both enrich the whitefly molecular resource and will aid the sequencing of the other species' mitogenomes. It will contribute significantly to resolving the systematics of the B. afer complex.

  8. The complete mitochondrial genome of Triphysa phryne (Lepidoptera: Nymphalidae: Satyrinae).

    Science.gov (United States)

    Zhang, Wei; Gan, Shanshan; Zuo, Ni; Chen, Chunhui; Wang, Ying; Hao, Jiasheng

    2016-01-01

    The complete mitochondrial genome (mitogenome) sequence of Triphysa phryne (Lepidoptera: Nymphalidae: Satyrinae) was determined in this study. The mitogenome is 15,143 bp in length, containing 37 typical animal mitochondrial genes: 13 putative protein-coding genes (PCGs), 2 ribosomal RNAs, 22 transfer RNAs and a non-coding AT-rich region. Its gene content and order are identical to those of other lepidopteran mitogenomes. All protein-coding genes (PCGs) are initiated by ATN codons, except for COI gene which uses CGA as its start codon. Nine PCGs terminate in the common stop TAA, whereas the COI, COII, ND5 and ND4 genes end with single T. All tRNA genes showed typical secondary cloverleaf structures except for the tRNA(Ser)(AGN), which has a simple loop with the absence of its DHU stem. The 316 bp AT-rich region contains several features common to the other lepidopterans, such as the motif ATAGA followed by an 19-bp poly-T stretch and two microsatellite-like (TA)8(AT) and (TA)4 elements preceded by the ATTTA motif.

  9. From simple to supercomplex: mitochondrial genomes of euglenozoan protists [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Drahomíra Faktorová

    2016-11-01

    Full Text Available Mitochondria are double membrane organelles of endosymbiotic origin, best known for constituting the centre of energetics of a eukaryotic cell. They contain their own mitochondrial genome, which as a consequence of gradual reduction during evolution typically contains less than two dozens of genes. In this review, we highlight the extremely diverse architecture of mitochondrial genomes and mechanisms of gene expression between the three sister groups constituting the phylum Euglenozoa - Euglenida, Diplonemea and Kinetoplastea. The earliest diverging euglenids possess a simplified mitochondrial genome and a conventional gene expression, whereas both are highly complex in the two other groups. The expression of their mitochondrial-encoded proteins requires extensive post-transcriptional modifications guided by complex protein machineries and multiple small RNA molecules. Moreover, the least studied diplonemids, which have been recently discovered as a highly abundant component of the world ocean plankton, possess one of the most complicated mitochondrial genome organisations known to date.

  10. From simple to supercomplex: mitochondrial genomes of euglenozoan protists [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Drahomíra Faktorová

    2016-03-01

    Full Text Available Mitochondria are double membrane organelles of endosymbiotic origin, best known for constituting the centre of energetics of a eukaryotic cell. They contain their own mitochondrial genome, which as a consequence of gradual reduction during evolution typically contains less than two dozens of genes. In this review, we highlight the extremely diverse architecture of mitochondrial genomes and mechanisms of gene expression between the three sister groups constituting the phylum Euglenozoa - Euglenida, Diplonemea and Kinetoplastea. The earliest diverging euglenids possess a simplified mitochondrial genome and a conventional gene expression, whereas both are highly complex in the two other groups. The expression of their mitochondrial-encoded proteins requires extensive post-transcriptional modifications guided by complex protein machineries and multiple small RNA molecules. Moreover, the least studied diplonemids, which have been recently discovered as a highly abundant component of the world ocean plankton, possess one of the most complicated mitochondrial genome organisations known to date.

  11. Complete mitochondrial genomes of two flat-backed millipedes by next-generation sequencing (Diplopoda, Polydesmida

    Directory of Open Access Journals (Sweden)

    Yan Dong

    2016-11-01

    Full Text Available A lack of mitochondrial genome data from myriapods is hampering progress across genetic, systematic, phylogenetic and evolutionary studies. Here, the complete mitochondrial genomes of two millipedes, Asiomorpha coarctata Saussure, 1860 (Diplopoda: Polydesmida: Paradoxosomatidae and Xystodesmus sp. (Diplopoda: Polydesmida: Xystodesmidae were assembled with high coverage using Illumina sequencing data. The mitochondrial genomes of the two newly sequenced species are circular molecules of 15,644 bp and 15,791 bp, within which the typical mitochondrial genome complement of 13 protein-coding genes, 22 tRNAs and two ribosomal RNA genes could be identified. The mitochondrial genome of A. coarctata is the first complete sequence in the family Paradoxosomatidae (Diplopoda: Polydesmida and the gene order of the two flat-backed millipedes is novel among known myriapod mitochondrial genomes. Unique translocations have occurred, including inversion of one half of the two genomes with respect to other millipede genomes. Inversion of the entire side of a genome (trnF-nad5-trnH-nad4-nad4L, trnP, nad1-trnL2-trnL1-rrnL-trnV-rrnS, trnQ, trnC and trnY could constitute a common event in the order Polydesmida. Last, our phylogenetic analyses recovered the monophyletic Progoneata, subphylum Myriapoda and four internal classes.

  12. Complete mitochondrial genomes of two flat-backed millipedes by next-generation sequencing (Diplopoda, Polydesmida)

    Science.gov (United States)

    Dong, Yan; Zhu, Lixin; Bai, Yu; Ou, Yongyue; Wang, Changbao

    2016-01-01

    Abstract A lack of mitochondrial genome data from myriapods is hampering progress across genetic, systematic, phylogenetic and evolutionary studies. Here, the complete mitochondrial genomes of two millipedes, Asiomorpha coarctata Saussure, 1860 (Diplopoda: Polydesmida: Paradoxosomatidae) and Xystodesmus sp. (Diplopoda: Polydesmida: Xystodesmidae) were assembled with high coverage using Illumina sequencing data. The mitochondrial genomes of the two newly sequenced species are circular molecules of 15,644 bp and 15,791 bp, within which the typical mitochondrial genome complement of 13 protein-coding genes, 22 tRNAs and two ribosomal RNA genes could be identified. The mitochondrial genome of Asiomorpha coarctata is the first complete sequence in the family Paradoxosomatidae (Diplopoda: Polydesmida) and the gene order of the two flat-backed millipedes is novel among known myriapod mitochondrial genomes. Unique translocations have occurred, including inversion of one half of the two genomes with respect to other millipede genomes. Inversion of the entire side of a genome (trnF-nad5-trnH-nad4-nad4L, trnP, nad1-trnL2-trnL1-rrnL-trnV-rrnS, trnQ, trnC and trnY) could constitute a common event in the order Polydesmida. Last, our phylogenetic analyses recovered the monophyletic Progoneata, subphylum Myriapoda and four internal classes. PMID:28138271

  13. Complete sequence of the mitochondrial genome of Odontamblyopus rubicundus (Perciformes: Gobiidae): genome characterization and phylogenetic analysis

    Indian Academy of Sciences (India)

    Tianxing Liu; Xiaoxiao Jin; Rixin Wang; Tianjun Xu

    2013-12-01

    Odontamblyopus rubicundus is a species of gobiid fishes, inhabits muddy-bottomed coastal waters. In this paper, the first complete mitochondrial genome sequence of O. rubicundus is reported. The complete mitochondrial genome sequence is 17119 bp in length and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a control region and an L-strand origin as in other teleosts. Most mitochondrial genes are encoded on H-strand except for ND6 and seven tRNA genes. Some overlaps occur in protein-coding genes and tRNAs ranging from 1 to 7 bp. The possibly nonfunctional L-strand origin folded into a typical stem-loop secondary structure and a conserved motif (5′-GCCGG-3′) was found at the base of the stem within the $tRNA^{Cys}$ gene. The TAS, CSB-2 and CSB-3 could be detected in the control region. However, in contrast to most of other fishes, the central conserved sequence block domain and the CSB-1 could not be recognized in O. rubicundus, which is consistent with Acanthogobius hasta (Gobiidae). In addition, phylogenetic analyses based on different sequences of species of Gobiidae and different methods showed that the classification of O. rubicundus into Odontamblyopus due to morphology is debatable.

  14. Complete sequence of the mitochondrial genome of Odontamblyopus rubicundus (Perciformes: Gobiidae): genome characterization and phylogenetic analysis.

    Science.gov (United States)

    Liu, Tianxing; Jin, Xiaoxiao; Wang, Rixin; Xu, Tianjun

    2013-12-01

    Odontamblyopus rubicundus is a species of gobiid fishes, inhabits muddy-bottomed coastal waters. In this paper, the first complete mitochondrial genome sequence of O. rubicundus is reported. The complete mitochondrial genome sequence is 17119 bp in length and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a control region and an L-strand origin as in other teleosts. Most mitochondrial genes are encoded on H-strand except for ND6 and seven tRNA genes. Some overlaps occur in protein-coding genes and tRNAs ranging from 1 to 7 bp. The possibly nonfunctional L-strand origin folded into a typical stem-loop secondary structure and a conserved motif (5'-GCCGG-3') was found at the base of the stem within the tRNACys gene. The TAS, CSB-2 and CSB-3 could be detected in the control region. However, in contrast to most of other fishes, the central conserved sequence block domain and the CSB-1 could not be recognized in O. rubicundus, which is consistent with Acanthogobius hasta (Gobiidae). In addition, phylogenetic analyses based on different sequences of species of Gobiidae and different methods showed that the classification of O. rubicundus into Odontamblyopus due to morphology is debatable.

  15. The complete sequence of the mitochondrial genome of Rongchang pig (Sus Scrofa).

    Science.gov (United States)

    Wang, Ling-Yu; Xu, Dong; Ma, Hai-Ming

    2016-01-01

    Rongchang pig is one of the native breeds in Sichuan province in China. The total length of mitochondrial genome of Rongchang pig is 16,710 bp, including 34.67% A, 26.18% C, 25.82% T and 13.33% G, and in the order A > C > T > G. Mitochondrial genome contains a major non-coding control region (D-Loop region), 2 ribosomal RNA genes, 13 protein-coding genes (PCGs) and 22 transfer RNA genes. This is the first report of the complete mitochondrial genome sequence about Rongchang pig. The mitochondrial genome of Rongchang pig subsequently provides an important information in genetic mechanism and the evolution genomes.

  16. The mitochondrial genome of the ascalaphid owlfly Libelloides macaronius and comparative evolutionary mitochondriomics of neuropterid insects.

    Science.gov (United States)

    Negrisolo, Enrico; Babbucci, Massimiliano; Patarnello, Tomaso

    2011-05-10

    The insect order Neuroptera encompasses more than 5,700 described species. To date, only three neuropteran mitochondrial genomes have been fully and one partly sequenced. Current knowledge on neuropteran mitochondrial genomes is limited, and new data are strongly required. In the present work, the mitochondrial genome of the ascalaphid owlfly Libelloides macaronius is described and compared with the known neuropterid mitochondrial genomes: Megaloptera, Neuroptera and Raphidioptera. These analyses are further extended to other endopterygotan orders. The mitochondrial genome of L. macaronius is a circular molecule 15,890 bp long. It includes the entire set of 37 genes usually present in animal mitochondrial genomes. The gene order of this newly sequenced genome is unique among Neuroptera and differs from the ancestral type of insects in the translocation of trnC. The L. macaronius genome shows the lowest A+T content (74.50%) among known neuropterid genomes. Protein-coding genes possess the typical mitochondrial start codons, except for cox1, which has an unusual ACG. Comparisons among endopterygotan mitochondrial genomes showed that A+T content and AT/GC-skews exhibit a broad range of variation among 84 analyzed taxa. Comparative analyses showed that neuropterid mitochondrial protein-coding genes experienced complex evolutionary histories, involving features ranging from codon usage to rate of substitution, that make them potential markers for population genetics/phylogenetics studies at different taxonomic ranks. The 22 tRNAs show variable substitution patterns in Neuropterida, with higher sequence conservation in genes located on the α strand. Inferred secondary structures for neuropterid rrnS and rrnL genes largely agree with those known for other insects. For the first time, a model is provided for domain I of an insect rrnL. The control region in Neuropterida, as in other insects, is fast-evolving genomic region, characterized by AT-rich motifs. The new genome

  17. Comparative Analysis of Gender-Associated Complete Mitochondrial Genomes in Marine Mussels (Mytilus spp.)

    OpenAIRE

    Breton, Sophie; Burger, Gertraud; Stewart, Donald T.; Blier, Pierre U.

    2006-01-01

    Marine mussels of the genus Mytilus have an unusual mode of mitochondrial DNA (mtDNA) transmission termed doubly uniparental inheritance (DUI). Female mussels are homoplasmic for the F mitotype, which is inherited maternally, while males are usually heteroplasmic, carrying a mixture of the maternal F mitotype and the paternally inherited M genome. Two classes of M genomes have been observed: “standard” M genomes and “recently masculinized” M genomes. The latter are more similar to F genomes a...

  18. The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants.

    Science.gov (United States)

    Sugiyama, Y; Watase, Y; Nagase, M; Makita, N; Yagura, S; Hirai, A; Sugiura, M

    2005-02-01

    Tobacco is a valuable model system for investigating the origin of mitochondrial DNA (mtDNA) in amphidiploid plants and studying the genetic interaction between mitochondria and chloroplasts in the various functions of the plant cell. As a first step, we have determined the complete mtDNA sequence of Nicotiana tabacum. The mtDNA of N. tabacum can be assumed to be a master circle (MC) of 430,597 bp. Sequence comparison of a large number of clones revealed that there are four classes of boundaries derived from homologous recombination, which leads to a multipartite organization with two MCs and six subgenomic circles. The mtDNA of N. tabacum contains 36 protein-coding genes, three ribosomal RNA genes and 21 tRNA genes. Among the first class, we identified the genes rps1 and psirps14, which had previously been thought to be absent in tobacco mtDNA on the basis of Southern analysis. Tobacco mtDNA was compared with those of Arabidopsis thaliana, Beta vulgaris, Oryza sativa and Brassica napus. Since repeated sequences show no homology to each other among the five angiosperms, it can be supposed that these were independently acquired by each species during the evolution of angiosperms. The gene order and the sequences of intergenic spacers in mtDNA also differ widely among the five angiosperms, indicating multiple reorganizations of genome structure during the evolution of higher plants. Among the conserved genes, the same potential conserved nonanucleotide-motif-type promoter could only be postulated for rrn18-rrn5 in four of the dicotyledonous plants, suggesting that a coding sequence does not necessarily move with the promoter upon reorganization of the mitochondrial genome.

  19. Discovery of cyanophage genomes which contain mitochondrial DNA polymerase.

    Science.gov (United States)

    Chan, Yi-Wah; Mohr, Remus; Millard, Andrew D; Holmes, Antony B; Larkum, Anthony W; Whitworth, Anna L; Mann, Nicholas H; Scanlan, David J; Hess, Wolfgang R; Clokie, Martha R J

    2011-08-01

    DNA polymerase γ is a family A DNA polymerase responsible for the replication of mitochondrial DNA in eukaryotes. The origins of DNA polymerase γ have remained elusive because it is not present in any known bacterium, though it has been hypothesized that mitochondria may have inherited the enzyme by phage-mediated nonorthologous displacement. Here, we present an analysis of two full-length homologues of this gene, which were found in the genomes of two bacteriophages, which infect the chlorophyll-d containing cyanobacterium Acaryochloris marina. Phylogenetic analyses of these phage DNA polymerase γ proteins show that they branch deeply within the DNA polymerase γ clade and therefore share a common origin with their eukaryotic homologues. We also found homologues of these phage polymerases in the environmental Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA) database, which fell in the same clade. An analysis of the CAMERA assemblies containing the environmental homologues together with the filter fraction metadata indicated some of these assemblies may be of bacterial origin. We also show that the phage-encoded DNA polymerase γ is highly transcribed as the phage genomes are replicated. These findings provide data that may assist in reconstructing the evolution of mitochondria.

  20. Mitochondrial genome sequences and comparative genomics ofPhytophthora ramorum and P. sojae

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Frank N.; Douda, Bensasson; Tyler, Brett M.; Boore,Jeffrey L.

    2007-01-01

    The complete sequences of the mitochondrial genomes of theoomycetes of Phytophthora ramorum and P. sojae were determined during thecourse of their complete nuclear genome sequencing (Tyler, et al. 2006).Both are circular, with sizes of 39,314 bp for P. ramorum and 42,975 bpfor P. sojae. Each contains a total of 37 identifiable protein-encodinggenes, 25 or 26 tRNAs (P. sojae and P. ramorum, respectively)specifying19 amino acids, and a variable number of ORFs (7 for P. ramorum and 12for P. sojae) which are potentially additional functional genes.Non-coding regions comprise approximately 11.5 percent and 18.4 percentof the genomes of P. ramorum and P. sojae, respectively. Relative to P.sojae, there is an inverted repeat of 1,150 bp in P. ramorum thatincludes an unassigned unique ORF, a tRNA gene, and adjacent non-codingsequences, but otherwise the gene order in both species is identical.Comparisons of these genomes with published sequences of the P. infestansmitochondrial genome reveals a number of similarities, but the gene orderin P. infestans differs in two adjacent locations due to inversions.Sequence alignments of the three genomes indicated sequence conservationranging from 75 to 85 percent and that specific regions were morevariable than others.

  1. Mitochondrial Genomics in the Peronosporales; Implications for Phylogenetics and Development of Molecular Markers

    Science.gov (United States)

    The mitochondrial genomes of the genera Pythium and Phytophthora encode a similar suite of genes but differ from each other by an inverted repeat (IR) in Pythium that can represent approximately 75% of the genome size. While an IR is not usually found in Phytophthora genomes, a small IR was observe...

  2. Draft Plastid and Mitochondrial Genome Sequences from Antarctic Alga Prasiola crispa

    Science.gov (United States)

    Carvalho, Evelise Leis; Wallau, Gabriel da Luz; Rangel, Darlene Lopes; Machado, Laís Ceschini; da Silva, Alexandre Freitas; da Silva, Luiz Fernando Duarte; Macedo, Pablo Echeverria; Pereira, Antonio Batista; Victoria, Filipe de Carvalho; Boldo, Juliano Tomazzoni; Dal Belo, Cháriston André

    2015-01-01

    The organelle genomes of the Antarctic alga Prasiola crispa (Lightfoot) Kützing have been sequenced. The plastid and mitochondrial genomes have a total length of 196,502 bp and 89,819 bp, respectively. These genomes have 19 putative photosynthesis-related genes and 17 oxidative metabolism-related genes, respectively. PMID:26450727

  3. Mitochondrial genomics in the Genus Phytophthora with a focus on Phytophthora ramorum

    Science.gov (United States)

    Frank N. Martin; Paul Richardson

    2008-01-01

    The mitochondrial genomes of Phytophthora infestans, P. ramorum and P. sojae have been sequenced and comparative genomics has provided an opportunity to examine the processes involved with genome evolution in the genus Phytophthora. This approach can also be useful in assessing intraspecific...

  4. The Complete Moss Mitochondrial Genome in the Angiosperm Amborella Is a Chimera Derived from Two Moss Whole-Genome Transfers.

    Directory of Open Access Journals (Sweden)

    Z Nathan Taylor

    Full Text Available Sequencing of the 4-Mb mitochondrial genome of the angiosperm Amborella trichopoda has shown that it contains unprecedented amounts of foreign mitochondrial DNA, including four blocks of sequences that together correspond almost perfectly to one entire moss mitochondrial genome. This implies whole-genome transfer from a single moss donor but conflicts with phylogenetic results from an earlier, PCR-based study that suggested three different moss donors to Amborella. To resolve this conflict, we conducted an expanded set of phylogenetic analyses with respect to both moss lineages and mitochondrial loci. The moss DNA in Amborella was consistently placed in either of two positions, depending on the locus analyzed, as sister to the Ptychomniales or within the Hookeriales. This agrees with two of the three previously suggested donors, whereas the third is no longer supported. These results, combined with synteny analyses and other considerations, lead us to favor a model involving two successive moss-to-Amborella whole-genome transfers, followed by recombination that produced a single intact and chimeric moss mitochondrial genome integrated in the Amborella mitochondrial genome. Eight subsequent recombination events account for the state of fragmentation, rearrangement, duplication, and deletion of this chimeric moss mitochondrial genome as it currently exists in Amborella. Five of these events are associated with short-to-intermediate sized repeats. Two of the five probably occurred by reciprocal homologous recombination, whereas the other three probably occurred in a non-reciprocal manner via microhomology-mediated break-induced replication (MMBIR. These findings reinforce and extend recent evidence for an important role of MMBIR in plant mitochondrial DNA evolution.

  5. The highly reduced and fragmented mitochondrial genome of the early-branching dinoflagellate Oxyrrhis marina shares characteristics with both apicomplexan and dinoflagellate mitochondrial genomes.

    Science.gov (United States)

    Slamovits, Claudio H; Saldarriaga, Juan F; Larocque, Allen; Keeling, Patrick J

    2007-09-14

    The mitochondrial genome and the expression of the genes within it have evolved to be highly unusual in several lineages. Within alveolates, apicomplexans and dinoflagellates share the most reduced mitochondrial gene content on record, but differ from one another in organisation and function. To clarify how these characteristics originated, we examined mitochondrial genome form and expression in a key lineage that arose close to the divergence of apicomplexans and dinoflagellates, Oxyrrhis marina. We show that Oxyrrhis is a basal member of the dinoflagellate lineage whose mitochondrial genome has some unique characteristics while sharing others with apicomplexans or dinoflagellates. Specifically, Oxyrrhis has the smallest gene complement known, with several rRNA fragments and only two protein coding genes, cox1 and a cob-cox3 fusion. The genome appears to be highly fragmented, like that of dinoflagellates, but genes are frequently arranged as tandem copies, reminiscent of the repeating nature of the Plasmodium genome. In dinoflagellates and Oxyrrhis, genes are found in many arrangements, but the Oxyrrhis genome appears to be more structured, since neighbouring genes or gene fragments are invariably the same: cox1 and the cob-cox3 fusion were never found on the same genomic fragment. Analysing hundreds of cDNAs for both genes and circularized mRNAs from cob-cox3 showed that neither uses canonical start or stop codons, although a UAA terminator is created in the cob-cox3 fusion mRNA by post-transcriptional oligoadenylation. mRNAs from both genes also use a novel 5' oligo(U) cap. Extensive RNA editing is characteristic of dinoflagellates, but we find no editing in Oxyrrhis. Overall, the combination of characteristics found in the Oxyrrhis genome allows us to plot the sequence of many events that led to the extreme organisation of apicomplexan and dinoflalgellate mitochondrial genomes.

  6. The complete mitochondrial genome of Pseudocellus pearsei (Chelicerata: Ricinulei and a comparison of mitochondrial gene rearrangements in Arachnida

    Directory of Open Access Journals (Sweden)

    Braband Anke

    2007-10-01

    Full Text Available Abstract Background Mitochondrial genomes are widely utilized for phylogenetic and population genetic analyses among animals. In addition to sequence data the mitochondrial gene order and RNA secondary structure data are used in phylogenetic analyses. Arachnid phylogeny is still highly debated and there is a lack of sufficient sequence data for many taxa. Ricinulei (hooded tickspiders are a morphologically distinct clade of arachnids with uncertain phylogenetic affinities. Results The first complete mitochondrial DNA genome of a member of the Ricinulei, Pseudocellus pearsei (Arachnida: Ricinulei was sequenced using a PCR-based approach. The mitochondrial genome is a typical circular duplex DNA molecule with a size of 15,099 bp, showing the complete set of genes usually present in bilaterian mitochondrial genomes. Five tRNA genes (trnW, trnY, trnN, trnL(CUN, trnV show different relative positions compared to other Chelicerata (e.g. Limulus polyphemus, Ixodes spp.. We propose that two events led to this derived gene order: (1 a tandem duplication followed by random deletion and (2 an independent translocation of trnN. Most of the inferred tRNA secondary structures show the common cloverleaf pattern except tRNA-Glu where the TψC-arm is missing. In phylogenetic analyses (maximum likelihood, maximum parsimony, Bayesian inference using concatenated amino acid and nucleotide sequences of protein-coding genes the basal relationships of arachnid orders remain unresolved. Conclusion Phylogenetic analyses (ML, MP, BI of arachnid mitochondrial genomes fail to resolve interordinal relationships of Arachnida and remain in a preliminary stage because there is still a lack of mitogenomic data from important taxa such as Opiliones and Pseudoscorpiones. Gene order varies considerably within Arachnida – only eight out of 23 species have retained the putative arthropod ground pattern. Some gene order changes are valuable characters in phylogenetic analysis of

  7. Sequencing and alignment of mitochondrial genomes of Tibetan chicken and two lowland chicken breeds

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Tibetan chicken lives in high-altitude area and has adapted well to hypoxia genetically. Shouguang chicken and Silky chicken are both lowland chicken breeds. In the present study, the complete mito-chondrial genome sequences of the three chicken breeds were all sequenced. The results showed that the mitochondrial DNAs (mtDNAs) of Shouguang chicken and Silky chicken consist of 16784 bp and 16785 bp respectively, and Tibetan chicken mitochondrial genome varies from 16784 bp to 16786 bp. After sequence analysis, 120 mutations, including 4 single nucleotide polymorphisms (SNPs) in tRNA genes, 9 SNPs and 1 insertion in rRNA genes, 38 SNPs and 1 deletion in D-LOOP, 66 SNPs in pro-tein-coding genes, were found. This work will provide clues for the future study on the association between mitochondrial genes and the adaptation to hypoxia.Tibetan chicken, lowland chicken, mitochondrial genome, hypoxia.

  8. The complete mitochondrial genome of the acid-tolerant fungus Penicillium ShG4C

    Directory of Open Access Journals (Sweden)

    Andrey V. Mardanov

    2016-12-01

    Full Text Available Complete mitochondrial genome of the acid-tolerant fungus Penicillium ShG4C, isolated from oxidized sediments of an abandoned polymetallic mine site, has been sequenced using high-throughput sequencing approach. The mitochondrial genome represents a circular DNA molecule with size of 26,725 bp. It encodes a usual set of mitochondrial genes, including 15 protein coding genes, large and small ribosomal RNAs and 27 tRNA genes. All genes are located on H-strand DNA and transcribed in one direction. Taxonomic analysis based on concatenated sequences of mitochondrial proteins confirmed taxonomic position of this fungus within the genus Penicillium. The sequence of the complete mitochondrial genome of Penicillium ShG4C was deposited in DBBJ/EMBL/GenBank under accession number KX931017.

  9. Organization and comparative analysis of the mitochondrial genomes of bioluminescent Elateroidea (Coleoptera: Polyphaga).

    Science.gov (United States)

    Amaral, Danilo T; Mitani, Yasuo; Ohmiya, Yoshihiro; Viviani, Vadim R

    2016-07-25

    Mitochondrial genome organization in the Elateroidea superfamily (Coleoptera), which include the main families of bioluminescent beetles, has been poorly studied and lacking information about Phengodidae family. We sequenced the mitochondrial genomes of Neotropical Lampyridae (Bicellonycha lividipennis), Phengodidae (Brasilocerus sp.2 and Phrixothrix hirtus) and Elateridae (Pyrearinus termitilluminans, Hapsodrilus ignifer and Teslasena femoralis). All species had a typical insect mitochondrial genome except for the following: in the elaterid T. femoralis genome there is a non-coding region between NADH2 and tRNA-Trp; in the phengodids Brasilocerus sp.2 and P. hirtus genomes we did not find the tRNA-Ile and tRNA-Gln. The P. hirtus genome showed a ~1.6kb non-coding region, the rearrangement of tRNA-Tyr, a new tRNA-Leu copy, and several regions with higher AT contents. Phylogenetics analysis using Bayesian and ML models indicated that the Phengodidae+Rhagophthalmidae are closely related to Lampyridae family, and included Drilus flavescens (Drilidae) as an internal clade within Elateridae. This is the first report that compares the mitochondrial genomes organization of the three main families of bioluminescent Elateroidea, including the first Neotropical Lampyridae and Phengodidae. The losses of tRNAs, and translocation and duplication events found in Phengodidae mt genomes, mainly in P. hirtus, may indicate different evolutionary rates in these mitochondrial genomes. The mitophylogenomics analysis indicates the monophyly of the three bioluminescent families and a closer relationship between Lampyridae and Phengodidae/Rhagophthalmidae, in contrast with previous molecular analysis.

  10. The complete mitochondrial genome of Articulate Brachiopod Terebratal ia transversa

    Energy Technology Data Exchange (ETDEWEB)

    Helfenbein, Kevin G.; Brown, Wesley M.; Boore, Jeffrey L.

    2001-07-01

    We have sequenced the complete mitochondrial DNA (mtDNA) of the articulate brachiopod Terebratalia transversa. The circular genome is 14,291 bp in size, relatively small compared to other published metazoan mtDNAs. The 37 genes commonly found in animal mtDNA are present; the size decrease is due to the truncation of several tRNA, rRNA, and protein genes, to some nucleotide overlaps, and to a paucity of non-coding nucleotides. Although the gene arrangement differs radically from those reported for other metazoans, some gene junctions are shared with two other articulate brachiopods, Laqueus rubellus and Terebratulina retusa. All genes in the T. transversa mtDNA, unlike those in most metazoan mtDNAs reported, are encoded by the same strand. The A+T content (59.1 percent) is low for a metazoan mtDNA, and there is a high propensity for homopolymer runs and a strong base-compositional strand bias. The coding strand is quite G+T-rich, a skew that is shared by the confamilial (laqueid) specie s L. rubellus, but opposite to that found in T. retusa, a cancellothyridid. These compositional skews are strongly reflected in the codon usage patterns and the amino acid compositions of the mitochondrial proteins, with markedly different usage observed between T. retusa and the two laqueids. This observation, plus the similarity of the laqueid non-coding regions to the reverse complement of the non-coding region of the cancellothyridid, suggest that an inversion that resulted in a reversal in the direction of first-strand replication has occurred in one of the two lineages. In addition to the presence of one non-coding region in T. transversa that is comparable to those in the other brachiopod mtDNAs, there are two others with the potential to form secondary structures; one or both of these may be involved in the process of transcript cleavage.

  11. The adaptive evolution of the mammalian mitochondrial genome

    Directory of Open Access Journals (Sweden)

    O'Brien Stephen J

    2008-03-01

    Full Text Available Abstract Background The mitochondria produce up to 95% of a eukaryotic cell's energy through oxidative phosphorylation. The proteins involved in this vital process are under high functional constraints. However, metabolic requirements vary across species, potentially modifying selective pressures. We evaluate the adaptive evolution of 12 protein-coding mitochondrial genes in 41 placental mammalian species by assessing amino acid sequence variation and exploring the functional implications of observed variation in secondary and tertiary protein structures. Results Wide variation in the properties of amino acids were observed at functionally important regions of cytochrome b in species with more-specialized metabolic requirements (such as adaptation to low energy diet or large body size, such as in elephant, dugong, sloth, and pangolin, and adaptation to unusual oxygen requirements, for example diving in cetaceans, flying in bats, and living at high altitudes in alpacas. Signatures of adaptive variation in the NADH dehydrogenase complex were restricted to the loop regions of the transmembrane units which likely function as protons pumps. Evidence of adaptive variation in the cytochrome c oxidase complex was observed mostly at the interface between the mitochondrial and nuclear-encoded subunits, perhaps evidence of co-evolution. The ATP8 subunit, which has an important role in the assembly of F0, exhibited the highest signal of adaptive variation. ATP6, which has an essential role in rotor performance, showed a high adaptive variation in predicted loop areas. Conclusion Our study provides insight into the adaptive evolution of the mtDNA genome in mammals and its implications for the molecular mechanism of oxidative phosphorylation. We present a framework for future experimental characterization of the impact of specific mutations in the function, physiology, and interactions of the mtDNA encoded proteins involved in oxidative phosphorylation.

  12. Complete mitochondrial genome of the endangered roughskin sculpin Trachidermus fasciatus (Scorpaeniformes, Cottidae).

    Science.gov (United States)

    Zeng, Zhen; Liu, Zhi Zhi; Pan, Lian De; Tang, Shou Jie; Wang, Cong Tao; Tang, Wen Qiao; Yang, Jin Quan

    2012-12-01

    In this study, the complete mitochondrial genome of the endangered roughskin sculpin, Trachidermus fasciatus, was first determined. The mitogenome (16,536 bp) consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. Except for the eight tRNA and ND6 genes, all other mitochondrial genes were encoded on the heavy strand. Mitochondrial DNA information can assist in species identification and conservation of the species' natural resources.

  13. The complete mitochondrial genome of the silvertip tetra, Hasemania nana (Characiformes: Characidae).

    Science.gov (United States)

    Xu, Ru; Zhao, Zi-Xia; Xu, Peng; Sun, Xiao-Wen

    2015-01-01

    We first sequenced the complete mitochondrial genome of silvertip tetra (Hasemania nana). The mitogenome was determined to be 16,581 bp long circular molecule with a typical gene arrangement of vertebrate mitochondrial DNA. All genes were encoded on the heavy strand with the exception of ND6 and eight tRNA genes. Mitochondrial DNA information provided the basis for the studies in species identification and conservation of the species' natural resources.

  14. The complete mitochondrial genome sequence of Diannan small-ear pig (Sus Scrofa).

    Science.gov (United States)

    Wang, Ling-Yu; Xu, Dong; Xiao, Ding-Fu; Ma, Hai-Ming

    2016-01-01

    In this study, the complete mitochondrial genome sequence of Diannan small-ear pig in Yunnan Province was firstly reported, which was determined through polymerase chain reaction (PCR) method. The total length of mitochondrial genome of Diannan small-ear pig was 16720 bp, including 34.77% A, 26.18% C, 25.81% T and 13.24% G, and in the order A > C > T > G. Mitochondrial genome contained a major non-coding control region (D-Loop region), 2 ribosomal RNA genes, 13 protein-coding genes (PCGs) and 22 transfer RNA genes. The mitochondrial genome of Diannan small-ear pig provides an important data set for the study on genetic mechanism.

  15. The mitochondrial genome of the wood-degrading basidiomycete Trametes cingulata.

    Science.gov (United States)

    Haridas, Sajeet; Gantt, J Stephen

    2010-07-01

    We present the 91,500 bp mitochondrial genome of the wood-degrading basidiomycete Trametes cingulata and compare it with the mitochondrial genomes of five additional Basidiomycota species. The Trametes mitochondrial genome encodes 15 proteins, 25 tRNAs and the small and large rRNAs. All of the genes, except one tRNA, are found on the same DNA strand. Several additional ORFs have also been identified; however, their sequences have not been conserved across the species we compared and they show no similarity to any known gene, suggesting that they may not correspond to authentic genes. The presence of endonuclease-like sequences in introns suggests a mechanism that explains the diversity of mitochondrial genome sizes that are unrelated to the gene content.

  16. Complete DNA sequence of the linear mitochondrial genome of the pathogenic yeast Candida parapsilosis

    DEFF Research Database (Denmark)

    Nosek, J.; Novotna, M.; Hlavatovicova, Z.

    2004-01-01

    The complete sequence of the mitochondrial DNA of the opportunistic yeast pathogen Candida parapsilosis was determined. The mitochondrial genome is represented by linear DNA molecules terminating with tandem repeats of a 738-bp unit. The number of repeats varies, thus generating a population...

  17. Complete DNA sequence of the linear mitochondrial genome of the pathogenic yeast Candida parapsilosis

    DEFF Research Database (Denmark)

    Nosek, J.; Novotna, M.; Hlavatovicova, Z.

    2004-01-01

    The complete sequence of the mitochondrial DNA of the opportunistic yeast pathogen Candida parapsilosis was determined. The mitochondrial genome is represented by linear DNA molecules terminating with tandem repeats of a 738-bp unit. The number of repeats varies, thus generating a population...

  18. Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore

    Science.gov (United States)

    Brian J. Knaus; Richard Cronn; Aaron Liston; Kristine Pilgrim; Michael K. Schwartz

    2011-01-01

    Science-based wildlife management relies on genetic information to infer population connectivity and identify conservation units. The most commonly used genetic marker for characterizing animal biodiversity and identifying maternal lineages is the mitochondrial genome. Mitochondrial genotyping figures prominently in conservation and management plans, with much of the...

  19. Evolution along the mutation gradient in the dynamic mitochondrial genome of salamanders.

    Science.gov (United States)

    Chong, Rebecca A; Mueller, Rachel Lockridge

    2013-01-01

    Mitochondria are intracellular organelles where oxidative phosphorylation is carried out to complete ATP synthesis. Mitochondria have their own genome; in metazoans, this is a small, circular molecule encoding 13 electron transport proteins, 22 tRNAs, and 2 rRNAs. In invertebrates, mitochondrial gene rearrangement is common, and it is correlated with increased substitution rates. In vertebrates, mitochondrial gene rearrangement is rare, and its relationship to substitution rate remains unexplored. Mitochondrial genes can also show spatial variation in substitution rates around the genome due to the mechanism of mtDNA replication, which produces a mutation gradient. To date, however, the strength of the mutation gradient and whether movement along the gradient in rearranged (or otherwise modified) genomes impacts genic substitution rates remain unexplored in the majority of vertebrates. Salamanders include both normal mitochondrial genomes and independently derived rearrangements and expansions, providing a rare opportunity to test the effects of large-scale changes to genome architecture on vertebrate mitochondrial gene sequence evolution. We show that: 1) rearranged/expanded genomes have higher substitution rates; 2) most genes in rearranged/expanded genomes maintain their position along the mutation gradient, substitution rates of the genes that do move are unaffected by their new position, and the gradient in salamanders is weak; and 3) genomic rearrangements/expansions occur independent of levels of selective constraint on genes. Together, our results demonstrate that large-scale changes to genome architecture impact mitochondrial gene evolution in predictable ways; however, despite these impacts, the same functional constraints act on mitochondrial protein-coding genes in both modified and normal genomes.

  20. CHCHD10 mutations promote loss of mitochondrial cristae junctions with impaired mitochondrial genome maintenance and inhibition of apoptosis.

    Science.gov (United States)

    Genin, Emmanuelle C; Plutino, Morgane; Bannwarth, Sylvie; Villa, Elodie; Cisneros-Barroso, Eugenia; Roy, Madhuparna; Ortega-Vila, Bernardo; Fragaki, Konstantina; Lespinasse, Françoise; Pinero-Martos, Estefania; Augé, Gaëlle; Moore, David; Burté, Florence; Lacas-Gervais, Sandra; Kageyama, Yusuke; Itoh, Kie; Yu-Wai-Man, Patrick; Sesaki, Hiromi; Ricci, Jean-Ehrland; Vives-Bauza, Cristofol; Paquis-Flucklinger, Véronique

    2016-01-01

    CHCHD10-related diseases include mitochondrial DNA instability disorder, frontotemporal dementia-amyotrophic lateral sclerosis (FTD-ALS) clinical spectrum, late-onset spinal motor neuropathy (SMAJ), and Charcot-Marie-Tooth disease type 2 (CMT2). Here, we show that CHCHD10 resides with mitofilin, CHCHD3 and CHCHD6 within the "mitochondrial contact site and cristae organizing system" (MICOS) complex. CHCHD10 mutations lead to MICOS complex disassembly and loss of mitochondrial cristae with a decrease in nucleoid number and nucleoid disorganization. Repair of the mitochondrial genome after oxidative stress is impaired in CHCHD10 mutant fibroblasts and this likely explains the accumulation of deleted mtDNA molecules in patient muscle. CHCHD10 mutant fibroblasts are not defective in the delivery of mitochondria to lysosomes suggesting that impaired mitophagy does not contribute to mtDNA instability. Interestingly, the expression of CHCHD10 mutant alleles inhibits apoptosis by preventing cytochrome c release.

  1. The complete mitochondrial genomes of two band-winged grasshoppers, Gastrimargus marmoratus and Oedaleus asiaticus

    Directory of Open Access Journals (Sweden)

    Kang Le

    2009-04-01

    Full Text Available Abstract Background The two closely related species of band-winged grasshoppers, Gastrimargus marmoratus and Oedaleus asiaticus, display significant differences in distribution, biological characteristics and habitat preferences. They are so similar to their respective congeneric species that it is difficult to differentiate them from other species within each genus. Hoppers of the two species have quite similar morphologies to that of Locusta migratoria, hence causing confusion in species identification. Thus we determined and compared the mitochondrial genomes of G. marmoratus and O. asiaticus to address these questions. Results The complete mitochondrial genomes of G. marmoratus and O. asiaticus are 15,924 bp and 16,259 bp in size, respectively, with O. asiaticus being the largest among all known mitochondrial genomes in Orthoptera. Both mitochondrial genomes contain a standard set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and an A+T-rich region in the same order as those of the other analysed caeliferan species, but different from those of the ensiferan species by the rearrangement of trnD and trnK. The putative initiation codon for the cox1 gene in the two species is ATC. The presence of different sized tandem repeats in the A+T-rich region leads to size variation between their mitochondrial genomes. Except for nad2, nad4L, and nad6, most of the caeliferan mtDNA genes exhibit low levels of divergence. In phylogenetic analyses, the species from the suborder Caelifera form a monophyletic group, as is the case for the Ensifera. Furthermore, the two suborders cluster as sister groups, supporting the monophyly of Orthoptera. Conclusion The mitochondrial genomes of both G. marmoratus and O. asiaticus harbor the typical 37 genes and an A+T-rich region, exhibiting similar characters to those of other grasshopper species. Characterization of the two mitochondrial genomes has enriched our knowledge on mitochondrial

  2. Complete Mitochondrial Genome Sequence of the Eastern Gorilla (Gorilla beringei) and Implications for African Ape Biogeography

    OpenAIRE

    Das, Ranajit; Hergenrother, Scott D.; Soto-Calderón, Iván D.; Dew, J. Larry; Anthony, Nicola M; Jensen-Seaman, Michael I

    2014-01-01

    The Western and Eastern species of gorillas (Gorilla gorilla and Gorilla beringei) began diverging in the mid-Pleistocene, but in a complex pattern with ongoing gene flow following their initial split. We sequenced the complete mitochondrial genomes of 1 Eastern and 1 Western gorilla to provide the most accurate date for their mitochondrial divergence, and to analyze patterns of nucleotide substitutions. The most recent common ancestor of these genomes existed about 1.9 million years ago, sli...

  3. The Complete Mitochondrial Genome of the Foodborne Parasitic Pathogen Cyclospora cayetanensis.

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    Hediye Nese Cinar

    Full Text Available Cyclospora cayetanensis is a human-specific coccidian parasite responsible for several food and water-related outbreaks around the world, including the most recent ones involving over 900 persons in 2013 and 2014 outbreaks in the USA. Multicopy organellar DNA such as mitochondrion genomes have been particularly informative for detection and genetic traceback analysis in other parasites. We sequenced the C. cayetanensis genomic DNA obtained from stool samples from patients infected with Cyclospora in Nepal using the Illumina MiSeq platform. By bioinformatically filtering out the metagenomic reads of non-coccidian origin sequences and concentrating the reads by targeted alignment, we were able to obtain contigs containing Eimeria-like mitochondrial, apicoplastic and some chromosomal genomic fragments. A mitochondrial genomic sequence was assembled and confirmed by cloning and sequencing targeted PCR products amplified from Cyclospora DNA using primers based on our draft assembly sequence. The results show that the C. cayetanensis mitochondrion genome is 6274 bp in length, with 33% GC content, and likely exists in concatemeric arrays as in Eimeria mitochondrial genomes. Phylogenetic analysis of the C. cayetanensis mitochondrial genome places this organism in a tight cluster with Eimeria species. The mitochondrial genome of C. cayetanensis contains three protein coding genes, cytochrome (cytb, cytochrome C oxidase subunit 1 (cox1, and cytochrome C oxidase subunit 3 (cox3, in addition to 14 large subunit (LSU and nine small subunit (SSU fragmented rRNA genes.

  4. The Armc10/SVH gene: genome context, regulation of mitochondrial dynamics and protection against Aβ-induced mitochondrial fragmentation

    Science.gov (United States)

    Serrat, R; Mirra, S; Figueiro-Silva, J; Navas-Pérez, E; Quevedo, M; López-Doménech, G; Podlesniy, P; Ulloa, F; Garcia-Fernàndez, J; Trullas, R; Soriano, E

    2014-01-01

    Mitochondrial function and dynamics are essential for neurotransmission, neural function and neuronal viability. Recently, we showed that the eutherian-specific Armcx gene cluster (Armcx1–6 genes), located in the X chromosome, encodes for a new family of proteins that localise to mitochondria, regulating mitochondrial trafficking. The Armcx gene cluster evolved by retrotransposition of the Armc10 gene mRNA, which is present in all vertebrates and is considered to be the ancestor gene. Here we investigate the genomic organisation, mitochondrial functions and putative neuroprotective role of the Armc10 ancestor gene. The genomic context of the Armc10 locus shows considerable syntenic conservation among vertebrates, and sequence comparisons and CHIP-data suggest the presence of at least three conserved enhancers. We also show that the Armc10 protein localises to mitochondria and that it is highly expressed in the brain. Furthermore, we show that Armc10 levels regulate mitochondrial trafficking in neurons, but not mitochondrial aggregation, by controlling the number of moving mitochondria. We further demonstrate that the Armc10 protein interacts with the KIF5/Miro1-2/Trak2 trafficking complex. Finally, we show that overexpression of Armc10 in neurons prevents Aβ-induced mitochondrial fission and neuronal death. Our data suggest both conserved and differential roles of the Armc10/Armcx gene family in regulating mitochondrial dynamics in neurons, and underscore a protective effect of the Armc10 gene against Aβ-induced toxicity. Overall, our findings support a further degree of regulation of mitochondrial dynamics in the brain of more evolved mammals. PMID:24722288

  5. Complete mitochondrial genome sequence of the polychaete annelidPlatynereis dumerilii

    Energy Technology Data Exchange (ETDEWEB)

    Boore, Jeffrey L.

    2004-08-15

    Complete mitochondrial genome sequences are now available for 126 metazoans (see Boore 1999; Mitochondrial Genomics link at http://www.jgi.doe.gov), but the taxonomic representation is highly biased. For example, 80 are from a single phylum, Chordata, and show little variation for many molecular features. Arthropoda is represented by 16 taxa, Mollusca by eight, and Echinodermata by five, with only 17 others from the remaining {approx}30 metazoan phyla. With few exceptions (see Wolstenholme 1992 and Boore 1999) these are circular DNA molecules, about 16 kb in size, and encode the same set of 37 genes. A variety of non-standard names are sometimes used for animal mitochondrial genes; see Boore (1999) for gene nomenclature and a table of synonyms. Mitochondrial genome comparisons serve as a model of genome evolution. In this system, much smaller and simpler than that of the nucleus, are all of the same factors of genome evolution, where one may find tractable the changes in tRNA structure, base composition, genetic code, gene arrangement, etc. Further, patterns of mitochondrial gene rearrangements are an exceptionally reliable indicator of phylogenetic relationships (Smith et al.1993; Boore et al. 1995; Boore, Lavrov, and Brown 1998; Boore and Brown 1998, 2000; Dowton 1999; Stechmann and Schlegel 1999; Kurabayashi and Ueshima 2000). To these ends, we are sampling further the variation among major animal groups in features of their mitochondrial genomes.

  6. Comparing models on the genealogical relationships among Neandertal, Cro-Magnoid and modern Europeans by serial coalescent simulations.

    Science.gov (United States)

    Belle, E M S; Benazzo, A; Ghirotto, S; Colonna, V; Barbujani, G

    2009-03-01

    Populations of anatomically archaic (Neandertal) and early modern (Cro-Magnoid) humans are jointly documented in the European fossil record, in the period between 40 000 and 25 000 years BP, but the large differences between their cultures, morphologies and DNAs suggest that the two groups were not close relatives. However, it is still unclear whether any genealogical continuity between them can be ruled out. Here, we simulated a broad range of demographic scenarios by means of a serial coalescence algorithm in which Neandertals, Cro-Magnoids and modern Europeans were either part of the same mitochondrial genealogy or of two separate genealogies. Mutation rates, population sizes, population structure and demographic growth rates varied across simulations. All models in which anatomically modern (that is, Cro-Magnoid and current) Europeans belong to a distinct genealogy performed better than any model in which the three groups were assigned to the same mitochondrial genealogy. The maximum admissible level of gene flow between Neandertals and the ancestors of current Europeans is 0.001% per generation, one order of magnitude lower than estimated in previous studies not considering genetic data on Cro-Magnoid people.

  7. MITOS: improved de novo metazoan mitochondrial genome annotation.

    Science.gov (United States)

    Bernt, Matthias; Donath, Alexander; Jühling, Frank; Externbrink, Fabian; Florentz, Catherine; Fritzsch, Guido; Pütz, Joern; Middendorf, Martin; Stadler, Peter F

    2013-11-01

    About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. This annotation information, which has accumulated over two decades, has been obtained with a diverse set of computational tools and annotation strategies. Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations in particular for the RNA genes. Taken together, this causes substantial problems for fully automatic pipelines that aim to use these data comprehensively for studies of animal phylogenetics and the molecular evolution of mitogenomes. The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences. We show that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality. At the same time we avoid biases, inconsistencies of nomenclature, and typos originating from manual curation strategies. The MITOS pipeline is accessible online at http://mitos.bioinf.uni-leipzig.de. Copyright © 2012 Elsevier Inc. All rights reserved.

  8. The mitochondrial genome of the butterfly Polyura schreiber (Lepidoptera: Nymphalidae).

    Science.gov (United States)

    Song, Fan; Cao, Tianwen; Cao, Liangming; Li, Hu; Wang, Juping; Xuan, Shanbin

    2016-09-01

    The nearly complete mitochondrial genome (mitogenome) of the butterfly, Polyura schreiber, was determined. The sequenced mitogenome is a typical circular DNA molecule of 15 320 bp, containing 13 protein-coding genes, two rRNA genes, 21 tRNA genes, and a putative control region. tRNA(Phe) was failed to sequence, which was presumed to be located between tRNA(Glu) and ND5. Protein-coding genes all initiate with ATN codons and terminate with TAA codons except for COII and ND5 use a single T residue as the termination codon. All tRNAs have the clover-leaf structure except for the tRNA(Ser(AGN)) and the length of them range from 65 to 71 bp. The control region is 412 bp long with an A + T content of 90.5%. Our phylogenetic analysis recovered the sister-group relationship between Charaxinae and Satyrinae.

  9. Complete mitochondrial genome of Zebra tilapia, Tilapia buttikoferi.

    Science.gov (United States)

    Mu, Xi-Dong; Liu, Chao; Wang, Xue-Jie; Liu, Yi; Hu, Yin-Chang; Luo, Jian-Ren

    2016-01-01

    We determined the complete mitochondrial genome of Tilapia buttikoferi, which was 16,577 bp in length with an A + T content of 53.0%, containing 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a complete control region. The gene arrangement was similar to that of typical fishes. The total base composition of the mitogenome was 25.6% T, 30.8% C, 27.4% A and 16.2% G. Of the 13 protein-coding genes, 12 genes start with an ATG codon, except for COX1 with GTG. Seven (ND1, ND2, COX1, ATPase8, ATPase6, ND4L and ND6) used TAA or AGA as the termination codon, whereas six (COX2, COX3, ND3, ND4, ND5 and cyt b) had incomplete stop codon T. Its control region was atypical in being short at 861 bp, and contained TACAT motif and one microsatellite-like region (TA)7. This mitogenome sequence data may be useful for phylogenetic and systematic analyses within the family Cichlaidae.

  10. Complete mitochondrial genome of yellow meal worm (Tenebrio molitor).

    Science.gov (United States)

    Liu, Li-Na; Wang, Cheng-Ye

    2014-11-18

    The yellow meal worm (Tenebrio molitor L.) is an important resource insect typically used as animal feed additive. It is also widely used for biological research. The first complete mitochondrial genome of T. molitor was determined for the first time by long PCR and conserved primer walking approaches. The results showed that the entire mitogenome of T. molitor was 15 785 bp long, with 72.35% A+T content [deposited in GenBank with accession number KF418153]. The gene order and orientation were the same as the most common type suggested as ancestral for insects. Two protein-coding genes used atypical start codons (CTA in ND2 and AAT in COX1), and the remaining 11 protein-coding genes started with a typical insect initiation codon ATN. All tRNAs showed standard clover-leaf structure, except for tRNA(Ser) (AGN), which lacked a dihydrouridine (DHU) arm. The newly added T. molitor mitogenome could provide information for future studies on yellow meal worm.

  11. RECG maintains plastid and mitochondrial genome stability by suppressing extensive recombination between short dispersed repeats.

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    Masaki Odahara

    2015-03-01

    Full Text Available Maintenance of plastid and mitochondrial genome stability is crucial for photosynthesis and respiration, respectively. Recently, we have reported that RECA1 maintains mitochondrial genome stability by suppressing gross rearrangements induced by aberrant recombination between short dispersed repeats in the moss Physcomitrella patens. In this study, we studied a newly identified P. patens homolog of bacterial RecG helicase, RECG, some of which is localized in both plastid and mitochondrial nucleoids. RECG partially complements recG deficiency in Escherichia coli cells. A knockout (KO mutation of RECG caused characteristic phenotypes including growth delay and developmental and mitochondrial defects, which are similar to those of the RECA1 KO mutant. The RECG KO cells showed heterogeneity in these phenotypes. Analyses of RECG KO plants showed that mitochondrial genome was destabilized due to a recombination between 8-79 bp repeats and the pattern of the recombination partly differed from that observed in the RECA1 KO mutants. The mitochondrial DNA (mtDNA instability was greater in severe phenotypic RECG KO cells than that in mild phenotypic ones. This result suggests that mitochondrial genomic instability is responsible for the defective phenotypes of RECG KO plants. Some of the induced recombination caused efficient genomic rearrangements in RECG KO mitochondria. Such loci were sometimes associated with a decrease in the levels of normal mtDNA and significant decrease in the number of transcripts derived from the loci. In addition, the RECG KO mutation caused remarkable plastid abnormalities and induced recombination between short repeats (12-63 bp in the plastid DNA. These results suggest that RECG plays a role in the maintenance of both plastid and mitochondrial genome stability by suppressing aberrant recombination between dispersed short repeats; this role is crucial for plastid and mitochondrial functions.

  12. Evolution of the mitochondrial genome in snakes: Gene rearrangements and phylogenetic relationships

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    Zhou Kaiya

    2008-11-01

    Full Text Available Abstract Background Snakes as a major reptile group display a variety of morphological characteristics pertaining to their diverse behaviours. Despite abundant analyses of morphological characters, molecular studies using mitochondrial and nuclear genes are limited. As a result, the phylogeny of snakes remains controversial. Previous studies on mitochondrial genomes of snakes have demonstrated duplication of the control region and translocation of trnL to be two notable features of the alethinophidian (all serpents except blindsnakes and threadsnakes mtDNAs. Our purpose is to further investigate the gene organizations, evolution of the snake mitochondrial genome, and phylogenetic relationships among several major snake families. Results The mitochondrial genomes were sequenced for four taxa representing four different families, and each had a different gene arrangement. Comparative analyses with other snake mitochondrial genomes allowed us to summarize six types of mitochondrial gene arrangement in snakes. Phylogenetic reconstruction with commonly used methods of phylogenetic inference (BI, ML, MP, NJ arrived at a similar topology, which was used to reconstruct the evolution of mitochondrial gene arrangements in snakes. Conclusion The phylogenetic relationships among the major families of snakes are in accordance with the mitochondrial genomes in terms of gene arrangements. The gene arrangement in Ramphotyphlops braminus mtDNA is inferred to be ancestral for snakes. After the divergence of the early Ramphotyphlops lineage, three types of rearrangements occurred. These changes involve translocations within the IQM tRNA gene cluster and the duplication of the CR. All phylogenetic methods support the placement of Enhydris plumbea outside of the (Colubridae + Elapidae cluster, providing mitochondrial genomic evidence for the familial rank of Homalopsidae.

  13. Complete mitochondrial genome of the Kikuchi's minnow Aphyocypris kikuchii (Teleostei, Cyprinidae).

    Science.gov (United States)

    Jang-Liaw, Nian-Hong; Tsai, Chi-Li; Watanabe, Katsutoshi

    2013-02-01

    We have sequenced the complete mitochondrial genome of the Kikuchi's minnow, Aphyocypris kikuchii (Oshima 1919), which is an endemic species to Taiwan. The complete mitochondrial genome is 16,601 bp in size, containing 37 genes coding for 13 proteins, 2 rRNAs, 22 tRNAs, and 1 control region. It has the typical vertebrate mitochondrial gene arrangement. The sequence information could play an important role in resolving the conflict on its current taxonomic position and preservation of genetic resources for helping conservation of the endangered species.

  14. The complete chloroplast and mitochondrial genome sequences of Boea hygrometrica: insights into the evolution of plant organellar genomes.

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    Tongwu Zhang

    Full Text Available The complete nucleotide sequences of the chloroplast (cp and mitochondrial (mt genomes of resurrection plant Boea hygrometrica (Bh, Gesneriaceae have been determined with the lengths of 153,493 bp and 510,519 bp, respectively. The smaller chloroplast genome contains more genes (147 with a 72% coding sequence, and the larger mitochondrial genome have less genes (65 with a coding faction of 12%. Similar to other seed plants, the Bh cp genome has a typical quadripartite organization with a conserved gene in each region. The Bh mt genome has three recombinant sequence repeats of 222 bp, 843 bp, and 1474 bp in length, which divide the genome into a single master circle (MC and four isomeric molecules. Compared to other angiosperms, one remarkable feature of the Bh mt genome is the frequent transfer of genetic material from the cp genome during recent Bh evolution. We also analyzed organellar genome evolution in general regarding genome features as well as compositional dynamics of sequence and gene structure/organization, providing clues for the understanding of the evolution of organellar genomes in plants. The cp-derived sequences including tRNAs found in angiosperm mt genomes support the conclusion that frequent gene transfer events may have begun early in the land plant lineage.

  15. The complete chloroplast and mitochondrial genome sequences of Boea hygrometrica: insights into the evolution of plant organellar genomes.

    Science.gov (United States)

    Zhang, Tongwu; Fang, Yongjun; Wang, Xumin; Deng, Xin; Zhang, Xiaowei; Hu, Songnian; Yu, Jun

    2012-01-01

    The complete nucleotide sequences of the chloroplast (cp) and mitochondrial (mt) genomes of resurrection plant Boea hygrometrica (Bh, Gesneriaceae) have been determined with the lengths of 153,493 bp and 510,519 bp, respectively. The smaller chloroplast genome contains more genes (147) with a 72% coding sequence, and the larger mitochondrial genome have less genes (65) with a coding faction of 12%. Similar to other seed plants, the Bh cp genome has a typical quadripartite organization with a conserved gene in each region. The Bh mt genome has three recombinant sequence repeats of 222 bp, 843 bp, and 1474 bp in length, which divide the genome into a single master circle (MC) and four isomeric molecules. Compared to other angiosperms, one remarkable feature of the Bh mt genome is the frequent transfer of genetic material from the cp genome during recent Bh evolution. We also analyzed organellar genome evolution in general regarding genome features as well as compositional dynamics of sequence and gene structure/organization, providing clues for the understanding of the evolution of organellar genomes in plants. The cp-derived sequences including tRNAs found in angiosperm mt genomes support the conclusion that frequent gene transfer events may have begun early in the land plant lineage.

  16. Presence of two mitochondrial genomes in the mytilid Perumytilus purpuratus: Phylogenetic evidence for doubly uniparental inheritance

    Science.gov (United States)

    Vargas, Jaime; Pérez, Montse; Toro, Jorge; Astorga, Marcela P.

    2015-01-01

    This study presents evidence, using sequences of ribosomal 16S and COI mtDNA, for the presence of two mitochondrial genomes in Perumytilus purpuratus. This may be considered evidence of doubly uniparental mtDNA inheritance. The presence of the two types of mitochondrial genomes differentiates females from males. The F genome was found in the somatic and gonadal tissues of females and in the somatic tissues of males; the M genome was found in the gonads and mantle of males only. For the mitochondrial 16S region, ten haplotypes were found for the F genome (nucleotide diversity 0.004), and 7 haplotypes for the M genome (nucleotide diversity 0.001), with a distance Dxy of 0.125 and divergence Kxy of 60.33%. For the COI gene 17 haplotypes were found for the F genome (nucleotide diversity 0.009), and 10 haplotypes for the M genome (nucleotide diversity 0.010), with a genetic distance Dxy of 0.184 and divergence Kxy of 99.97%. Our results report the presence of two well-differentiated, sex-specific types of mitochondrial genome (one present in the male gonad, the other in the female gonad), implying the presence of DUI in P. purpuratus. These results indicate that care must be taken in phylogenetic comparisons using mtDNA sequences of P. purpuratus without considering the sex of the individuals. PMID:26273220

  17. A complete mitochondrial genome of wheat (Triticum aestivum cv. Chinese Yumai), and fast evolving mitochondrial genes in higher plants

    Indian Academy of Sciences (India)

    Peng Cui; Huitao Liu; Qiang Lin; Feng Ding; Guoyin Zhuo; Songnian Hu; Dongcheng Liu; Wenlong Yang; Kehui Zhan; Aimin Zhang; Jun Yu

    2009-12-01

    Plant mitochondrial genomes, encoding necessary proteins involved in the system of energy production, play an important role in the development and reproduction of the plant. They occupy a specific evolutionary pattern relative to their nuclear counterparts. Here, we determined the winter wheat (Triticum aestivum cv. Chinese Yumai) mitochondrial genome in a length of 452 and 526 bp by shotgun sequencing its BAC library. It contains 202 genes, including 35 known protein-coding genes, three rRNA and 17 tRNA genes, as well as 149 open reading frames (ORFs; greater than 300 bp in length). The sequence is almost identical to the previously reported sequence of the spring wheat (T. aestivum cv. Chinese Spring); we only identified seven SNPs (three transitions and four transversions) and 10 indels (insertions and deletions) between the two independently acquired sequences, and all variations were found in non-coding regions. This result confirmed the accuracy of the previously reported mitochondrial sequence of the Chinese Spring wheat. The nucleotide frequency and codon usage of wheat are common among the lineage of higher plant with a high AT-content of 58%. Molecular evolutionary analysis demonstrated that plant mitochondrial genomes evolved at different rates, which may correlate with substantial variations in metabolic rate and generation time among plant lineages. In addition, through the estimation of the ratio of non-synonymous to synonymous substitution rates between orthologous mitochondrion-encoded genes of higher plants, we found an accelerated evolutionary rate that seems to be the result of relaxed selection.

  18. A novel mitochondrial genome architecture in thrips (Insecta: Thysanoptera): extreme size asymmetry among chromosomes and possible recent control region duplication

    Science.gov (United States)

    Multi-partite mitochondrial genomes are very rare in animals but have been found previously in two insect orders with highly rearranged genomes, the Phthiraptera (parasitic lice), and the Psocoptera (booklice/barklice). We provide the first report of a multi-partite mitochondrial genome architecture...

  19. Horizontal transfer of DNA from the mitochondrial to the plastid genome and its subsequent evolution in milkweeds (Apocynaceae)

    Science.gov (United States)

    Shannon C.K. Straub; Richard C. Cronn; Christopher Edwards; Mark Fishbein; Aaron. Liston

    2013-01-01

    Horizontal gene transfer (HGT) of DNA from the plastid to the nuclear and mitochondrial genomes of higher plants is a common phenomenon; however, plastid genomes (plastomes) are highly conserved and have generally been regarded as impervious to HGT. We sequenced the 158 kb plastome and the 690 kb mitochondrial genome of common milkweed (Asclepias syriaca [Apocynaceae...

  20. Small inverted repeats drive mitochondrial genome evolution in Lake Baikal sponges.

    Science.gov (United States)

    Lavrov, Dennis V; Maikova, Olga O; Pett, Walker; Belikov, Sergey I

    2012-08-15

    Demosponges, the largest and most diverse class in the phylum Porifera, possess mitochondrial DNA (mtDNA) markedly different from that in other animals. Although several studies investigated evolution of demosponge mtDNA among major lineages of the group, the changes within these groups remain largely unexplored. Recently we determined mitochondrial genomic sequence of the Lake Baikal sponge Lubomirskia baicalensis and described proliferation of small inverted repeats (hairpins) that occurred in it since the divergence between L. baicalensis and the most closely related cosmopolitan freshwater sponge Ephydatia muelleri. Here we report mitochondrial genomes of three additional species of Lake Baikal sponges: Swartschewskia papyracea, Rezinkovia echinata and Baikalospongia intermedia morpha profundalis (Demospongiae, Haplosclerida, Lubomirskiidae) and from a more distantly related freshwater sponge Corvomeyenia sp. (Demospongiae, Haplosclerida, Metaniidae). We use these additional sequences to explore mtDNA evolution in Baikalian sponges, paying particular attention to the variation in the rates of nucleotide substitutions and the distribution of hairpins, abundant in these genomes. We show that most of the changes in Lubomirskiidae mitochondrial genomes are due to insertion/deletion/duplication of these elements rather than single nucleotide substitutions. Thus inverted repeats can act as an important force in evolution of mitochondrial genome architecture and be a valuable marker for population- and species-level studies in this group. In addition, we infer (((Rezinkovia+Lubomirskia)+Swartschewskia)+Baikalospongia) phylogeny for the family Lubomirskiidae based on the analysis of mitochondrial coding sequences from freshwater sponges.

  1. The mitochondrial genome structure of Xenoturbella bocki (phylum Xenoturbellida is ancestral within the deuterostomes

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    Lanfear Robert

    2009-05-01

    Full Text Available Abstract Background Mitochondrial genome comparisons contribute in multiple ways when inferring animal relationships. As well as primary sequence data, rare genomic changes such as gene order, shared gene boundaries and genetic code changes, which are unlikely to have arisen through convergent evolution, are useful tools in resolving deep phylogenies. Xenoturbella bocki is a morphologically simple benthic marine worm recently found to belong among the deuterostomes. Here we present analyses comparing the Xenoturbella bocki mitochondrial gene order, genetic code and control region to those of other metazoan groups. Results The complete mitochondrial genome sequence of Xenoturbella bocki was determined. The gene order is most similar to that of the chordates and the hemichordates, indicating that this conserved mitochondrial gene order might be ancestral to the deuterostome clade. Using data from all phyla of deuterostomes, we infer the ancestral mitochondrial gene order for this clade. Using inversion and breakpoint analyses of metazoan mitochondrial genomes, we test conflicting hypotheses for the phylogenetic placement of Xenoturbella and find a closer affinity to the hemichordates than to other metazoan groups. Comparative analyses of the control region reveal similarities in the transcription initiation and termination sites and origin of replication of Xenoturbella with those of the vertebrates. Phylogenetic analyses of the mitochondrial sequence indicate a weakly supported placement as a basal deuterostome, a result that may be the effect of compositional bias. Conclusion The mitochondrial genome of Xenoturbella bocki has a very conserved gene arrangement in the deuterostome group, strikingly similar to that of the hemichordates and the chordates, and thus to the ancestral deuterostome gene order. Similarity to the hemichordates in particular is suggested by inversion and breakpoint analysis. Finally, while phylogenetic analyses of the

  2. Predictive role of mitochondrial genome in the stress resistance of insects and nematodes.

    Science.gov (United States)

    Pandey, Akshay; Suman, Shubhankar; Chandna, Sudhir

    2010-06-24

    Certain insects (e.g., moths and butterflies; order Lepidoptera) and nematodes are considered as excellent experimental models to study the cellular stress signaling mechanisms since these organisms are far more stress-resistant as compared to mammalian system. Multiple factors have been implicated in this unusual response, including the oxidative stress response mechanisms. Radiation or chemical-induced mitochondrial oxidative stress occurs through damage caused to the components of electron transport chain (ETC) leading to leakage of electrons and generation of superoxide radicals. This may be countered through quick replacement of damaged mitochondrial proteins by upregulated expression. Since the ETC comprises of various proteins coded by mitochondrial DNA, variation in the composition, expressivity and regulation of mitochondrial genome could greatly influence mitochondrial role under oxidative stress conditions. Therefore, we carried out in silico analysis of mitochondrial DNA in these organisms and compared it with that of the stress-sensitive humans/mammals. Parameters such as mitochondrial genome organization, codon bias, gene expressivity and GC(3) content were studied. Gene arrangement and Shine-Dalgarno (SD) sequence patterns indicating translational regulation were distinct in insect and nematodes as compared to humans. A higher codon bias (ENC≫35) and lower GC(3) content (≫0.20) were observed in mitochondrial genes of insect and nematodes as compared to humans (ENC>42; GC3>0.20), coupled with low codon adaptation index among insects. These features indeed favour higher expressivity of mitochondrial proteins and might help maintain the mitochondrial physiology under stress conditions. Therefore, our study indicates that mitochondrial genome organization may influence stress-resistance of insects and nematodes.

  3. A whole mitochondrial genome screening in a MELAS patient: A novel mitochondrial tRNA{sup Val} mutation

    Energy Technology Data Exchange (ETDEWEB)

    Mezghani, Najla [Laboratoire de Genetique Moleculaire Humaine, Faculte de Medecine de Sfax, Universite de Sfax (Tunisia); Mnif, Mouna [Service d' endocrinologie, C.H.U. Habib Bourguiba de Sfax (Tunisia); Kacem, Maha [Service de Medecine interne, C.H.U. Fattouma Bourguiba de Monastir (Tunisia); Mkaouar-Rebai, Emna, E-mail: emna_mkaouar@mail2world.com [Laboratoire de Genetique Moleculaire Humaine, Faculte de Medecine de Sfax, Universite de Sfax (Tunisia); Hadj Salem, Ikhlass [Laboratoire de Genetique Moleculaire Humaine, Faculte de Medecine de Sfax, Universite de Sfax (Tunisia); Kallel, Nozha; Charfi, Nadia; Abid, Mohamed [Service d' endocrinologie, C.H.U. Habib Bourguiba de Sfax (Tunisia); Fakhfakh, Faiza [Laboratoire de Genetique Moleculaire Humaine, Faculte de Medecine de Sfax, Universite de Sfax (Tunisia)

    2011-04-22

    Highlights: {yields} We report a young Tunisian patient with clinical features of MELAS syndrome. {yields} Reported mitochondrial mutations were absent after a mutational screening of the whole mtDNA. {yields} We described a novel m.1640A>G mutation in the tRNA{sup Val} gene which was absent in 150 controls. {yields} Mitochondrial deletions and POLG1 gene mutations were absent. {yields} The m.1640A>G mutation could be associated to MELAS syndrome. -- Abstract: Mitochondrial encephalopathy, lactic acidosis and strokelike episodes (MELAS) syndrome is a mitochondrial disorder characterized by a wide variety of clinical presentations and a multisystemic organ involvement. In this study, we report a Tunisian girl with clinical features of MELAS syndrome who was negative for the common m.3243A>G mutation, but also for the reported mitochondrial DNA (mtDNA) mutations and deletions. Screening of the entire mtDNA genome showed several known mitochondrial variants besides to a novel transition m.1640A>G affecting a wobble adenine in the anticodon stem region of the tRNA{sup Val}. This nucleotide was conserved and it was absent in 150 controls suggesting its pathogenicity. In addition, no mutations were found in the nuclear polymerase gamma-1 gene (POLG1). These results suggest further investigation nuclear genes encoding proteins responsible for stability and structural components of the mtDNA or to the oxidative phosphorylation machinery to explain the phenotypic variability in the studied family.

  4. Complete sequence of heterogenous-composition mitochondrial genome (Brassica napus and its exogenous source

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    Wang Juan

    2012-11-01

    Full Text Available Abstract Background Unlike maternal inheritance of mitochondria in sexual reproduction, somatic hybrids follow no obvious pattern. The introgressed segment orf138 from the mitochondrial genome of radish (Raphanus sativus to its counterpart in rapeseed (Brassica napus demonstrates that this inheritance mode derives from the cytoplasm of both parents. Sequencing of the complete mitochondrial genome of five species from Brassica family allowed the prediction of other extraneous sources of the cybrids from the radish parent, and the determination of their mitochondrial rearrangement. Results We obtained the complete mitochondrial genome of Ogura-cms-cybrid (oguC rapeseed. To date, this is the first time that a heterogeneously composed mitochondrial genome was sequenced. The 258,473 bp master circle constituted of 33 protein-coding genes, 3 rRNA sequences, and 23 tRNA sequences. This mitotype noticeably holds two copies of atp9 and is devoid of cox2-2. Relative to nap mitochondrial genome, 40 point mutations were scattered in the 23 protein-coding genes. atp6 even has an abnormal start locus whereas tatC has an abnormal end locus. The rearrangement of the 22 syntenic regions that comprised 80.11% of the genome was influenced by short repeats. A pair of large repeats (9731 bp was responsible for the multipartite structure. Nine unique regions were detected when compared with other published Brassica mitochondrial genome sequences. We also found six homologous chloroplast segments (Brassica napus. Conclusions The mitochondrial genome of oguC is quite divergent from nap and pol, which are more similar with each other. We analyzed the unique regions of every genome of the Brassica family, and found that very few segments were specific for these six mitotypes, especially cam, jun, and ole, which have no specific segments at all. Therefore, we conclude that the most specific regions of oguC possibly came from radish. Compared with the chloroplast genome

  5. Complete mitochondrial genome sequencing reveals novel haplotypes in a Polynesian population.

    Directory of Open Access Journals (Sweden)

    Miles Benton

    Full Text Available The high risk of metabolic disease traits in Polynesians may be partly explained by elevated prevalence of genetic variants involved in energy metabolism. The genetics of Polynesian populations has been shaped by island hoping migration events which have possibly favoured thrifty genes. The aim of this study was to sequence the mitochondrial genome in a group of Maoris in an effort to characterise genome variation in this Polynesian population for use in future disease association studies. We sequenced the complete mitochondrial genomes of 20 non-admixed Maori subjects using Affymetrix technology. DNA diversity analyses showed the Maori group exhibited reduced mitochondrial genome diversity compared to other worldwide populations, which is consistent with historical bottleneck and founder effects. Global phylogenetic analysis positioned these Maori subjects specifically within mitochondrial haplogroup--B4a1a1. Interestingly, we identified several novel variants that collectively form new and unique Maori motifs--B4a1a1c, B4a1a1a3 and B4a1a1a5. Compared to ancestral populations we observed an increased frequency of non-synonymous coding variants of several mitochondrial genes in the Maori group, which may be a result of positive selection and/or genetic drift effects. In conclusion, this study reports the first complete mitochondrial genome sequence data for a Maori population. Overall, these new data reveal novel mitochondrial genome signatures in this Polynesian population and enhance the phylogenetic picture of maternal ancestry in Oceania. The increased frequency of several mitochondrial coding variants makes them good candidates for future studies aimed at assessment of metabolic disease risk in Polynesian populations.

  6. A Cost-Effective Approach to Sequence Hundreds of Complete Mitochondrial Genomes.

    Science.gov (United States)

    Nunez, Joaquin C B; Oleksiak, Marjorie F

    2016-01-01

    We present a cost-effective approach to sequence whole mitochondrial genomes for hundreds of individuals. Our approach uses small reaction volumes and unmodified (non-phosphorylated) barcoded adaptors to minimize reagent costs. We demonstrate our approach by sequencing 383 Fundulus sp. mitochondrial genomes (192 F. heteroclitus and 191 F. majalis). Prior to sequencing, we amplified the mitochondrial genomes using 4-5 custom-made, overlapping primer pairs, and sequencing was performed on an Illumina HiSeq 2500 platform. After removing low quality and short sequences, 2.9 million and 2.8 million reads were generated for F. heteroclitus and F. majalis respectively. Individual genomes were assembled for each species by mapping barcoded reads to a reference genome. For F. majalis, the reference genome was built de novo. On average, individual consensus sequences had high coverage: 61-fold for F. heteroclitus and 57-fold for F. majalis. The approach discussed in this paper is optimized for sequencing mitochondrial genomes on an Illumina platform. However, with the proper modifications, this approach could be easily applied to other small genomes and sequencing platforms.

  7. Study on the Mitochondrial Genome of Sea Island Cotton (Gossypium barbadense) by BAC Library Screening

    Institute of Scientific and Technical Information of China (English)

    SU Ai-guo; LI Shuang-shuang; LIU Guo-zheng; LEI Bin-bin; KANG Ding-ming; LI Zhao-hu; MA Zhi-ying; HUA Jin-ping

    2014-01-01

    The plant mitochondrial genome displays complex features, particularly in terms of cytoplasmic male sterility (CMS). Therefore, research on the cotton mitochondrial genome may provide important information for analyzing genome evolution and exploring the molecular mechanism of CMS. In this paper, we present a preliminary study on the mitochondrial genome of sea island cotton (Gossypium barbadense) based on positive clones from the bacterial artiifcial chromosome (BAC) library. Thirty-ifve primers designed with the conserved sequences of functional genes and exons of mitochondria were used to screen positive clones in the genome library of the sea island cotton variety called Pima 90-53. Ten BAC clones were obtained and veriifed for further study. A contig was obtained based on six overlapping clones and subsequently laid out primarily on the mitochondrial genome. One BAC clone, clone 6 harbored with the inserter of approximate 115 kb mtDNA sequence, in which more than 10 primers fragments could be ampliifed, was sequenced and assembled using the Solexa strategy. Fifteen mitochondrial functional genes were revealed in clone 6 by gene annotation. The characteristics of the syntenic gene/exon of the sequences and RNA editing were preliminarily predicted.

  8. Mitochondrial genomes of Vanhornia eucnemidarum (Apocrita: Vanhorniidae) and Primeuchroeus spp. (Aculeata: Chrysididae): Evidence of rearranged mitochondrial genomes within the Apocrita (Insecta: Hymenoptera).

    Science.gov (United States)

    Castro, Lyda Raquel; Ruberu, Kalani; Dowton, Mark

    2006-07-01

    We sequenced most of the mitochondrial (mt) genomes of 2 apocritan taxa: Vanhornia eucnemidarum and Primeuchroeus spp. These mt genomes have similar nucleotide composition and codon usage to those of mt genomes reported for other Hymenoptera, with a total A + T content of 80.1% and 78.2%, respectively. Gene content corresponds to that of other metazoan mt genomes, but gene organization is not conserved. There are a total of 6 tRNA genes rearranged in V. eucnemidarum and 9 in Primeuchroeus spp. Additionally, several noncoding regions were found in the mt genome of V. eucnemidarum, as well as evidence of a sustained gene duplication involving 3 tRNA genes. We also report an inversion of the large and small ribosomal RNA genes in Primeuchroeus spp. mt genome. However, none of the rearrangements reported are phylogenetically informative with respect to the current taxon sample.

  9. Sequencing of the mitochondrial genome of the avocado lace bug Pseudacysta perseae (Heteroptera, Tingidae) using a genome skimming approach.

    Science.gov (United States)

    Kocher, Arthur; Guilbert, Éric; Lhuillier, Émeline; Murienne, Jerôme

    2015-03-01

    Lace bugs (Tingidae) are a family of phytophagous heteropterans, some of which are important agricultural and forestry pests. They currently comprise around 2500 species distributed worldwide, for which only one mitochondrial genome has been described so far. We sequenced the complete mitochondrial genome and the nuclear ribosomal gene segment of the avocado lace bug Pseudacysta perseae using a genome skimming approach on an Illumina Hiseq 2000 platform. Fifty-four additional heteropteran mitogenomes, including the one of the sycamore lace bug Corythucha ciliata, were retrieved to allow for comparisons and phylogenetic analyses. P. perseae mitochondrial genome was determined to be 15,850 bp long, and presented the typical organisation of insect mitogenomes. The phylogenetic analysis placed P. perseae as a sister to C. ciliata but did not confirm the monophyly of Miroidae including Tingidae. Our results contradicted widely accepted phylogenetic hypothesis, which highlights the limits of analyses based on mitochondrial data only. Shotgun sequencing approaches should provide substantial improvements in harmonizing mitochondrial and nuclear databases.

  10. Complete mitochondrial genome of the freshwater sculpin Cottus koreanus (Scorpaeniformes, Cottidae).

    Science.gov (United States)

    Hwang, Dae-Sik; Byeon, Hwa-Kun; Lee, Jae-Seong

    2013-10-01

    The complete mitochondrial genome was sequenced from the freshwater sculpin Cottus koreanus. The genome sequence was 16,560 bp in size, and the gene order and contents were identical with those of previously reported fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), 3 genes (CO2, ND4, Cytb) had incomplete stop codons. The base composition of C. koreanus mitogenome showed anti-G bias (13.94% and 12.73%) on the second and third positions of PCGs, respectively.

  11. The complete sequence of mitochondrial genome of Laiwu Black pig (Sus Scrofa).

    Science.gov (United States)

    Yang, Hu; Xu, Xing-Li; Ma, Hai-Ming

    2016-01-01

    In the present study, the ear tissue of an adult Laiwu Black pig is from the Shandong province of China. The complete mitochondrial genome of Laiwu Black pig was determined by polymerase chain reaction (PCR). The complete mitochondrial genome is 16,710 bp, and it contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, a control region (D-loop), with the genome organization and gene order being identical to that of the typical vertebrates.

  12. Complete genome sequence of mitochondrial DNA (mtDNA) of Chlorella sorokiniana.

    Science.gov (United States)

    Orsini, Massimiliano; Costelli, Cristina; Malavasi, Veronica; Cusano, Roberto; Concas, Alessandro; Angius, Andrea; Cao, Giacomo

    2016-01-01

    The complete sequence of mitochondrial genome of the Chlorella sorokiniana strain (SAG 111-8 k) is presented in this work. Within the Chlorella genus, it represents the second species with a complete sequenced and annotated mitochondrial genome (GenBank accession no. KM241869). The genome consists of circular chromosomes of 52,528 bp and encodes a total of 31 protein coding genes, 3 rRNAs and 26 tRNAs. The overall AT contents of the C. sorokiniana mtDNA is 70.89%, while the coding sequence is of 97.4%.

  13. The complete mitochondrial genome of the Asian particolored bat Vespertilio sinensis (Chiroptera: Vespertilionidae) in Korea.

    Science.gov (United States)

    Yoon, Kwang Bae; Lee, Jin Hong; Cho, Jae Youl; Park, Yung Chul

    2016-01-01

    The complete nucleotide sequence of the mitochondrial genome of the Asian particolored bat, Vespertilio sinensis, was determined. The genome organization, gene contents, and codon usage conformed to those of other bat mitochondrial genomes. The total length of the mitogenome of Vespertilio sinensis is 16,971 bp with a total base composition of 32.6% A, 29.6% T, 23.7% C and 14.0% G. The mitogenome consists of 13 protein-coding genes, 2 rRNA (12S and 16S RNA) genes, 22 tRNA genes and 1 control region.

  14. Complete mitochondrial genome of the argentine ant, Linepithema humile (Hymenoptera: Formicidae).

    Science.gov (United States)

    Zhao, Ezi; Bi, Guiqi; Yang, Junqing; Zhang, Zhen; Liu, Guoqiang; Du, Qingwei; Shang, Erlei

    2017-03-01

    In this study, the complete mitochondrial genome of the widespread invasive Argentine ant (Linepithema humile) was first determined. The mitochondrial genome is 16 098 bp in length, and encodes one D-loop region, two ribosomal RNA genes, 13 protein-coding genes, and 18 transfer RNA genes. Average GC content of this genome is 19.68%. nad6 and cob genes were overlapped by 4 bp. The phylogenetic tree involving 13 available closely related species further validated the new determined sequences and phylogeny of L. humile.

  15. Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution.

    Science.gov (United States)

    Slack, Kerryn E; Jones, Craig M; Ando, Tatsuro; Harrison, G L Abby; Fordyce, R Ewan; Arnason, Ulfur; Penny, David

    2006-06-01

    Testing models of macroevolution, and especially the sufficiency of microevolutionary processes, requires good collaboration between molecular biologists and paleontologists. We report such a test for events around the Late Cretaceous by describing the earliest penguin fossils, analyzing complete mitochondrial genomes from an albatross, a petrel, and a loon, and describe the gradual decline of pterosaurs at the same time modern birds radiate. The penguin fossils comprise four naturally associated skeletons from the New Zealand Waipara Greensand, a Paleocene (early Tertiary) formation just above a well-known Cretaceous/Tertiary boundary site. The fossils, in a new genus (Waimanu), provide a lower estimate of 61-62 Ma for the divergence between penguins and other birds and thus establish a reliable calibration point for avian evolution. Combining fossil calibration points, DNA sequences, maximum likelihood, and Bayesian analysis, the penguin calibrations imply a radiation of modern (crown group) birds in the Late Cretaceous. This includes a conservative estimate that modern sea and shorebird lineages diverged at least by the Late Cretaceous about 74 +/- 3 Ma (Campanian). It is clear that modern birds from at least the latest Cretaceous lived at the same time as archaic birds including Hesperornis, Ichthyornis, and the diverse Enantiornithiformes. Pterosaurs, which also coexisted with early crown birds, show notable changes through the Late Cretaceous. There was a decrease in taxonomic diversity, and small- to medium-sized species disappeared well before the end of the Cretaceous. A simple reading of the fossil record might suggest competitive interactions with birds, but much more needs to be understood about pterosaur life histories. Additional fossils and molecular data are still required to help understand the role of biotic interactions in the evolution of Late Cretaceous birds and thus to test that the mechanisms of microevolution are sufficient to explain

  16. Arthropod phylogenetics in light of three novel millipede (myriapoda: diplopoda mitochondrial genomes with comments on the appropriateness of mitochondrial genome sequence data for inferring deep level relationships.

    Directory of Open Access Journals (Sweden)

    Michael S Brewer

    Full Text Available BACKGROUND: Arthropods are the most diverse group of eukaryotic organisms, but their phylogenetic relationships are poorly understood. Herein, we describe three mitochondrial genomes representing orders of millipedes for which complete genomes had not been characterized. Newly sequenced genomes are combined with existing data to characterize the protein coding regions of myriapods and to attempt to reconstruct the evolutionary relationships within the Myriapoda and Arthropoda. RESULTS: The newly sequenced genomes are similar to previously characterized millipede sequences in terms of synteny and length. Unique translocations occurred within the newly sequenced taxa, including one half of the Appalachioria falcifera genome, which is inverted with respect to other millipede genomes. Across myriapods, amino acid conservation levels are highly dependent on the gene region. Additionally, individual loci varied in the level of amino acid conservation. Overall, most gene regions showed low levels of conservation at many sites. Attempts to reconstruct the evolutionary relationships suffered from questionable relationships and low support values. Analyses of phylogenetic informativeness show the lack of signal deep in the trees (i.e., genes evolve too quickly. As a result, the myriapod tree resembles previously published results but lacks convincing support, and, within the arthropod tree, well established groups were recovered as polyphyletic. CONCLUSIONS: The novel genome sequences described herein provide useful genomic information concerning millipede groups that had not been investigated. Taken together with existing sequences, the variety of compositions and evolution of myriapod mitochondrial genomes are shown to be more complex than previously thought. Unfortunately, the use of mitochondrial protein-coding regions in deep arthropod phylogenetics appears problematic, a result consistent with previously published studies. Lack of phylogenetic

  17. The Neandertal vertebral column 2: The lumbar spine.

    Science.gov (United States)

    Gómez-Olivencia, Asier; Arlegi, Mikel; Barash, Alon; Stock, Jay T; Been, Ella

    2017-05-01

    Here we provide the most extensive metric and morphological analysis performed to date on the Neandertal lumbar spine. Neandertal lumbar vertebrae show differences from modern humans in both the vertebral body and in the neural arch, although not all Neandertal lumbar vertebrae differ from modern humans in the same way. Differences in the vertebral foramen are restricted to the lowermost lumbar vertebrae (L4 and L5), differences in the orientation of the upper articular facets appear in the uppermost lumbar vertebrae (probably in L1 and L2-L3), and differences in the horizontal angle of the transverse process appear in L2-L4. Neandertals, when compared to modern humans, show a smaller degree of lumbar lordosis. Based on a still limited fossil sample, early hominins (australopiths and Homo erectus) had a lumbar lordosis that was similar to but below the mean of modern humans. Here, we hypothesize that from this ancestral degree of lumbar lordosis, the Neandertal lineage decreased their lumbar lordosis and Homo sapiens slightly increased theirs. From a postural point of view, the lower degree of lordosis is related to a more vertical position of the sacrum, which is also positioned more ventrally with respect to the dorsal end of the pelvis. This results in a spino-pelvic alignment that, though different from modern humans, maintained an economic postural equilibrium. Some features, such as a lower degree of lumbar lordosis, were already present in the middle Pleistocene populations ancestral to Neandertals. However, these middle Pleistocene populations do not show the full suite of Neandertal lumbar morphologies, which probably means that the characteristic features of the Neandertal lumbar spine did not arise all at once. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Reconstructing the plant mitochondrial genome for marker discovery: a case study using Pinus.

    Science.gov (United States)

    Donnelly, Kevin; Cottrell, Joan; Ennos, Richard A; Vendramin, Giovanni Guiseppe; A'Hara, Stuart; King, Sarah; Perry, Annika; Wachowiak, Witold; Cavers, Stephen

    2016-12-20

    Whole-genome-shotgun (WGS) sequencing of total genomic DNA was used to recover ~1 Mbp of novel mitochondrial (mtDNA) sequence from Pinus sylvestris (L.) and three members of the closely-related Pinus mugo species complex. DNA was extracted from megagametophyte tissue from six mother trees from locations across Europe and 100 bp paired-end sequencing was performed on the Illumina HiSeq platform. Candidate mtDNA sequences were identified by their size and coverage characteristics, and by comparison with published plant mitochondrial genomes. Novel variants were identified, and primers targeting these loci were trialled on a set of 28 individuals from across Europe. In total, 31 SNP loci were successfully resequenced, characterising 15 unique haplotypes. This approach offers a cost effective means of developing marker resources for mitochondrial genomes in other plant species where reference sequences are unavailable. This article is protected by copyright. All rights reserved.

  19. The complete mitochondrial genome of the codling moth Cydia pomonella (Lepidoptera: Tortricidae).

    Science.gov (United States)

    Shi, Bao-Cai; Liu, Wei; Wei, Shu-Jun

    2013-02-01

    The complete mitochondrial genome of the codling moth Cydia pomonella (Lepidoptera: Tortricidae) was determined. The genome is 15,253 bp long with 37 typical animal mitochondrial genes and an A+T-rich region. All genes are arranged in their conserved positions compared with the pupative ancestral arrangement of insects except for trnM, which was translocated to the upstream of the transfer RNA cluster trnI-trnQ as in all previously reported lepidopteran mitochondiral genomes. Seven portein-coding genes use ATG start codon and five use ATT. However, the cox1 gene uses the CGA start codon as it is found in all previous reported mitochondrial genomes of Lepidoptera. Nine protein-coding genes stop with termination codon TAA. Four protein-coding genes use incomplete stop codons TA or T. The A+T region is located between rrnS and trnM with a length of 331 bp.

  20. The complete sequence of mitochondrial genome of Wuzhishan pig (Sus Scrofa).

    Science.gov (United States)

    Chai, Yu-Lan; Xu, Dong; Ma, Hai-Ming

    2016-01-01

    In the present study, we sequenced the complete mitochondrial genome of Wuzhishan pig, which was 16,741 bp in size and had a nucleotide composition in A and T (60.46%). The genome consisted of a major non-coding control region (D-loop region) and 37 genes, including 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), and 22 transfer RNA (tRNA) genes. The genes in the mitochondrial genomes of Wuzhishan pig used three kinds of initiation codons (ATA, ATG, and GTG) and four kinds of termination codons (TAA, AGA, TAG, and an incomplete termination codons T-). The complete mitochondrial genome sequence of Wuzhishan pig provides an important data set for further study on genetic mechanism.

  1. The complete sequence of the mitochondrial genome of Lantang pig (Sus scrofa).

    Science.gov (United States)

    Ran, Mao-Liang; Liu, Zhen; Yang, An-Qi; Li, Zhi; Chen, Bin

    2016-01-01

    Lantang pig is a native breed of Guangzhou Province in China. It is the first time that the complete mitochondrial genome sequence of Lantang pig is reported in this work, which is determined through the PCR-based method. The total length of the mitognome is 16,709 bp, which contains 2 ribosomal RNA genes, 22 tRNA genes, 13 PCGs and 1 conntrol region (D-loop region, Table 1). The total base composition of Lantang pig mitochondrial genome is 34.69% for A, 26.18% for C, 25.82% for T and 13.31% for G, in the order A>C>T>G. The complete mitochondrial genome of Lantang pig provides an important data in genetic mechanism and the evolution genomes.

  2. The mitochondrial subgenomes of the nematode Globodera pallida are mosaics: evidence of recombination in an animal mitochondrial genome.

    Science.gov (United States)

    Gibson, Tracey; Blok, Vivian C; Phillips, Mark S; Hong, Gary; Kumarasinghe, Duminda; Riley, Ian T; Dowton, Mark

    2007-04-01

    We sequenced four mitochondrial subgenomes from the potato cyst nematode Globodera pallida, previously characterized as one of the few animals to have a multipartite mitochondrial genome. The sequence data indicate that three of these subgenomic mitochondrial circles are mosaics, comprising long, multigenic fragments derived from fragments of the other circles. This pattern is consistent with the operation of intermitochondrial recombination, a process generally considered absent in animal mitochondria. We also report that many of the duplicated genes contain deleterious mutations, ones likely to render the gene nonfunctional; gene conversion does not appear to be homogenizing the different gene copies. The proposed nonfunctional copies are clustered on particular circles, whereas copies that are likely to code functional gene products are clustered on others.

  3. Double-strand break repair processes drive evolution of the mitochondrial genome in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Shedge Vikas

    2011-09-01

    Full Text Available Abstract Background The mitochondrial genome of higher plants is unusually dynamic, with recombination and nonhomologous end-joining (NHEJ activities producing variability in size and organization. Plant mitochondrial DNA also generally displays much lower nucleotide substitution rates than mammalian or yeast systems. Arabidopsis displays these features and expedites characterization of the mitochondrial recombination surveillance gene MSH1 (MutS 1 homolog, lending itself to detailed study of de novo mitochondrial genome activity. In the present study, we investigated the underlying basis for unusual plant features as they contribute to rapid mitochondrial genome evolution. Results We obtained evidence of double-strand break (DSB repair, including NHEJ, sequence deletions and mitochondrial asymmetric recombination activity in Arabidopsis wild-type and msh1 mutants on the basis of data generated by Illumina deep sequencing and confirmed by DNA gel blot analysis. On a larger scale, with mitochondrial comparisons across 72 Arabidopsis ecotypes, similar evidence of DSB repair activity differentiated ecotypes. Forty-seven repeat pairs were active in DNA exchange in the msh1 mutant. Recombination sites showed asymmetrical DNA exchange within lengths of 50- to 556-bp sharing sequence identity as low as 85%. De novo asymmetrical recombination involved heteroduplex formation, gene conversion and mismatch repair activities. Substoichiometric shifting by asymmetrical exchange created the appearance of rapid sequence gain and loss in association with particular repeat classes. Conclusions Extensive mitochondrial genomic variation within a single plant species derives largely from DSB activity and its repair. Observed gene conversion and mismatch repair activity contribute to the low nucleotide substitution rates seen in these genomes. On a phenotypic level, these patterns of rearrangement likely contribute to the reproductive versatility of higher plants.

  4. The mitochondrial genome sequence and molecular phylogeny of the turkey, Meleagris gallopavo.

    Science.gov (United States)

    Guan, X; Silva, P; Gyenai, K B; Xu, J; Geng, T; Tu, Z; Samuels, D C; Smith, E J

    2009-04-01

    The mitochondrial genome (mtGenome) has been little studied in the turkey (Meleagris gallopavo), a species for which there is no publicly available mtGenome sequence. Here, we used PCR-based methods with 19 pairs of primers designed from the chicken and other species to develop a complete turkey mtGenome sequence. The entire sequence (16,717 bp) of the turkey mtGenome was obtained, and it exhibited 85% similarity to the chicken mtGenome sequence. Thirteen genes and 24 RNAs (22 tRNAs and 2 rRNAs) were annotated. An mtGenome-based phylogenetic analysis indicated that the turkey is most closely related to the chicken, Gallus gallus, and quail, Corturnix japonica. Given the importance of the mtGenome, the present work adds to the growing genomic resources needed to define the genetic mechanisms that underlie some economically significant traits in the turkey.

  5. Accelerated evolution of mitochondrial but not nuclear genomes of Hymenoptera: new evidence from crabronid wasps.

    Directory of Open Access Journals (Sweden)

    Martin Kaltenpoth

    Full Text Available Mitochondrial genes in animals are especially useful as molecular markers for the reconstruction of phylogenies among closely related taxa, due to the generally high substitution rates. Several insect orders, notably Hymenoptera and Phthiraptera, show exceptionally high rates of mitochondrial molecular evolution, which has been attributed to the parasitic lifestyle of current or ancestral members of these taxa. Parasitism has been hypothesized to entail frequent population bottlenecks that increase rates of molecular evolution by reducing the efficiency of purifying selection. This effect should result in elevated substitution rates of both nuclear and mitochondrial genes, but to date no extensive comparative study has tested this hypothesis in insects. Here we report the mitochondrial genome of a crabronid wasp, the European beewolf (Philanthus triangulum, Hymenoptera, Crabronidae, and we use it to compare evolutionary rates among the four largest holometabolous insect orders (Coleoptera, Diptera, Hymenoptera, Lepidoptera based on phylogenies reconstructed with whole mitochondrial genomes as well as four single-copy nuclear genes (18S rRNA, arginine kinase, wingless, phosphoenolpyruvate carboxykinase. The mt-genome of P. triangulum is 16,029 bp in size with a mean A+T content of 83.6%, and it encodes the 37 genes typically found in arthropod mt genomes (13 protein-coding, 22 tRNA, and two rRNA genes. Five translocations of tRNA genes were discovered relative to the putative ancestral genome arrangement in insects, and the unusual start codon TTG was predicted for cox2. Phylogenetic analyses revealed significantly longer branches leading to the apocritan Hymenoptera as well as the Orussoidea, to a lesser extent the Cephoidea, and, possibly, the Tenthredinoidea than any of the other holometabolous insect orders for all mitochondrial but none of the four nuclear genes tested. Thus, our results suggest that the ancestral parasitic lifestyle of

  6. Mitochondrial genome rearrangements in glomus species triggered by homologous recombination between distinct mtDNA haplotypes.

    Science.gov (United States)

    Beaudet, Denis; Terrat, Yves; Halary, Sébastien; de la Providencia, Ivan Enrique; Hijri, Mohamed

    2013-01-01

    Comparative mitochondrial genomics of arbuscular mycorrhizal fungi (AMF) provide new avenues to overcome long-lasting obstacles that have hampered studies aimed at understanding the community structure, diversity, and evolution of these multinucleated and genetically polymorphic organisms.AMF mitochondrial (mt) genomes are homogeneous within isolates, and their intergenic regions harbor numerous mobile elements that have rapidly diverged, including homing endonuclease genes, small inverted repeats, and plasmid-related DNA polymerase genes (dpo), making them suitable targets for the development of reliable strain-specific markers. However, these elements may also lead to genome rearrangements through homologous recombination, although this has never previously been reported in this group of obligate symbiotic fungi. To investigate whether such rearrangements are present and caused by mobile elements in AMF, the mitochondrial genomes from two Glomeraceae members (i.e., Glomus cerebriforme and Glomus sp.) with substantial mtDNA synteny divergence,were sequenced and compared with available glomeromycotan mitochondrial genomes. We used an extensive nucleotide/protein similarity network-based approach to investigated podiversity in AMF as well as in other organisms for which sequences are publicly available. We provide strong evidence of dpo-induced inter-haplotype recombination, leading to a reshuffled mitochondrial genome in Glomus sp. These findings raise questions as to whether AMF single spore cultivations artificially underestimate mtDNA genetic diversity.We assessed potential dpo dispersal mechanisms in AMF and inferred a robust phylogenetic relationship with plant mitochondrial plasmids. Along with other indirect evidence, our analyses indicate that members of the Glomeromycota phylum are potential donors of mitochondrial plasmids to plants.

  7. Genomic resources for sea lice: analysis of ESTs and mitochondrial genomes.

    Science.gov (United States)

    Yasuike, Motoshige; Leong, Jong; Jantzen, Stuart G; von Schalburg, Kristian R; Nilsen, Frank; Jones, Simon R M; Koop, Ben F

    2012-04-01

    Sea lice are common parasites of both farmed and wild salmon. Salmon farming constitutes an important economic market in North America, South America, and Northern Europe. Infections with sea lice can result in significant production losses. A compilation of genomic information on different genera of sea lice is an important resource for understanding their biology as well as for the study of population genetics and control strategies. We report on over 150,000 expressed sequence tags (ESTs) from five different species (Pacific Lepeophtheirus salmonis (49,672 new ESTs in addition to 14,994 previously reported ESTs), Atlantic L. salmonis (57,349 ESTs), Caligus clemensi (14,821 ESTs), Caligus rogercresseyi (32,135 ESTs), and Lernaeocera branchialis (16,441 ESTs)). For each species, ESTs were assembled into complete or partial genes and annotated by comparisons to known proteins in public databases. In addition, whole mitochondrial (mt) genome sequences of C. clemensi (13,440 bp) and C. rogercresseyi (13,468 bp) were determined and compared to L. salmonis. Both nuclear and mtDNA genes show very high levels of sequence divergence between these ectoparastic copepods suggesting that the different species of sea lice have been in existence for 37-113 million years and that parasitic association with salmonids is also quite ancient. Our ESTs and mtDNA data provide a novel resource for the study of sea louse biology, population genetics, and control strategies. This genomic information provides the material basis for the development of a 38K sea louse microarray that can be used in conjunction with our existing 44K salmon microarray to study host-parasite interactions at the molecular level. This report represents the largest genomic resource for any copepod species to date.

  8. AB036. Analysis of human mitochondrial genome mutations of Vietnamese patients tentatively diagnosed with encephalomyopathy

    Science.gov (United States)

    Nghia, Phan Tuan; Thai, Trinh Hong; Hue, Truong Thi; Van Minh, Nguyen; Khanh, Phung Bao; Hiep, Tran Duc; Anh, Tran Kieu; Loan, Nguyen Thi Hong; Van, Nguyen Thi Hong; Anh, Pham Van; Hung, Cao Vu; Anh, Le Ngoc

    2015-01-01

    Human mitochondrial genome consists of 16,569 bp, and replicates independently from the nuclear genome. Mutations in mitochondrial genome are usually causative factors of various metabolic disorders, especially those of encephalomyopathy. DNA analysis is the most reliable method for detection of mitochondrial genome mutations, and accordingly an excellent diagnostic tool for mitochondrial mutation-related diseases. In this study, 19 different mitochondrial genome mutations including A3243G, A3251G, T3271C and T3291C (MELAS); A8344G, T8356C and G8363A (MERRF); G3460A, G11778A and T14484C (LHON); T8993G/C and T9176G (Leigh); A1555G (deafness) and A4225G, G4298A, T10010C, T14727C, T14728C, T14709C (encephalomyopathy in general) were analyzed using PCR-RFLP in combination with DNA sequencing. In addition, a real-time PCR method using locked nucleic acid (LNA) Taqman probe was set up for heteroplasmy determination. Screening of 283 tentatively diagnosed encephalomyopathy patients revealed 7 cases of A3243G, 1 case of G11778A, 1 case of A1555G, 1 case of A4225G, 1 case G4298A, and 1 case of 6 bp (ACTCCT/CTCCTA) deletion. Using the LNA Taqman probe real-time PCR, the heteroplasmy of some point mutations was determined and the results support a potential relationship between heteroplasmy level and severity of the disease.

  9. The mitochondrial genome of the egg-laying flatworm Aglaiogyrodactylus forficulatus (Platyhelminthes: Monogenoidea).

    Science.gov (United States)

    Bachmann, Lutz; Fromm, Bastian; Patella de Azambuja, Luciana; Boeger, Walter A

    2016-05-17

    The rather species-poor oviparous gyrodactylids are restricted to South America. It was suggested that they have a basal position within the otherwise viviparous Gyrodactylidae. Accordingly, it was proposed that the species-rich viviparous gyrodactylids diversified and dispersed from there. The mitochondrial genome of Aglaiogyrodactylus forficulatus was bioinformatically assembled from next-generation illumina MiSeq sequencing reads, annotated, and compared to previously published mitochondrial genomes of other monogenoidean flatworm species. The mitochondrial genome of A. forficulatus consists of 14,371 bp with an average A + T content of 75.12 %. All expected 12 protein coding, 22 tRNA, and 2 rRNA genes were identified. Furthermore, there were two repetitive non-coding regions essentially consisting of 88 bp and 233 bp repeats, respectively. Maximum Likelihood analyses placed the mitochondrial genome of A. forficulatus in a well-supported clade together with the viviparous Gyrodactylidae species. The gene order differs in comparison to that of other monogenoidean species, with rearrangements mainly affecting tRNA genes. In comparison to Paragyrodactylus variegatus, four gene order rearrangements, i.e. three transpositions and one complex tandem-duplication-random-loss event, were detected. Mitochondrial genome sequence analyses support a basal position of the oviparous A. forficulatus within Gyrodactylidae, and a sister group relationship of the oviparous and viviparous forms.

  10. Mitochondrial genomes and Doubly Uniparental Inheritance: new insights from Musculista senhousia sex-linked mitochondrial DNAs (Bivalvia Mytilidae

    Directory of Open Access Journals (Sweden)

    Milani Liliana

    2011-09-01

    Full Text Available Abstract Background Doubly Uniparental Inheritance (DUI is a fascinating exception to matrilinear inheritance of mitochondrial DNA (mtDNA. Species with DUI are characterized by two distinct mtDNAs that are inherited either through females (F-mtDNA or through males (M-mtDNA. DUI sex-linked mitochondrial genomes share several unusual features, such as additional protein coding genes and unusual gene duplications/structures, which have been related to the functionality of DUI. Recently, new evidence for DUI was found in the mytilid bivalve Musculista senhousia. This paper describes the complete sex-linked mitochondrial genomes of this species. Results Our analysis highlights that both M and F mtDNAs share roughly the same gene content and order, but with some remarkable differences. The Musculista sex-linked mtDNAs have differently organized putative control regions (CR, which include repeats and palindromic motifs, thought to provide sites for DNA-binding proteins involved in the transcriptional machinery. Moreover, in male mtDNA, two cox2 genes were found, one (M-cox2b 123bp longer. Conclusions The complete mtDNA genome characterization of DUI bivalves is the first step to unravel the complex genetic signals allowing Doubly Uniparental Inheritance, and the evolutionary implications of such an unusual transmission route in mitochondrial genome evolution in Bivalvia. The observed redundancy of the palindromic motifs in Musculista M-mtDNA may have a role on the process by which sperm mtDNA becomes dominant or exclusive of the male germline of DUI species. Moreover, the duplicated M-COX2b gene may have a different, still unknown, function related to DUI, in accordance to what has been already proposed for other DUI species in which a similar cox2 extension has been hypothesized to be a tag for male mitochondria.

  11. Phylogenetic analysis of the true water bugs (Insecta: Hemiptera: Heteroptera: Nepomorpha: evidence from mitochondrial genomes

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    Xie Qiang

    2009-06-01

    Full Text Available Abstract Background The true water bugs are grouped in infraorder Nepomorpha (Insecta: Hemiptera: Heteroptera and are of great economic importance. The phylogenetic relationships within Nepomorpha and the taxonomic hierarchies of Pleoidea and Aphelocheiroidea are uncertain. Most of the previous studies were based on morphological characters without algorithmic assessment. In the latest study, the molecular markers employed in phylogenetic analyses were partial sequences of 16S rDNA and 18S rDNA with a total length about 1 kb. Up to now, no mitochondrial genome of the true water bugs has been sequenced, which is one of the largest data sets that could be compared across animal taxa. In this study we analyzed the unresolved problems in Nepomorpha using evidence from mitochondrial genomes. Results Nine mitochondrial genomes of Nepomorpha and five of other hemipterans were sequenced. These mitochondrial genomes contain the commonly found 37 genes without gene rearrangements. Based on the nucleotide sequences of mt-genomes, Pleoidea is not a member of the Nepomorpha and Aphelocheiroidea should be grouped back into Naucoroidea. Phylogenetic relationships among the superfamilies of Nepomorpha were resolved robustly. Conclusion The mt-genome is an effective data source for resolving intraordinal phylogenetic problems at the superfamily level within Heteroptera. The mitochondrial genomes of the true water bugs are typical insect mt-genomes. Based on the nucleotide sequences of the mt-genomes, we propose the Pleoidea to be a separate heteropteran infraorder. The infraorder Nepomorpha consists of five superfamilies with the relationships (Corixoidea + ((Naucoroidea + Notonectoidea + (Ochteroidea + Nepoidea.

  12. A complete mitochondrial genome sequence from a mesolithic wild aurochs (Bos primigenius).

    LENUS (Irish Health Repository)

    Edwards, Ceiridwen J

    2010-01-01

    BACKGROUND: The derivation of domestic cattle from the extinct wild aurochs (Bos primigenius) has been well-documented by archaeological and genetic studies. Genetic studies point towards the Neolithic Near East as the centre of origin for Bos taurus, with some lines of evidence suggesting possible, albeit rare, genetic contributions from locally domesticated wild aurochsen across Eurasia. Inferences from these investigations have been based largely on the analysis of partial mitochondrial DNA sequences generated from modern animals, with limited sequence data from ancient aurochsen samples. Recent developments in DNA sequencing technologies, however, are affording new opportunities for the examination of genetic material retrieved from extinct species, providing new insight into their evolutionary history. Here we present DNA sequence analysis of the first complete mitochondrial genome (16,338 base pairs) from an archaeologically-verified and exceptionally-well preserved aurochs bone sample. METHODOLOGY: DNA extracts were generated from an aurochs humerus bone sample recovered from a cave site located in Derbyshire, England and radiocarbon-dated to 6,738+\\/-68 calibrated years before present. These extracts were prepared for both Sanger and next generation DNA sequencing technologies (Illumina Genome Analyzer). In total, 289.9 megabases (22.48%) of the post-filtered DNA sequences generated using the Illumina Genome Analyzer from this sample mapped with confidence to the bovine genome. A consensus B. primigenius mitochondrial genome sequence was constructed and was analysed alongside all available complete bovine mitochondrial genome sequences. CONCLUSIONS: For all nucleotide positions where both Sanger and Illumina Genome Analyzer sequencing methods gave high-confidence calls, no discrepancies were observed. Sequence analysis reveals evidence of heteroplasmy in this sample and places this mitochondrial genome sequence securely within a previously identified

  13. The complete chloroplast and mitochondrial genomes of the green macroalga Ulva sp. UNA00071828 (Ulvophyceae, Chlorophyta.

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    James T Melton

    Full Text Available Sequencing mitochondrial and chloroplast genomes has become an integral part in understanding the genomic machinery and the phylogenetic histories of green algae. Previously, only three chloroplast genomes (Oltmannsiellopsis viridis, Pseudendoclonium akinetum, and Bryopsis hypnoides and two mitochondrial genomes (O. viridis and P. akinetum from the class Ulvophyceae have been published. Here, we present the first chloroplast and mitochondrial genomes from the ecologically and economically important marine, green algal genus Ulva. The chloroplast genome of Ulva sp. was 99,983 bp in a circular-mapping molecule that lacked inverted repeats, and thus far, was the smallest ulvophycean plastid genome. This cpDNA was a highly compact, AT-rich genome that contained a total of 102 identified genes (71 protein-coding genes, 28 tRNA genes, and three ribosomal RNA genes. Additionally, five introns were annotated in four genes: atpA (1, petB (1, psbB (2, and rrl (1. The circular-mapping mitochondrial genome of Ulva sp. was 73,493 bp and follows the expanded pattern also seen in other ulvophyceans and trebouxiophyceans. The Ulva sp. mtDNA contained 29 protein-coding genes, 25 tRNA genes, and two rRNA genes for a total of 56 identifiable genes. Ten introns were annotated in this mtDNA: cox1 (4, atp1 (1, nad3 (1, nad5 (1, and rrs (3. Double-cut-and-join (DCJ values showed that organellar genomes across Chlorophyta are highly rearranged, in contrast to the highly conserved organellar genomes of the red algae (Rhodophyta. A phylogenomic investigation of 51 plastid protein-coding genes showed that Ulvophyceae is not monophyletic, and also placed Oltmannsiellopsis (Oltmannsiellopsidales and Tetraselmis (Chlorodendrophyceae closely to Ulva (Ulvales and Pseudendoclonium (Ulothrichales.

  14. Complete mitochondrial genome of Tree Sparrow Passer montanus saturatus (Passeriformes: Passeridae).

    Science.gov (United States)

    Yang, Fan; Li, Bo; Zhou, Lizhi; Bao, Di; Zhu, Hongyu

    2016-05-01

    Tree Sparrow Passer montanus is an Eurasian distribution passerine bird, which has 9 subspecies. In this study, we determined the complete mitochondrial genome of Passer montanus saturatus. The mitochondrial DNA is 16,904 bp long with A + T contents of 52.56%. The mitochondrial genome is typical circular that encodes the complete set of 37 genes. All protein-coding genes use the standard mitochondrial initiation codon ATG, except for COI starts with GTG and ND3 starts with ATA. TAN is the most frequent stop codon, and AGN and T- - are also occurred very common. All tRNAs possess the classic clover leaf secondary structure except for tRNA(Ser (AGN)) and tRNA(Cys (CUN)), which lack the "DHU" stem, only forming a simple loop.

  15. Sequencing and alignment of mitochondrial genomes of Tibetan chicken and two lowland chicken breeds

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Tibetan chicken lives in high-altitude area and has adapted well to hypoxia genetically. Shouguang chicken and Silky chicken are both lowland chicken breeds. In the present study, the complete mitochondrial genome sequences of the three chicken breeds were all sequenced. The results showed that the mitochondrial DNAs (mtDNAs) of Shouguang chicken and Silky chicken consist of 16784 bp and 16785 bp respectively, and Tibetan chicken mitochondrial genome varies from 16784 bp to 16786 bp. After sequence analysis, 120 mutations, including 4 single nucleotide polymorphisms (SNPs) in tRNA genes, 9 SNPs and 1 insertion in rRNA genes, 38 SNPs and 1 deletion in D-LOOP, 66 SNPs in protein-coding genes, were found. This work will provide clues for the future study on the association between mitochondrial genes and the adaptation to hypoxia.

  16. The evolutionary history of Saccharomyces species inferred from completed mitochondrial genomes and revision in the 'yeast mitochondrial genetic code'.

    Science.gov (United States)

    Sulo, Pavol; Szabóová, Dana; Bielik, Peter; Poláková, Silvia; Šoltys, Katarína; Jatzová, Katarína; Szemes, Tomáš

    2017-06-15

    The yeast Saccharomyces are widely used to test ecological and evolutionary hypotheses. A large number of nuclear genomic DNA sequences are available, but mitochondrial genomic data are insufficient. We completed mitochondrial DNA (mtDNA) sequencing from Illumina MiSeq reads for all Saccharomyces species. All are circularly mapped molecules decreasing in size with phylogenetic distance from Saccharomyces cerevisiae but with similar gene content including regulatory and selfish elements like origins of replication, introns, free-standing open reading frames or GC clusters. Their most profound feature is species-specific alteration in gene order. The genetic code slightly differs from well-established yeast mitochondrial code as GUG is used rarely as the translation start and CGA and CGC code for arginine. The multilocus phylogeny, inferred from mtDNA, does not correlate with the trees derived from nuclear genes. mtDNA data demonstrate that Saccharomyces cariocanus should be assigned as a separate species and Saccharomyces bayanus CBS 380T should not be considered as a distinct species due to mtDNA nearly identical to Saccharomyces uvarum mtDNA. Apparently, comparison of mtDNAs should not be neglected in genomic studies as it is an important tool to understand the origin and evolutionary history of some yeast species. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  17. The complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus (Bivalvia, Veneridae

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    Fabrizio Ghiselli

    2017-08-01

    Full Text Available Despite the large number of animal complete mitochondrial genomes currently available in public databases, knowledge about mitochondrial genomics in invertebrates is uneven. This paper reports, for the first time, the complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus, also known as the European clam. Ruditapes decussatus is morphologically and ecologically similar to the Manila clam Ruditapes philippinarum, which has been recently introduced for aquaculture in the very same habitats of Ruditapes decussatus, and that is replacing the native species. Currently the production of the European clam is almost insignificant, nonetheless it is considered a high value product, and therefore it is an economically important species, especially in Portugal, Spain and Italy. In this work we: (i assembled Ruditapes decussatus mitochondrial genome from RNA-Seq data, and validated it by Sanger sequencing; (ii analyzed and characterized the Ruditapes decussatus mitochondrial genome, comparing its features with those of other venerid bivalves; (iii assessed mitochondrial sequence polymorphism (SP and copy number variation (CNV of tandem repeats across 26 samples. Despite using high-throughput approaches we did not find evidence for the presence of two sex-linked mitochondrial genomes, typical of the doubly uniparental inheritance of mitochondria, a phenomenon known in ∼100 bivalve species. According to our analyses, Ruditapes decussatus is more genetically similar to species of the Genus Paphia than to the congeneric Ruditapes philippinarum, a finding that bolsters the already-proposed need of a taxonomic revision. We also found a quite low genetic variability across the examined samples, with few SPs and little variability of the sequences flanking the control region (Largest Unassigned Regions (LURs. Strikingly, although we found low nucleotide variability along the entire mitochondrial genome, we observed high levels of length

  18. Distinct patterns of mitochondrial genome diversity in bonobos (Pan paniscus and humans

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    Zsurka Gábor

    2010-09-01

    Full Text Available Abstract Background We have analyzed the complete mitochondrial genomes of 22 Pan paniscus (bonobo, pygmy chimpanzee individuals to assess the detailed mitochondrial DNA (mtDNA phylogeny of this close relative of Homo sapiens. Results We identified three major clades among bonobos that separated approximately 540,000 years ago, as suggested by Bayesian analysis. Incidentally, we discovered that the current reference sequence for bonobo likely is a hybrid of the mitochondrial genomes of two distant individuals. When comparing spectra of polymorphic mtDNA sites in bonobos and humans, we observed two major differences: (i Of all 31 bonobo mtDNA homoplasies, i.e. nucleotide changes that occurred independently on separate branches of the phylogenetic tree, 13 were not homoplasic in humans. This indicates that at least a part of the unstable sites of the mitochondrial genome is species-specific and difficult to be explained on the basis of a mutational hotspot concept. (ii A comparison of the ratios of non-synonymous to synonymous changes (dN/dS among polymorphic positions in bonobos and in 4902 Homo sapiens mitochondrial genomes revealed a remarkable difference in the strength of purifying selection in the mitochondrial genes of the F0F1-ATPase complex. While in bonobos this complex showed a similar low value as complexes I and IV, human haplogroups displayed 2.2 to 7.6 times increased dN/dS ratios when compared to bonobos. Conclusions Some variants of mitochondrially encoded subunits of the ATPase complex in humans very likely decrease the efficiency of energy conversion leading to production of extra heat. Thus, we hypothesize that the species-specific release of evolutionary constraints for the mitochondrial genes of the proton-translocating ATPase is a consequence of altered heat homeostasis in modern humans.

  19. Mitochondrial genome sequence and expression profiling for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae.

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    Venu M Margam

    Full Text Available We report the assembly of the 14,054 bp near complete sequencing of the mitochondrial genome of the legume pod borer (LPB, Maruca vitrata (Lepidoptera: Crambidae, which we subsequently used to estimate divergence and relationships within the lepidopteran lineage. The arrangement and orientation of the 13 protein-coding, 2 rRNA, and 19 tRNA genes sequenced was typical of insect mitochondrial DNA sequences described to date. The sequence contained a high A+T content of 80.1% and a bias for the use of codons with A or T nucleotides in the 3rd position. Transcript mapping with midgut and salivary gland ESTs for mitochondrial genome annotation showed that translation from protein-coding genes initiates and terminates at standard mitochondrial codons, except for the coxI gene, which may start from an arginine CGA codon. The genomic copy of coxII terminates at a T nucleotide, and a proposed polyadenylation mechanism for completion of the TAA stop codon was confirmed by comparisons to EST data. EST contig data further showed that mature M. vitrata mitochondrial transcripts are monocistronic, except for bicistronic transcripts for overlapping genes nd4/nd4L and nd6/cytb, and a tricistronic transcript for atp8/atp6/coxIII. This processing of polycistronic mitochondrial transcripts adheres to the tRNA punctuated cleavage mechanism, whereby mature transcripts are cleaved only at intervening tRNA gene sequences. In contrast, the tricistronic atp8/atp6/coxIII in Drosophila is present as separate atp8/atp6 and coxIII transcripts despite the lack of an intervening tRNA. Our results indicate that mitochondrial processing mechanisms vary between arthropod species, and that it is crucial to use transcriptional information to obtain full annotation of mitochondrial genomes.

  20. The complete mitochondrial genome of the rare and endangered Orthotrichum rogeri (Orthotrichaceae, Bryophyta).

    Science.gov (United States)

    Jakub, Sawicki; Szczecińska, Monika; Kulik, Tomasz; Myszczyński, Kamil; Ślipiko, Monika; Wołosz, Katarzyna; Plášek, Vítězslav

    2016-09-01

    The mitogenome of the Orthotrichum rogeri (GenBank accession number KM873610) has a total length of 106,634 bp and consist of 40 protein-coding genes, 3 ribosomal RNA (rRNA) and 24 transfer RNA. The gene order is identical to other known moss mitogenomes. A complete mitochondrial genome sequence of O. rogeri will help the development of primers for examining mitochondrial variation across bryophytes.

  1. The mitochondrial genome and transcriptome of the basal dinoflagellate Hematodinium sp.: character evolution within the highly derived mitochondrial genomes of dinoflagellates.

    Science.gov (United States)

    Jackson, C J; Gornik, S G; Waller, R F

    2012-01-01

    The sister phyla dinoflagellates and apicomplexans inherited a drastically reduced mitochondrial genome (mitochondrial DNA, mtDNA) containing only three protein-coding (cob, cox1, and cox3) genes and two ribosomal RNA (rRNA) genes. In apicomplexans, single copies of these genes are encoded on the smallest known mtDNA chromosome (6 kb). In dinoflagellates, however, the genome has undergone further substantial modifications, including massive genome amplification and recombination resulting in multiple copies of each gene and gene fragments linked in numerous combinations. Furthermore, protein-encoding genes have lost standard stop codons, trans-splicing of messenger RNAs (mRNAs) is required to generate complete cox3 transcripts, and extensive RNA editing recodes most genes. From taxa investigated to date, it is unclear when many of these unusual dinoflagellate mtDNA characters evolved. To address this question, we investigated the mitochondrial genome and transcriptome character states of the deep branching dinoflagellate Hematodinium sp. Genomic data show that like later-branching dinoflagellates Hematodinium sp. also contains an inflated, heavily recombined genome of multicopy genes and gene fragments. Although stop codons are also lacking for cox1 and cob, cox3 still encodes a conventional stop codon. Extensive editing of mRNAs also occurs in Hematodinium sp. The mtDNA of basal dinoflagellate Hematodinium sp. indicates that much of the mtDNA modification in dinoflagellates occurred early in this lineage, including genome amplification and recombination, and decreased use of standard stop codons. Trans-splicing, on the other hand, occurred after Hematodinium sp. diverged. Only RNA editing presents a nonlinear pattern of evolution in dinoflagellates as this process occurs in Hematodinium sp. but is absent in some later-branching taxa indicating that this process was either lost in some lineages or developed more than once during the evolution of the highly unusual

  2. Major genomic mitochondrial lineages delineate early human expansions

    OpenAIRE

    Flores Carlos; Larruga José M; González Ana M; Maca-Meyer Nicole; Cabrera Vicente M

    2001-01-01

    Abstract Background The phylogeographic distribution of human mitochondrial DNA variations allows a genetic approach to the study of modern Homo sapiens dispersals throughout the world from a female perspective. As a new contribution to this study we have phylogenetically analysed complete mitochondrial DNA(mtDNA) sequences from 42 human lineages, representing major clades with known geographic assignation. Results We show the relative relationships among the 42 lineages and present more accu...

  3. The complete mitochondrial genome of the rayfish Raja porosa (Chondrichthyes, Rajidae).

    Science.gov (United States)

    Kim, Il-Chan; Jung, Sang-Oun; Lee, Young-Mi; Lee, Chang Joo; Park, Joong-Ki; Lee, Jae-Seong

    2005-06-01

    We isolated mitochondrial DNA from the rayfish Raja porosa by long-polymerase chain reaction (Long-PCR) with conserved primers, and sequenced it by primer walking method using flanking sequences as sequencing primers. R. porosa mitochondrial DNA consists of 16,972 bp and its structural organization is conserved in comparison with other fishes and mammals. Based on the mitochondrial cytochrome b (cyt b) sequence, the phylogenetic position of R. porosa among cartilaginous fishes was inferred using different phylogenetic methods (ML-based quartet puzzling, Neighbor-joining (NJ) and Bayesian approaches). In this paper, we report the characteristics of the R. porosa mitochondrial genome including structural organization, base composition of rRNAs, tRNAs and protein-encoding genes and characteristics of mitochondrial tRNAs. These findings are applicable to comparative mitogenomics of R. porosa with other related taxa.

  4. Complete mitochondrial genomes of the Northern (Salvelinus malma) and Southern (Salvelinus curilus) Dolly Varden chars (Salmoniformes, Salmonidae).

    Science.gov (United States)

    Balakirev, Evgeniy S; Romanov, Nikolai S; Ayala, Francisco J

    2016-01-01

    The complete mitochondrial genomes were sequenced from the Northern and Southern Dolly Varden chars, Salvelinus malma and S. curilus. The genome sequences are 16,654 bp in size in both species, and the gene arrangement, composition, and size are very similar to the salmonid fish genomes published previously. The level of sequence divergence between S. malma and S. curilus inferred from the complete mitochondrial genomes is relatively low (1.88%) indicating recent divergence of the species and/or historical hybridization.

  5. The first mitochondrial genome for the butterfly family Riodinidae (Abisara fylloides) and its systematic implications.

    Science.gov (United States)

    Zhao, Fang; Huang, Dun-Yuan; Sun, Xiao-Yan; Shi, Qing-Hui; Hao, Jia-Sheng; Zhang, Lan-Lan; Yang, Qun

    2013-10-01

    The Riodinidae is one of the lepidopteran butterfly families. This study describes the complete mitochondrial genome of the butterfly species Abisara fylloides, the first mitochondrial genome of the Riodinidae family. The results show that the entire mitochondrial genome of A. fylloides is 15 301 bp in length, and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a 423 bp A+T-rich region. The gene content, orientation and order are identical to the majority of other lepidopteran insects. Phylogenetic reconstruction was conducted using the concatenated 13 protein-coding gene (PCG) sequences of 19 available butterfly species covering all the five butterfly families (Papilionidae, Nymphalidae, Peridae, Lycaenidae and Riodinidae). Both maximum likelihood and Bayesian inference analyses highly supported the monophyly of Lycaenidae+Riodinidae, which was standing as the sister of Nymphalidae. In addition, we propose that the riodinids be categorized into the family Lycaenidae as a subfamilial taxon.

  6. Total mitochondrial genome of mantis shrimp, Squilloides leptosquilla (Brooks, 1886) (Crustacea: Stomatopoda: Squillidae) in Korean waters.

    Science.gov (United States)

    Kang, Hye-Eun; Kim, Jung Nyun; Yoon, Tae-Ho; Park, Kyeong Dong; Park, Won Gyu; Park, Hyun; Kim, Hyun Woo

    2016-07-01

    We characterized the complete mitochondrial genome of Squilloides leptosquilla (Brooks, 1886) collected from the southern waters of Korea, which is newly recorded into the Korean carcinological fauna. The total mitochondrial genome length of S. leptosquilla was 16,376 bp. This circular DNA encodes 13 proteins, two ribosomal RNAs, and 22 transfer RNAs, as well as a putative control region. Compared with other decapod crustacean mitochondrial genomes, the overall A + T content was relatively high (71.1%) as those among other stomatopod species. Nine and four protein-coding genes are encoded on the H-strand and on the L-strand, respectively. The short non-coding region (210 bp) between tRNA(Glu) and tRNA(Phe) may be the good candidate as the molecular marker to discriminate S. leptosequilla from other stomatopods.

  7. The complete mitochondrial genome of the invasive house crow Corvus splendens (Passeriformes: Corvidae).

    Science.gov (United States)

    Krzeminska, Urszula; Wilson, Robyn; Rahman, Sadequr; Song, Beng Kah; Gan, Han Ming; Tan, Mun Hua; Austin, Christopher M

    2016-01-01

    The complete mitochondrial genome of the invasive house crow (Corvus splendens) was sequenced (GenBank accession number: KJ766304) using the MiSeq Personal Sequencer (Illumina, San Diego, CA). The mitochondrial genome is 16,962 bp in length, comprising 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal subunit genes and a non-coding control region. The mitogenome structural organization is identical to that of the other Corvus species and related genera. The overall base composition of C. splendens is 30.65% for A, 29.71% for C, 14.84% for G and 24.80% for T, with an AT content of 55.45%. We propose to use full mitochondrial genome to address taxonomic issues and to study the population genetics of crows.

  8. Determination and analysis of the complete mitochondrial genome sequence of Taoyuan chicken.

    Science.gov (United States)

    Liu, Li-Li; Xie, Hong-Bing; Yu, Qi-Fang; He, Shao-Ping; He, Jian-Hua

    2016-01-01

    Taoyuan chicken is excellent native breeds in China. This study firstly determined the complete mitochondrial genome sequence of Taoyuan chicken using PCR-based amplification and Sanger sequencing. The characteristic of the entire mitochondrial genome was analyzed in detail, with the base composition of 30.26% A, 23.79% T, 32.44% C, 13.50% G in the Taoyuan chicken (16,784 bp in length). It contained 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and a major non-coding control region (D-loop region). The complete mitochondrial genome sequence of Taoyuan chicken will be useful for the phylogenetics of poultry, and be available as basic data for the genetics and breeding.

  9. The complete sequence of the mitochondrial genome of Duroc pig (Sus Scrofa).

    Science.gov (United States)

    Wang, Ling-Yu; Chai, Yu-Lan; Ma, Hai-Ming

    2016-01-01

    In this study, the total length of mitochondrial genome of Duroc pig is 16,731 bp, including 34.66% A, 26.27% C, 25.74% T and 13.33% G. Mitochondrial genome contains a major non-coding control region (D-Loop region), 2 ribosomal RNA genes, 13 protein-coding genes (PCGs) and 22 transfer RNA genes. ND2 selects ATT as the initiation codon, and ATA is chose as an initiation codon in ND3 and ND5, the nonstandard start codon is GTG in ND4L and the rest protein common start codon is ATG. The mitochondrial genome of Duroc pig provides an important data in genetic mechanism, which plays an important role in the three-way crossbred pigs.

  10. The complete mitochondrial genome of the Jacobin pigeon (Columba livia breed Jacobin).

    Science.gov (United States)

    He, Wen-Xiao; Jia, Jin-Feng

    2015-06-01

    The Jacobin is a breed of fancy pigeon developed over many years of selective breeding that originated in Asia. In the present work, we report the complete mitochondrial genome sequence of Jacobin pigeon for the first time. The total length of the mitogenome was 17,245 bp with the base composition of 30.18% for A, 23.98% for T, 31.88% for C, and 13.96% for G and an A-T (54.17 %)-rich feature was detected. It harbored 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 non-coding control region. The arrangement of all genes was identical to the typical mitochondrial genomes of pigeon. The complete mitochondrial genome sequence of Jacobin pigeon would serve as an important data set of the germplasm resources for further study.

  11. The complete mitochondrial genome of the ice pigeon (Columba livia breed ice).

    Science.gov (United States)

    Zhang, Rui-Hua; He, Wen-Xiao

    2015-02-01

    The ice pigeon is a breed of fancy pigeon developed over many years of selective breeding. In the present work, we report the complete mitochondrial genome sequence of ice pigeon for the first time. The total length of the mitogenome was 17,236 bp with the base composition of 30.2% for A, 24.0% for T, 31.9% for C, and 13.9% for G and an A-T (54.2 %)-rich feature was detected. It harbored 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). The arrangement of all genes was identical to the typical mitochondrial genomes of pigeon. The complete mitochondrial genome sequence of ice pigeon would serve as an important data set of the germplasm resources for further study.

  12. The complete mitochondrial genome of the Fancy Pigeon, Columba livia (Columbiformes: Columbidae).

    Science.gov (United States)

    Zhang, Rui-Hua; Xu, Ming-Ju; Wang, Cun-Lian; Xu, Tong; Wei, Dong; Liu, Bao-Jian; Wang, Guo-Hua

    2015-02-01

    The fancy pigeons are domesticated varieties of the rock pigeon developed over many years of selective breeding. In the present work, we report the complete mitochondrial genome sequence of fancy pigeon for the first time. The total length of the mitogenome was 17,233 bp with the base composition of 30.1% for A, 24.0% for T, 31.9% for C, and 14.0% for G and an A-T (54.2 %)-rich feature was detected. It harbored 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). The arrangement of all genes was identical to the typical mitochondrial genomes of pigeon. The complete mitochondrial genome sequence of fancy pigeon would serve as an important data set of the germplasm resources for further study.

  13. The complete mitochondrial genome of the Feral Rock Pigeon (Columba livia breed feral).

    Science.gov (United States)

    Li, Chun-Hong; Liu, Fang; Wang, Li

    2014-10-01

    Abstract In the present work, we report the complete mitochondrial genome sequence of feral rock pigeon for the first time. The total length of the mitogenome was 17,239 bp with the base composition of 30.3% for A, 24.0% for T, 31.9% for C, and 13.8% for G and an A-T (54.3 %)-rich feature was detected. It harbored 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). The arrangement of all genes was identical to the typical mitochondrial genomes of pigeon. The complete mitochondrial genome sequence of feral rock pigeon would serve as an important data set of the germplasm resources for further study.

  14. Characterization of the complete mitochondrial genome of the king pigeon (Columba livia breed king).

    Science.gov (United States)

    Zhang, Rui-Hua; He, Wen-Xiao; Xu, Tong

    2015-06-01

    The king pigeon is a breed of pigeon developed over many years of selective breeding primarily as a utility breed. In the present work, we report the complete mitochondrial genome sequence of king pigeon for the first time. The total length of the mitogenome was 17,221 bp with the base composition of 30.14% for A, 24.05% for T, 31.82% for C, and 13.99% for G and an A-T (54.22 %)-rich feature was detected. It harbored 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one non-coding control region (D-loop region). The arrangement of all genes was identical to the typical mitochondrial genomes of pigeon. The complete mitochondrial genome sequence of king pigeon would serve as an important data set of the germplasm resources for further study.

  15. The complete mitochondrial genome of Bos taurus coreanae (Korean native cattle).

    Science.gov (United States)

    Wang, Xi; Zhang, Yuan Qing; He, Dong Chang; Yang, Xiao Ming; Li, Bo; Wang, Dong Cai; Guang, Jin; Xu, Fang; Li, Jun Ya; Gao, Xue; Gao, Hui Jiang; Zhang, Lu Pei; Zhang, Xi Zhong

    2016-01-01

    Korean native cattle is one of the famous native breeds in Korean. In the present work, we report the complete mitochondrial genome sequence of Korean native cattle for the first time. The total length of the mitogenome was 16,339 bp with the base composition of 33.4% for A, 27.2% for T, 26.0% for C, and 13.4% for G, and an A-T (60.6%)-rich feature was detected. It harbored 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). The arrangement of all genes was identical to the typical mitochondrial genomes of cattle. The complete mitochondrial genome sequence of Korean native cattle would serve as an important data set of the germplasm resources for further study.

  16. The phylogenetic position of Acoela as revealed by the complete mitochondrial genome of Symsagittifera roscoffensis

    Directory of Open Access Journals (Sweden)

    Littlewood D Timothy J

    2010-10-01

    Full Text Available Abstract Background Acoels are simply organized unsegmented worms, lacking hindgut and anus. Several publications over recent years challenge the long-held view that acoels are early offshoots of the flatworms. Instead a basal position as sister group to all other bilaterian animals was suggested, mainly based on molecular evidence. This led to the view that features of acoels might reflect those of the last common ancestor of Bilateria, and resulted in several evo-devo studies trying to interpret bilaterian evolution using acoels as a proxy model for the "Urbilateria". Results We describe the first complete mitochondrial genome sequence of a member of the Acoela, Symsagittifera roscoffensis. Gene content and circular organization of the mitochondrial genome does not significantly differ from other bilaterian animals. However, gene order shows no similarity to any other mitochondrial genome within the Metazoa. Phylogenetic analyses of concatenated alignments of amino acid sequences from protein coding genes support a position of Acoela and Nemertodermatida as the sister group to all other Bilateria. Our data provided no support for a sister group relationship between Xenoturbellida and Acoela or Acoelomorpha. The phylogenetic position of Xenoturbella bocki as sister group to or part of the deuterostomes was also unstable. Conclusions Our phylogenetic analysis supports the view that acoels and nemertodermatids are the earliest divergent extant lineage of Bilateria. As such they remain a valid source for seeking primitive characters present in the last common ancestor of Bilateria. Gene order of mitochondrial genomes seems to be very variable among Acoela and Nemertodermatida and the groundplan for the metazoan mitochondrial genome remains elusive. More data are needed to interpret mitochondrial genome evolution at the base of Bilateria.

  17. Genetic variation architecture of mitochondrial genome reveals the differentiation in Korean landrace and weedy rice.

    Science.gov (United States)

    Tong, Wei; He, Qiang; Park, Yong-Jin

    2017-03-03

    Mitochondrial genome variations have been detected despite the overall conservation of this gene content, which has been valuable for plant population genetics and evolutionary studies. Here, we describe mitochondrial variation architecture and our performance of a phylogenetic dissection of Korean landrace and weedy rice. A total of 4,717 variations across the mitochondrial genome were identified adjunct with 10 wild rice. Genetic diversity assessment revealed that wild rice has higher nucleotide diversity than landrace and/or weedy, and landrace rice has higher diversity than weedy rice. Genetic distance was suggestive of a high level of breeding between landrace and weedy rice, and the landrace showing a closer association with wild rice than weedy rice. Population structure and principal component analyses showed no obvious difference in the genetic backgrounds of landrace and weedy rice in mitochondrial genome level. Phylogenetic, population split, and haplotype network evaluations were suggestive of independent origins of the indica and japonica varieties. The origin of weedy rice is supposed to be more likely from cultivated rice rather than from wild rice in mitochondrial genome level.

  18. Changes in the human mitochondrial genome after treatment of malignant disease

    Energy Technology Data Exchange (ETDEWEB)

    Wardell, Theresa M.; Ferguson, Elaine; Chinnery, Patrick F.; Borthwick, Gillian M.; Taylor, Robert W.; Jackson, Graham; Craft, Alan; Lightowlers, Robert N.; Howell, Neil; Turnbull, Douglass M

    2003-04-09

    Mitochondrial DNA (mtDNA) is the only extrachromosomal DNA in human cells. The mitochondrial genome encodes essential information for the synthesis of the mitochondrial respiratory chain. Inherited defects of this genome are an important cause of human disease. In addition, the mitochondrial genome seems to be particularly prone to DNA damage and acquired mutations may have a role in ageing, cancer and neurodegeneration. We wished to determine if radiotherapy and chemotherapy used in the treatment of cancer could induce changes in the mitochondrial genome. Such changes would be an important genetic marker of DNA damage and may explain some of the adverse effects of treatment. We studied samples from patients who had received radiotherapy and chemotherapy for point mutations within the mtDNA control region, and for large-scale deletions. In blood samples from patients, we found a significantly increased number of point mutations compared to the control subjects. In muscle biopsies from 7 of 8 patients whom had received whole body irradiation as well as chemotherapy, the level of a specific mtDNA deletion was significantly greater than in control subjects. Our studies have shown that in patients who have been treated for cancer there is an increased level of mtDNA damage.

  19. Genetic variation architecture of mitochondrial genome reveals the differentiation in Korean landrace and weedy rice

    Science.gov (United States)

    Tong, Wei; He, Qiang; Park, Yong-Jin

    2017-01-01

    Mitochondrial genome variations have been detected despite the overall conservation of this gene content, which has been valuable for plant population genetics and evolutionary studies. Here, we describe mitochondrial variation architecture and our performance of a phylogenetic dissection of Korean landrace and weedy rice. A total of 4,717 variations across the mitochondrial genome were identified adjunct with 10 wild rice. Genetic diversity assessment revealed that wild rice has higher nucleotide diversity than landrace and/or weedy, and landrace rice has higher diversity than weedy rice. Genetic distance was suggestive of a high level of breeding between landrace and weedy rice, and the landrace showing a closer association with wild rice than weedy rice. Population structure and principal component analyses showed no obvious difference in the genetic backgrounds of landrace and weedy rice in mitochondrial genome level. Phylogenetic, population split, and haplotype network evaluations were suggestive of independent origins of the indica and japonica varieties. The origin of weedy rice is supposed to be more likely from cultivated rice rather than from wild rice in mitochondrial genome level. PMID:28256554

  20. Complex Mutation and Weak Selection together Determined the Codon Usage Bias in Bryophyte Mitochondrial Genomes

    Institute of Scientific and Technical Information of China (English)

    Bin Wang; Jing Liu; Liang Jin; Xue-Ying Feng; Jian-Qun Chen

    2010-01-01

    Mutation and selection are two major forces causing codon usage biases. How these two forces influence the codon usages in green plant mitochondrial genomes has not been well investigated. In the present study, we surveyed five bryophyte mitochondrial genomes to reveal their codon usagepatterns as well as the determining forces. Three interesting findings were made. First, comparing to Chara vulgaris, an algal species sister to all extant land plants, bryophytes have more G, C-ending codon usages in their mitochondrial genes. This is consistent with the generally higher genomic GC content in bryophyte mitochondria, suggesting an increased mutational pressure toward GC. Second, as indicated by Wright's Nc-GC3s plot, mutation, not selection, is the major force affecting codon usages of bryophyte mitochondrial genes. However, the real mutational dynamics seem very complex. Context-dependent analysis indicated that nucleotide at the 2nd codon position would slightly affect synonymous codon choices. Finally, in bryophyte mitochondria, tRNA genes would apply a weak selection force to finetune the synonymous codon frequencies, as revealed by data of Ser4-Pro-Thr-Val families. In summary,complex mutation and weak selection together determined the codon usages in bryophyte mitochondrial genomes.

  1. The complete mitochondrial genome of cultivated radish WK10039 (Raphanus sativus L.).

    Science.gov (United States)

    Jeong, Young-Min; Chung, Won-Hyung; Choi, Ah Young; Mun, Jeong-Hwan; Kim, Namshin; Yu, Hee-Ju

    2016-01-01

    We determined the complete nucleotide sequence of the mitochondrial genome of radish cultivar WK10039 (Raphanus sativus L.). The total length of the mtDNA sequence is 244,054 bp, with GC content of 45.3%. The radish mtDNA contains 82 protein-coding genes, 17 tRNA genes, and 3 rRNA genes. Among the protein-coding genes, 34 encode proteins with known functions. There are two 5529 bp repeats in the radish mitochondrial genome that may contribute to DNA recombination resulting in at least three different forms of mtDNA in radish.

  2. Complete mitochondrial genome of the Walking goby Scartelaos histophorus (Perceformes, Gobiidae).

    Science.gov (United States)

    Quan, Xianqing; Jin, Xiaoxiao; Wang, Rixin; Xu, Tianjun; Shi, Ge

    2012-08-01

    The Walking goby Scartelaos histophorus (Perciformes, Gobiidae) is an amphibious gobioid fish. In this paper, the complete mitochondrial genome of S. histophorus was first determined. The genome is 16,496 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 1 control region. The overall base composition of S. histophorus is 27.5% for T, 28.0% for C, 28.3% for A, and 16.1% for G, with a slight A+T bias of 55.8%. It has the typical vertebrate mitochondrial gene arrangement.

  3. Complete mitochondrial genome of the Oriental Hornet, Vespa orientalis F. (Hymenoptera: Vespidae)

    DEFF Research Database (Denmark)

    Haddad, Nizar Jamal; Al-Nakeeb, Kosai Ali Ahmed; Petersen, Bent

    2017-01-01

    The Oriental Hornet (Vespa orientalis) is a social insect belonging to the Vespiade family (Wasps, Hornets, Yellowjackets), genus Vespa (true Hornets). The oriental hornet is a scavenger and an agricultural pest, especially to bee farmers, but is also recently described as a harvester of solar...... energy. Here, we report the mitochondrial genome sequence of the Oriental Hornet, Vespa orientalis F., which may play a vital role in understanding this wasp biology, light trapping and generation of electricity. The mitochondrial genome of this hornet is 16,099 bp in length, containing 13 protein...

  4. Complete female mitochondrial genome of Anodonta anatina (Mollusca: Unionidae): confirmation of a novel protein-coding gene (F ORF).

    Science.gov (United States)

    Soroka, Marianna; Burzyński, Artur

    2015-04-01

    Freshwater mussels are among animals having two different, gender-specific mitochondrial genomes. We sequenced complete female mitochondrial genomes from five individuals of Anodonta anatina, a bivalve species common in palearctic ecozone. The length of the genome was variable: 15,637-15,653 bp. This variation was almost entirely confined to the non-coding parts, which constituted approximately 5% of the genome. Nucleotide diversity was moderate, at 0.3%. Nucleotide composition was typically biased towards AT (66.0%). All genes normally seen in animal mtDNA were identified, as well as the ORF characteristic for unionid mitochondrial genomes, bringing the total number of genes present to 38. If this additional ORF does encode a protein, it must evolve under a very relaxed selection since all substitutions within this gene were non-synonymous. The gene order and structure of the genome were identical to those of all female mitochondrial genomes described in unionid bivalves except the Gonideini.

  5. A Comprehensive Genomic Analysis Reveals the Genetic Landscape of Mitochondrial Respiratory Chain Complex Deficiencies.

    Directory of Open Access Journals (Sweden)

    Masakazu Kohda

    2016-01-01

    Full Text Available Mitochondrial disorders have the highest incidence among congenital metabolic disorders characterized by biochemical respiratory chain complex deficiencies. It occurs at a rate of 1 in 5,000 births, and has phenotypic and genetic heterogeneity. Mutations in about 1,500 nuclear encoded mitochondrial proteins may cause mitochondrial dysfunction of energy production and mitochondrial disorders. More than 250 genes that cause mitochondrial disorders have been reported to date. However exact genetic diagnosis for patients still remained largely unknown. To reveal this heterogeneity, we performed comprehensive genomic analyses for 142 patients with childhood-onset mitochondrial respiratory chain complex deficiencies. The approach includes whole mtDNA and exome analyses using high-throughput sequencing, and chromosomal aberration analyses using high-density oligonucleotide arrays. We identified 37 novel mutations in known mitochondrial disease genes and 3 mitochondria-related genes (MRPS23, QRSL1, and PNPLA4 as novel causative genes. We also identified 2 genes known to cause monogenic diseases (MECP2 and TNNI3 and 3 chromosomal aberrations (6q24.3-q25.1, 17p12, and 22q11.21 as causes in this cohort. Our approaches enhance the ability to identify pathogenic gene mutations in patients with biochemically defined mitochondrial respiratory chain complex deficiencies in clinical settings. They also underscore clinical and genetic heterogeneity and will improve patient care of this complex disorder.

  6. A Comprehensive Genomic Analysis Reveals the Genetic Landscape of Mitochondrial Respiratory Chain Complex Deficiencies

    Science.gov (United States)

    Nyuzuki, Hiromi; Moriyama, Yohsuke; Mizuno, Yosuke; Hirata, Tomoko; Yatsuka, Yukiko; Yamashita-Sugahara, Yzumi; Nakachi, Yutaka; Kato, Hidemasa; Okuda, Akihiko; Tamaru, Shunsuke; Borna, Nurun Nahar; Banshoya, Kengo; Aigaki, Toshiro; Sato-Miyata, Yukiko; Ohnuma, Kohei; Suzuki, Tsutomu; Nagao, Asuteka; Maehata, Hazuki; Matsuda, Fumihiko; Higasa, Koichiro; Nagasaki, Masao; Yasuda, Jun; Yamamoto, Masayuki; Fushimi, Takuya; Shimura, Masaru; Kaiho-Ichimoto, Keiko; Harashima, Hiroko; Yamazaki, Taro; Mori, Masato; Murayama, Kei; Ohtake, Akira; Okazaki, Yasushi

    2016-01-01

    Mitochondrial disorders have the highest incidence among congenital metabolic disorders characterized by biochemical respiratory chain complex deficiencies. It occurs at a rate of 1 in 5,000 births, and has phenotypic and genetic heterogeneity. Mutations in about 1,500 nuclear encoded mitochondrial proteins may cause mitochondrial dysfunction of energy production and mitochondrial disorders. More than 250 genes that cause mitochondrial disorders have been reported to date. However exact genetic diagnosis for patients still remained largely unknown. To reveal this heterogeneity, we performed comprehensive genomic analyses for 142 patients with childhood-onset mitochondrial respiratory chain complex deficiencies. The approach includes whole mtDNA and exome analyses using high-throughput sequencing, and chromosomal aberration analyses using high-density oligonucleotide arrays. We identified 37 novel mutations in known mitochondrial disease genes and 3 mitochondria-related genes (MRPS23, QRSL1, and PNPLA4) as novel causative genes. We also identified 2 genes known to cause monogenic diseases (MECP2 and TNNI3) and 3 chromosomal aberrations (6q24.3-q25.1, 17p12, and 22q11.21) as causes in this cohort. Our approaches enhance the ability to identify pathogenic gene mutations in patients with biochemically defined mitochondrial respiratory chain complex deficiencies in clinical settings. They also underscore clinical and genetic heterogeneity and will improve patient care of this complex disorder. PMID:26741492

  7. Complete mitochondrial genome sequence of a phytophagous ladybird beetle, Henosepilachna pusillanima (Mulsant) (Coleoptera: Coccinellidae).

    Science.gov (United States)

    Behere, G T; Firake, D M; Tay, W T; Azad Thakur, N S; Ngachan, S V

    2016-01-01

    Ladybird beetles are generally considered as agriculturally beneficial insects, but the ladybird beetles in the coleopteran subfamily Epilachninae are phytophagous and major plant feeding pest species which causes severe economic losses to cucurbitaceous and solanaceous crops. Henosepilachna pusillanima (Mulsant) is one of the important pest species of ladybird beetle. In this report, we sequenced and characterized the complete mitochondrial genome of H. pusillanima. For sequencing of the complete mitochondrial genome, we used the Ion Torrent sequencing platform. The complete circular mitochondrial genome of the H. pusillanima was determined to be 16,216 bp long. There were totally 13 protein coding genes, 22 transfer RNA, 2 ribosomal RNA and a control (A + T-rich) region estimated to be 1690 bp. The gene arrangement and orientations of assembled mitogenome were identical to the reported predatory ladybird beetle Coccinella septempunctata L. This is the first completely sequenced coleopteran mitochondrial genome from the beetle subfamily Epilachninae from India. Data generated in this study will benefit future comparative genomics studies for understanding the evolutionary relationships between predatory and phytophagous coccinellid beetles.

  8. Nuclear genomic control of naturally occurring variation in mitochondrial function in Drosophila melanogaster.

    Science.gov (United States)

    Jumbo-Lucioni, Patricia; Bu, Su; Harbison, Susan T; Slaughter, Juanita C; Mackay, Trudy F C; Moellering, Douglas R; De Luca, Maria

    2012-11-22

    Mitochondria are organelles found in nearly all eukaryotic cells that play a crucial role in cellular survival and function. Mitochondrial function is under the control of nuclear and mitochondrial genomes. While the latter has been the focus of most genetic research, we remain largely ignorant about the nuclear-encoded genomic control of inter-individual variability in mitochondrial function. Here, we used Drosophila melanogaster as our model organism to address this question. We quantified mitochondrial state 3 and state 4 respiration rates and P:O ratio in mitochondria isolated from the thoraces of 40 sequenced inbred lines of the Drosophila Genetic Reference Panel. We found significant within-population genetic variability for all mitochondrial traits. Hence, we performed genome-wide association mapping and identified 141 single nucleotide polymorphisms (SNPs) associated with differences in mitochondrial respiration and efficiency (P ≤1 × 10-5). Gene-centered regression models showed that 2-3 SNPs can explain 31, 13, and 18% of the phenotypic variation in state 3, state 4, and P:O ratio, respectively. Most of the genes tagged by the SNPs are involved in organ development, second messenger-mediated signaling pathways, and cytoskeleton remodeling. One of these genes, sallimus (sls), encodes a component of the muscle sarcomere. We confirmed the direct effect of sls on mitochondrial respiration using two viable mutants and their coisogenic wild-type strain. Furthermore, correlation network analysis revealed that sls functions as a transcriptional hub in a co-regulated module associated with mitochondrial respiration and is connected to CG7834, which is predicted to encode a protein with mitochondrial electron transfer flavoprotein activity. This latter finding was also verified in the sls mutants. Our results provide novel insights into the genetic factors regulating natural variation in mitochondrial function in D. melanogaster. The integrative genomic

  9. The complete mitochondrial genomes of Schistosoma haematobium and Schistosoma spindale and the evolutionary history of mitochondrial genome changes among parasitic flatworms.

    Science.gov (United States)

    Littlewood, D Timothy J; Lockyer, Anne E; Webster, Bonnie L; Johnston, David A; Le, Thanh Hoa

    2006-05-01

    Complete mitochondrial genome sequences for the schistosomes Schistosoma haematobium and Schistosoma. spindale have been characterized. S. haematobium is the causative agent of urinary schistosomiasis in humans and S. spindale uses ruminants as its definitive host; both are transmitted by freshwater snail intermediate hosts. Results confirm a major gene order rearrangement among schistosomes in all traditional Schistosoma species groups other than Schistosoma japonicum; i.e., species groups S. mansoni, S. haematobium, and S. indicum. These data lend support to the 'out of Asia' (East and Southeast Asia) hypothesis for Schistosoma. The gene order change involves translocation of atp6-nad2-trnA and a rearrangement of nad3-nad1 relative to other parasitic flatworm mt genomes so far sequenced. Gene order and tRNA secondary structure changes (loss and acquisition of the DHU and/or TPsiC arms of trnC, trnF, and trnR) between mitochondrial genomes of these and other (digenean and cestode) flatworms were inferred by character mapping onto a phylogeny estimated from nuclear small subunit rRNA gene sequences of these same species, in order to find additional rare genomic changes suitable as synapomorphies. Denser and wider taxon sampling of mt genomes across the Platyhelminthes will validate these putative characters.

  10. Evidence for paternal transmission and heteroplasmy in the mitochondrial genome of Silene vulgaris, a gynodioecious plant.

    Science.gov (United States)

    McCauley, D E; Bailey, M F; Sherman, N A; Darnell, M Z

    2005-07-01

    Gynodioecy refers to the co-occurrence of females and hermaphrodites in the same population. In many gynodioecious plants, sex is determined by an epistatic interaction between mitochondrial and nuclear genes, resulting in intragenomic evolutionary conflict, should the mitochondrial genome be maternally inherited. While maternal inheritance of the mitochondrial genome is common in angiosperms, few gynodioecious species have been studied. Here, the inheritance of the mitochondrial genes atpA and coxI was studied in 318 Silene vulgaris individuals distributed among 23 crosses. While maternal inheritance was indicated in 96% of the individuals studied, one or more individuals from each of four sib groups displayed a genotype that was identical to the father, or that did not match either parent. Given evidence that inheritance is not strictly maternal, it was hypothesized that some individuals could carry a mixture of maternally and paternally derived copies of the mitochondrial genome, a condition known as heteroplasmy. Since heteroplasmy might be difficult to detect should multiple versions of the mitochondrial genome co-occur in highly unequal copy number, a method was devised to amplify low-copy number forms of atpA differentially. Evidence for heteroplasmy was found in 23 of the 99 individuals studied, including cases in which the otherwise cryptic form of atpA matched the paternal genotype. The distribution of shared nucleotide sequence polymorphism among atpA haplotypes and the results of a population survey of the joint distribution of atpA and coxI haplotypes across individuals supports the hypothesis that heteroplasmy facilitates formation of novel mitochondrial genotypes by recombination.

  11. Complete mitochondrial genome of the Seoul frog Rana chosenica (Amphibia, Ranidae): comparison of R. chosenica and R. plancyi.

    Science.gov (United States)

    Ryu, Shi Hyun; Hwang, Ui Wook

    2011-06-01

    Here, we have sequenced the complete mitochondrial genome of the Seoul frog Rana chosenica (Amphibia, Ranidae), which is known as a Korean endemic species. It is listed as a vulnerable species by IUCN Red List and also an endangered species in South Korea. The complete mitochondrial genome of R. chosenica consists of 18,357 bp. Its gene arrangement pattern was identical with those of other Rana frogs. We compared the mitochondrial genome of R. chosenica with that of the Peking frog Rana plancyi that has been known closely related to R. chosenica. Nucleotide sequence similarity between the two whole mitochondrial genomes was 95.7%, and the relatively low similarity seems to indicate that the two species are distinctly separated on the species level. The information of mitochondrial genome comparison of the two species was discussed in detail.

  12. Neandertal versus Modern Human Dietary Responses to Climatic Fluctuations.

    Science.gov (United States)

    El Zaatari, Sireen; Grine, Frederick E; Ungar, Peter S; Hublin, Jean-Jacques

    2016-01-01

    The Neandertal lineage developed successfully throughout western Eurasia and effectively survived the harsh and severely changing environments of the alternating glacial/interglacial cycles from the middle of the Pleistocene until Marine Isotope Stage 3. Yet, towards the end of this stage, at the time of deteriorating climatic conditions that eventually led to the Last Glacial Maximum, and soon after modern humans entered western Eurasia, the Neandertals disappeared. Western Eurasia was by then exclusively occupied by modern humans. We use occlusal molar microwear texture analysis to examine aspects of diet in western Eurasian Paleolithic hominins in relation to fluctuations in food supplies that resulted from the oscillating climatic conditions of the Pleistocene. There is demonstrable evidence for differences in behavior that distinguish Upper Paleolithic humans from members of the Neandertal lineage. Specifically, whereas the Neandertals altered their diets in response to changing paleoecological conditions, the diets of Upper Paleolithic humans seem to have been less affected by slight changes in vegetation/climatic conditions but were linked to changes in their technological complexes. The results of this study also indicate differences in resource exploitation strategies between these two hominin groups. We argue that these differences in subsistence strategies, if they had already been established at the time of the first contact between these two hominin taxa, may have given modern humans an advantage over the Neandertals, and may have contributed to the persistence of our species despite habitat-related changes in food availabilities associated with climate fluctuations.

  13. Neandertal versus Modern Human Dietary Responses to Climatic Fluctuations.

    Directory of Open Access Journals (Sweden)

    Sireen El Zaatari

    Full Text Available The Neandertal lineage developed successfully throughout western Eurasia and effectively survived the harsh and severely changing environments of the alternating glacial/interglacial cycles from the middle of the Pleistocene until Marine Isotope Stage 3. Yet, towards the end of this stage, at the time of deteriorating climatic conditions that eventually led to the Last Glacial Maximum, and soon after modern humans entered western Eurasia, the Neandertals disappeared. Western Eurasia was by then exclusively occupied by modern humans. We use occlusal molar microwear texture analysis to examine aspects of diet in western Eurasian Paleolithic hominins in relation to fluctuations in food supplies that resulted from the oscillating climatic conditions of the Pleistocene. There is demonstrable evidence for differences in behavior that distinguish Upper Paleolithic humans from members of the Neandertal lineage. Specifically, whereas the Neandertals altered their diets in response to changing paleoecological conditions, the diets of Upper Paleolithic humans seem to have been less affected by slight changes in vegetation/climatic conditions but were linked to changes in their technological complexes. The results of this study also indicate differences in resource exploitation strategies between these two hominin groups. We argue that these differences in subsistence strategies, if they had already been established at the time of the first contact between these two hominin taxa, may have given modern humans an advantage over the Neandertals, and may have contributed to the persistence of our species despite habitat-related changes in food availabilities associated with climate fluctuations.

  14. Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm Silene latifolia

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    Sloan Daniel B

    2010-09-01

    Full Text Available Abstract Background Mitochondrial gene loss and functional transfer to the nucleus is an ongoing process in many lineages of plants, resulting in substantial variation across species in mitochondrial gene content. The Caryophyllaceae represents one lineage that has experienced a particularly high rate of mitochondrial gene loss relative to other angiosperms. Results In this study, we report the first complete mitochondrial genome sequence from a member of this family, Silene latifolia. The genome can be mapped as a 253,413 bp circle, but its structure is complicated by a large repeated region that is present in 6 copies. Active recombination among these copies produces a suite of alternative genome configurations that appear to be at or near "recombinational equilibrium". The genome contains the fewest genes of any angiosperm mitochondrial genome sequenced to date, with intact copies of only 25 of the 41 protein genes inferred to be present in the common ancestor of angiosperms. As observed more broadly in angiosperms, ribosomal proteins have been especially prone to gene loss in the S. latifolia lineage. The genome has also experienced a major reduction in tRNA gene content, including loss of functional tRNAs of both native and chloroplast origin. Even assuming expanded wobble-pairing rules, the mitochondrial genome can support translation of only 17 of the 61 sense codons, which code for only 9 of the 20 amino acids. In addition, genes encoding 18S and, especially, 5S rRNA exhibit exceptional sequence divergence relative to other plants. Divergence in one region of 18S rRNA appears to be the result of a gene conversion event, in which recombination with a homologous gene of chloroplast origin led to the complete replacement of a helix in this ribosomal RNA. Conclusions These findings suggest a markedly expanded role for nuclear gene products in the translation of mitochondrial genes in S. latifolia and raise the possibility of altered

  15. Complete mitochondrial genome of the versicoloured emerald hummingbird Amazilia versicolor, a polymorphic species.

    Science.gov (United States)

    Prosdocimi, Francisco; Souto, Helena Magarinos; Ruschi, Piero Angeli; Furtado, Carolina; Jennings, W Bryan

    2016-09-01

    The genome of the versicoloured emerald hummingbird (Amazilia versicolor) was partially sequenced in one-sixth of an Illumina HiSeq lane. The mitochondrial genome was assembled using MIRA and MITObim software, yielding a circular molecule of 16,861 bp in length and deposited in GenBank under the accession number KF624601. The mitogenome contained 13 protein-coding genes, 22 transfer tRNAs, 2 ribosomal RNAs and 1 non-coding control region. The molecule was assembled using 21,927 sequencing reads of 100 bp each, resulting in ∼130 × coverage of uniformly distributed reads along the genome. This is the forth mitochondrial genome described for this highly diverse family of birds and may benefit further phylogenetic, phylogeographic, population genetic and species delimitation studies of hummingbirds.

  16. Characterization of the complete mitochondrial genomes from Polycladida (Platyhelminthes) using next-generation sequencing.

    Science.gov (United States)

    Aguado, M Teresa; Grande, Cristina; Gerth, Michael; Bleidorn, Christoph; Noreña, Carolina

    2016-01-10

    The complete mitochondrial genomes of three polycladids, the acotylean Hoploplana elisabelloi and the cotyleans Enchiridium sp. and Prosthiostomum siphunculus have been assembled with high coverage from Illumina sequencing data. The mt genomes contain 36 genes including 12 of the 13 protein-coding genes characteristic for metazoan mitochondrial genomes, two ribosomal RNA genes, and 22 transfer RNA genes. Gene annotation, gene order, genetic code, start and stop codons and codon bias have been identified. In comparison with the well investigated parasitic Neodermata, our analysis reveals a great diversity of gene orders within Polycladida and Platyhelminthes in general. By analyzing representative genomes of the main groups of Platyhelminthes we explored the phylogenetic relationships of this group. The phylogenetic analyses strongly supported the monophyly of Polycladida, and based on a small taxon sampling suggest the monophyly of Acotylea and Cotylea.

  17. The complete mitochondrial genome sequence and gene organization of Tridentiger trigonocephalus (Gobiidae: Gobionellinae) with phylogenetic consideration.

    Science.gov (United States)

    Wei, Hongqing; Ma, Hongyu; Ma, Chunyan; Zhang, Fengying; Wang, Wei; Chen, Wei; Ma, Lingbo

    2016-09-01

    The complete mitochondrial genome plays an important role in studies of genome-level characteristics and phylogenetic relationships. Here we determined the complete mitogenome sequence of Tridentiger trigonocephalus (Perciformes, Gobiidae), and discovered its phylogenetic relationship. This circular genome was 16 662 bp in length, and consisted of 37 typical genes, including 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. The gene order of T. trigonocephalus mitochondrial genome was identical to those observed in most other vertebrates. Of 37 genes, 28 were encoded by heavy strand, while the others were encoded by light strand. The phylogenetic tree constructed by 13 concatenated protein-coding genes showed that T. trigonocephalus was closest to T. bifasciatus, and then to T. barbatus among the 20 species within suborder Gobioidei. This work should facilitate the studies on population genetic diversity, and molecular evolution in Gobioidei fishes.

  18. An unexpectedly large and loosely packed mitochondrial genome in the charophycean green alga Chlorokybus atmophyticus

    Directory of Open Access Journals (Sweden)

    Lemieux Claude

    2007-05-01

    Full Text Available Abstract Background The Streptophyta comprises all land plants and six groups of charophycean green algae. The scaly biflagellate Mesostigma viride (Mesostigmatales and the sarcinoid Chlorokybus atmophyticus (Chlorokybales represent the earliest diverging lineages of this phylum. In trees based on chloroplast genome data, these two charophycean green algae are nested in the same clade. To validate this relationship and gain insight into the ancestral state of the mitochondrial genome in the Charophyceae, we sequenced the mitochondrial DNA (mtDNA of Chlorokybus and compared this genome sequence with those of three other charophycean green algae and the bryophytes Marchantia polymorpha and Physcomitrella patens. Results The Chlorokybus genome differs radically from its 42,424-bp Mesostigma counterpart in size, gene order, intron content and density of repeated elements. At 201,763-bp, it is the largest mtDNA yet reported for a green alga. The 70 conserved genes represent 41.4% of the genome sequence and include nad10 and trnL(gag, two genes reported for the first time in a streptophyte mtDNA. At the gene order level, the Chlorokybus genome shares with its Chara, Chaetosphaeridium and bryophyte homologues eight to ten gene clusters including about 20 genes. Notably, some of these clusters exhibit gene linkages not previously found outside the Streptophyta, suggesting that they originated early during streptophyte evolution. In addition to six group I and 14 group II introns, short repeated sequences accounting for 7.5% of the genome were identified. Mitochondrial trees were unable to resolve the correct position of Mesostigma, due to analytical problems arising from accelerated sequence evolution in this lineage. Conclusion The Chlorokybus and Mesostigma mtDNAs exemplify the marked fluidity of the mitochondrial genome in charophycean green algae. The notion that the mitochondrial genome was constrained to remain compact during charophycean

  19. Mitochondrial genome of the endangered marine gastropod Strombus gigas Linnaeus, 1758 (Mollusca: Gastropoda).

    Science.gov (United States)

    Márquez, Edna J; Castro, Erick R; Alzate, Juan F

    2016-01-01

    The queen conch Strombus gigas is an endangered marine gastropod of significant economic importance across the Greater Caribbean region. This work reports for the first time the complete mitochondrial genome of S. gigas, obtained by FLX 454 pyrosequencing. The mtDNA genome encodes for 13 proteins, 22 tRNAs and 2 ribosomal RNAs. In addition, the coding sequences and gene synteny were similar to other previously reported mitogenomes of gastropods.

  20. The complete mitochondrial genome of the golden snapper Lutjanus johnii (Perciformes: Lutjanidae).

    Science.gov (United States)

    Taillebois, Laura; Crook, David; Saunders, Thor; Ovenden, Jennifer

    2016-01-01

    We describe the complete mitochondrial genome of the golden snapper Lutjanus johnii. It was assembled from approximately 1.4 million reads produced by Ion Torrent next generation sequencing. The complete genome was 16,596 bp in length consisting of 13 protein-coding regions, 22 tRNA, 12S and 16S rRNA as well as two non-coding regions. The A+T base content (52.8%) is similar to other teleosts.

  1. The complete mitochondrial DNA genome of a greater horseshoe bat subspecies, Rhinolophus ferrumequinum quelpartis (Chiroptera: Rhinolophidae).

    Science.gov (United States)

    Yoon, Kwang Bae; Kim, Ji Young; Kim, Hye Ri; Cho, Jae Youl; Park, Yung Chul

    2013-02-01

    There are two subspecies of Rhinolophus ferrumequinum currently recognized in South Korea. The Korean greater horseshoe bat subspecies, Rhinolophus ferrumequinum quelpartis, is distributed only in Jeju Island. The complete mitochondrial genome of the island subspecies was determined and revealed 99.7% similarity to the mainland subspecies Rhinolophus ferrumequinum korai. If d-loop region is excluded, similarity of the two genomes was 99.9%.

  2. A revised timescale for human evolution based on ancient mitochondrial genomes

    Science.gov (United States)

    Johnson, Philip L.F.; Bos, Kirsten; Lari, Martina; Bollongino, Ruth; Sun, Chengkai; Giemsch, Liane; Schmitz, Ralf; Burger, Joachim; Ronchitelli, Anna Maria; Martini, Fabio; Cremonesi, Renata G.; Svoboda, Jiří; Bauer, Peter; Caramelli, David; Castellano, Sergi; Reich, David; Pääbo, Svante; Krause, Johannes

    2016-01-01

    Summary Background Recent analyses of de novo DNA mutations in modern humans have suggested a nuclear substitution rate that is approximately half that of previous estimates based on fossil calibration. This result has led to suggestions that major events in human evolution occurred far earlier than previously thought. Result Here we use mitochondrial genome sequences from 10 securely dated ancient modern humans spanning 40,000 years as calibration points for the mitochondrial clock, thus yielding a direct estimate of the mitochondrial substitution rate. Our clock yields mitochondrial divergence times that are in agreement with earlier estimates based on calibration points derived from either fossils or archaeological material. In particular, our results imply a separation of non-Africans from the most closely related sub-Saharan African mitochondrial DNAs (haplogroup L3) of less than 62,000-95,000 years ago. Conclusion Though single loci like mitochondrial DNA (mtDNA) can only provide biased estimates of population split times, they can provide valid upper bounds; our results exclude most of the older dates for African and non-African split times recently suggested by de novo mutation rate estimates in the nuclear genome. PMID:23523248

  3. The Psm locus controls paternal sorting of the cucumber mitochondrial genome.

    Science.gov (United States)

    Havey, M J; Park, Y H; Bartoszewski, G

    2004-01-01

    The mitochondrial genome of cucumber shows paternal transmission and there are no reports of variation for mitochondrial transmission in cucumber. We used a mitochondrially encoded mosaic (MSC) phenotype to reveal phenotypic variation for mitochondrial-genome transmission in cucumber. At least 10 random plants from each of 71 cucumber plant introductions (PIs) were crossed as the female with an inbred line (MSC16) possessing the MSC phenotype. Nonmosaic F1 progenies were observed at high frequencies (greater than 50%) in F1 families from 10 PIs, with the greatest proportions being from PI 401734. Polymorphisms near the mitochondrial cox1 gene and JLV5 region revealed that nonmosaic hybrid progenies from crosses of PI 401734 with MSC16 as the male possessed the nonmosaic-inducing mitochondrial DNA (mtDNA) from the paternal parent. F2) F3, and backcross progenies from nonmosaic F1 plants from PI 401734 x MSC16 were testcrossed with MSC16 as the male parent to reveal segregation of a nuclear locus (Psm for Paternal sorting of mitochondria) controlling sorting of mtDNA from the paternal parent. Psm is a unique locus at which the maternal genotype affects sorting of paternally transmitted mtDNA.

  4. Integrative genomics identifies MCU as an essential component of the mitochondrial calcium uniporter.

    Science.gov (United States)

    Baughman, Joshua M; Perocchi, Fabiana; Girgis, Hany S; Plovanich, Molly; Belcher-Timme, Casey A; Sancak, Yasemin; Bao, X Robert; Strittmatter, Laura; Goldberger, Olga; Bogorad, Roman L; Koteliansky, Victor; Mootha, Vamsi K

    2011-06-19

    Mitochondria from diverse organisms are capable of transporting large amounts of Ca(2+) via a ruthenium-red-sensitive, membrane-potential-dependent mechanism called the uniporter. Although the uniporter's biophysical properties have been studied extensively, its molecular composition remains elusive. We recently used comparative proteomics to identify MICU1 (also known as CBARA1), an EF-hand-containing protein that serves as a putative regulator of the uniporter. Here, we use whole-genome phylogenetic profiling, genome-wide RNA co-expression analysis and organelle-wide protein coexpression analysis to predict proteins functionally related to MICU1. All three methods converge on a novel predicted transmembrane protein, CCDC109A, that we now call 'mitochondrial calcium uniporter' (MCU). MCU forms oligomers in the mitochondrial inner membrane, physically interacts with MICU1, and resides within a large molecular weight complex. Silencing MCU in cultured cells or in vivo in mouse liver severely abrogates mitochondrial Ca(2+) uptake, whereas mitochondrial respiration and membrane potential remain fully intact. MCU has two predicted transmembrane helices, which are separated by a highly conserved linker facing the intermembrane space. Acidic residues in this linker are required for its full activity. However, an S259A point mutation retains function but confers resistance to Ru360, the most potent inhibitor of the uniporter. Our genomic, physiological, biochemical and pharmacological data firmly establish MCU as an essential component of the mitochondrial Ca(2+) uniporter.

  5. The complete mitochondrial genome of the sea spider Nymphon gracile (Arthropoda: Pycnogonida

    Directory of Open Access Journals (Sweden)

    Braband Anke

    2006-11-01

    Full Text Available Abstract Background Mitochondrial genomes form units of genetic information replicating indepentently from nuclear genomes. Sequence data (most often from protein-coding genes and other features (gene order, RNA secondary structure of mitochondrial genomes are often used in phylogenetic studies of metazoan animals from population to phylum level. Pycnogonids are primarily marine arthropods, often considered closely related to chelicerates (spiders, scorpions and allies. However, due to their aberrant morphology and to controversial results from molecular studies, their phylogenetic position is still under debate. Results This is the first report of a complete mitochondrial genome sequence from a sea spider (Nymphon gracile, class Pycnogonida. Gene order derives from that of other arthropods so that presumably 10 single tRNA gene translocations, a translocation of the mitochondrial control region, and one large inversion affecting protein-coding genes must have happened in the lineage leading to Nymphon gracile. Some of the changes in gene order seem not to be common to all pycnogonids, as those were not found in a partial mitochondrial genome of another species, Endeis spinosa. Four transfer RNAs of Nymphon gracile show derivations from the usual cloverleaf secondary structure (truncation or loss of an arm. Initial phylogenetic analyses using mitochondrial protein-coding gene sequences placed Pycnogonida as sister group to Acari. However, this is in contrast to the majority of all other studies using nuclear genes and/or morphology and was not recovered in a second analysis where two long-branching acarid species were omitted. Conclusion Extensive gene rearrangement characterizes the mitochondrial genome of Nymphon gracile. At least some of the events leading to this derived gene order happened after the split of pycnogonid subtaxa. Nucleotide and amino acid frequencies show strong differences between chelicerate taxa, presumably biasing

  6. The complete mitochondrial genome of the Java fat-nose goby Pseudogobius javanicus (Teleostei, Gobiidae).

    Science.gov (United States)

    Huang, Shih-Pin; Shen, Chia-Ning; Chen, I-Shiung

    2015-02-01

    In this study, the complete mitochondrial genome of the fat-nose goby Pseudogobius javanicus has been amplified. P. javanicus is widely contributed species in Southeast to East Asia. The complete mitochondrial genome is 16,493 base pairs (bp) in total length, had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 2 rRNAs, 22 tRNAs, 1 control region (CR) and 1 light-strand replication origin (OL). The overall base composition of P. javanicus is 27.1% for A, 27.3% for T, 28.6% for C, 17.0% for G, with higher AT content of 54.4%. This study will contribute for understanding the phylogenetic approach in genus Pseudogobius.

  7. The complete mitochondrial genome of Hoeven's mullet-goby Hemigobius hoevenii (Bleeker) (Teleostei, Gobiidae).

    Science.gov (United States)

    Huang, Shih-Pin; Shen, Chia-Ning; Chen, I-Shiung

    2016-01-01

    In this study, the complete mitochondrial genome of Hoeven's mullet-goby Hemigobius hoevenii (Bleeker, 1851) collected from Malay Peninsula has been amplified and sequenced. The complete mitochondrial genome is 16,469 base pairs (bp) in total length, had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 2 rRNAs, 22 tRNAs, 1 control region (CR) and 1 light-strand replication origin (OL). The overall base composition of H. hoevenii is 27.1% for A, 26.6% for T, 29.0% for C, 17.3% for G, with higher AT content 53.7%. This study will contribute for understanding the phylogenetic approach of Hemigobius species as well as the related genera of gobiid fishes.

  8. The complete mitochondrial genome of spotted hidden-teeth goby Apocryptodon punctatus Tomiyama (Perciformes, Gobiidae).

    Science.gov (United States)

    Wen, Zhong-Han; Chen, I-Shiung

    2016-01-01

    The complete mitochondrial genome of the oxudercine, spotted hidden-teeth goby Apocryptodon punctatus (Tomiyama, 1934) has been amplified in this study. Apocryptodon punctatus was found in Japan, Taiwan and Eastern Mainland China. The complete mitochondrial genome is 16,567 base pairs (bp) in total length, had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 2 rRNAs, 22 tRNAs, 1 control region (CR) and 1 light-strand replication origin (OL). The overall base composition of Apocryptodon punctatus is 29.2% for A, 28.6% for T, 25.9% for C, 16.3% for G, with higher AT content 57.8%. This study will contribute and be rather beneficial for understanding the phylogenetic approach of species of Apocryptodon and the related genera among gobioids.

  9. The complete mitochondrial genome of the redigoby Redigobius bikolanus (Perciformes, Gobiidae).

    Science.gov (United States)

    Huang, Shih-Pin; Shen, Chia-Ning; Chen, I-Shiung

    2016-01-01

    The complete mitochondrial genome of the Biko's redigoby Redigobius bikolanus (Herre, 1927) has been amplified in this study. R. bikolanus contributes in Taiwan, as well as Southeast Asia. The complete mitochondrial genome is 16,464 base pairs (bp) in total length, had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 2 rRNAs, 22 tRNAs, 1 control region (CR) and 1 light-strand replication origin (OL). The overall base composition of R. bikolanus is 28.9% for A, 26.7% for T, 28.5% for C, 15.9% for G, with higher AT content 55.6%. This study will contribute and be rather beneficial for understanding the phylogenetic approach of genus Redigobius.

  10. Efficient newly designed primers for the amplification and sequencing of bird mitochondrial genomes.

    Science.gov (United States)

    Amer, Sayed A M; Ahmed, Mohamed Mohamed; Shobrak, Mohammed

    2013-01-01

    In the present study, 27 mitochondrial genomes of diverse avian supra-orders were collected from the Genbank database and their genes were aligned separately. From the alignments, the conserved sequences were selected to design novel conserved primers for amplification and sequencing of the different mitochondrial genes. The reproducibility of these primers was tested in the amplification and sequencing of diverse avian supra-order mitochondrial genomes and was confirmed. This method helped in designing a new set of primers to accelerate both the amplification and the sequencing of bird mitogenomes. It also aids in building mitogenome markers in studying the genetic framework of endemic birds as a preliminary strategy for conservation management of them.

  11. The mitochondrial genome of Phallusia mammillata and Phallusia fumigata (Tunicata, Ascidiacea: high genome plasticity at intra-genus level

    Directory of Open Access Journals (Sweden)

    Pesole Graziano

    2007-08-01

    Full Text Available Abstract Background Within Chordata, the subphyla Vertebrata and Cephalochordata (lancelets are characterized by a remarkable stability of the mitochondrial (mt genome, with constancy of gene content and almost invariant gene order, whereas the limited mitochondrial data on the subphylum Tunicata suggest frequent and extensive gene rearrangements, observed also within ascidians of the same genus. Results To confirm this evolutionary trend and to better understand the evolutionary dynamics of the mitochondrial genome in Tunicata Ascidiacea, we have sequenced and characterized the complete mt genome of two congeneric ascidian species, Phallusia mammillata and Phallusia fumigata (Phlebobranchiata, Ascidiidae. The two mtDNAs are surprisingly rearranged, both with respect to one another and relative to those of other tunicates and chordates, with gene rearrangements affecting both protein-coding and tRNA genes. The new data highlight the extraordinary variability of ascidian mt genome in base composition, tRNA secondary structure, tRNA gene content, and non-coding regions (number, size, sequence and location. Indeed, both Phallusia genomes lack the trnD gene, show loss/acquisition of DHU-arm in two tRNAs, and have a G+C content two-fold higher than other ascidians. Moreover, the mt genome of P. fumigata presents two identical copies of trnI, an extra tRNA gene with uncertain amino acid specificity, and four almost identical sequence regions. In addition, a truncated cytochrome b, lacking a C-terminal tail that commonly protrudes into the mt matrix, has been identified as a new mt feature probably shared by all tunicates. Conclusion The frequent occurrence of major gene order rearrangements in ascidians both at high taxonomic level and within the same genus makes this taxon an excellent model to study the mechanisms of gene rearrangement, and renders the mt genome an invaluable phylogenetic marker to investigate molecular biodiversity and speciation

  12. Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants.

    Science.gov (United States)

    Drouin, Guy; Daoud, Hanane; Xia, Junnan

    2008-12-01

    Previous studies have estimated that, in angiosperms, the synonymous substitution rate of chloroplast genes is three times higher than that of mitochondrial genes and that of nuclear genes is twelve times higher than that of mitochondrial genes. Here we used 12 genes in 27 seed plant species to investigate whether these relative rates of substitutions are common to diverse seed plant groups. We find that the overall relative rate of synonymous substitutions of mitochondrial, chloroplast and nuclear genes of all seed plants is 1:3:10, that these ratios are 1:2:4 in gymnosperms but 1:3:16 in angiosperms and that they go up to 1:3:20 in basal angiosperms. Our results show that the mitochondrial, chloroplast and nuclear genomes of seed plant groups have different synonymous substitutions rates, that these rates are different in different seed plant groups and that gymnosperms have smaller ratios than angiosperms.

  13. Subvertical grooves of interproximal facets in Neandertal posterior teeth.

    Science.gov (United States)

    Villa, G; Giacobini, G

    1995-01-01

    Subvertical grooves, located on the interproximal facets of most Neandertal posterior teeth, are less frequently noted on the teeth of other hominids, including modern humans. These grooves, 0.1-0.5 mm in width, are strictly localized within the facet area. Scanning electron microscopic (SEM) examination of grooves present on Neandertal teeth from Caverna delle Fate (Liguria, Italy) and Genay (Côte d'Or, France) demonstrated that they were produced during the life of these individuals. Characteristics of the groove surface suggest an erosion-abrasion mechanism of formation. These grooves, which developed in parts of the dentition exposed to marked stress, originated in areas characterized by changes in the orientation of enamel prism bundles (i.e., Hunter-Schreger bands). Observations carried out on modern human molars showed a subvertical disposition of these bands near interproximal ridges facilitating subvertical microfractures. Possible correlations between enamel structure, masticatory stress, and interproximal groove formation in Neandertals are discussed.

  14. Rapidly Evolving Mitochondrial Genome and Directional Selection in Mitochondrial Genes in the Parasitic Wasp Nasonia (Hymenoptera: Pteromalidae)

    Science.gov (United States)

    Raychoudhury, Rhitoban; Lavrov, Dennis V.; Werren, John H.

    2008-01-01

    We sequenced the nearly complete mtDNA of 3 species of parasitic wasps, Nasonia vitripennis (2 strains), Nasonia giraulti, and Nasonia longicornis, including all 13 protein-coding genes and the 2 rRNAs, and found unusual patterns of mitochondrial evolution. The Nasonia mtDNA has a unique gene order compared with other insect mtDNAs due to multiple rearrangements. The mtDNAs of these wasps also show nucleotide substitution rates over 30 times faster than nuclear protein-coding genes, indicating among the highest substitution rates found in animal mitochondria (normally <10 times faster). A McDonald and Kreitman test shows that the between-species frequency of fixed replacement sites relative to silent sites is significantly higher compared with within-species polymorphisms in 2 mitochondrial genes of Nasonia, atp6 and atp8, indicating directional selection. Consistent with this interpretation, the Ka/Ks (nonsynonymous/synonymous substitution rates) ratios are higher between species than within species. In contrast, cox1 shows a signature of purifying selection for amino acid sequence conservation, although rates of amino acid substitutions are still higher than for comparable insects. The mitochondrial-encoded polypeptides atp6 and atp8 both occur in F0F1ATP synthase of the electron transport chain. Because malfunction in this fundamental protein severely affects fitness, we suggest that the accelerated accumulation of replacements is due to beneficial mutations necessary to compensate mild-deleterious mutations fixed by random genetic drift or Wolbachia sweeps in the fast evolving mitochondria of Nasonia. We further propose that relatively high rates of amino acid substitution in some mitochondrial genes can be driven by a “Compensation-Draft Feedback”; increased fixation of mildly deleterious mutations results in selection for compensatory mutations, which lead to fixation of additional deleterious mutations in nonrecombining mitochondrial genomes, thus

  15. Rapidly evolving mitochondrial genome and directional selection in mitochondrial genes in the parasitic wasp nasonia (hymenoptera: pteromalidae).

    Science.gov (United States)

    Oliveira, Deodoro C S G; Raychoudhury, Rhitoban; Lavrov, Dennis V; Werren, John H

    2008-10-01

    We sequenced the nearly complete mtDNA of 3 species of parasitic wasps, Nasonia vitripennis (2 strains), Nasonia giraulti, and Nasonia longicornis, including all 13 protein-coding genes and the 2 rRNAs, and found unusual patterns of mitochondrial evolution. The Nasonia mtDNA has a unique gene order compared with other insect mtDNAs due to multiple rearrangements. The mtDNAs of these wasps also show nucleotide substitution rates over 30 times faster than nuclear protein-coding genes, indicating among the highest substitution rates found in animal mitochondria (normally mitochondrial genes of Nasonia, atp6 and atp8, indicating directional selection. Consistent with this interpretation, the Ka/Ks (nonsynonymous/synonymous substitution rates) ratios are higher between species than within species. In contrast, cox1 shows a signature of purifying selection for amino acid sequence conservation, although rates of amino acid substitutions are still higher than for comparable insects. The mitochondrial-encoded polypeptides atp6 and atp8 both occur in F0F1ATP synthase of the electron transport chain. Because malfunction in this fundamental protein severely affects fitness, we suggest that the accelerated accumulation of replacements is due to beneficial mutations necessary to compensate mild-deleterious mutations fixed by random genetic drift or Wolbachia sweeps in the fast evolving mitochondria of Nasonia. We further propose that relatively high rates of amino acid substitution in some mitochondrial genes can be driven by a "Compensation-Draft Feedback"; increased fixation of mildly deleterious mutations results in selection for compensatory mutations, which lead to fixation of additional deleterious mutations in nonrecombining mitochondrial genomes, thus accelerating the process of amino acid substitutions.

  16. The Complete DNA Sequence of the Mitochondrial Genome of a ``living Fossil,'' the Coelacanth (Latimeria Chalumnae)

    Science.gov (United States)

    Zardoya, R.; Meyer, A.

    1997-01-01

    The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3' end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNAs, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship. PMID:9215903

  17. Incompatibility between Nuclear and Mitochondrial Genomes Contributes to an Interspecies Reproductive Barrier.

    Science.gov (United States)

    Ma, Hong; Marti Gutierrez, Nuria; Morey, Robert; Van Dyken, Crystal; Kang, Eunju; Hayama, Tomonari; Lee, Yeonmi; Li, Ying; Tippner-Hedges, Rebecca; Wolf, Don P; Laurent, Louise C; Mitalipov, Shoukhrat

    2016-08-09

    Vertebrate cells carry two different genomes, nuclear (nDNA) and mitochondrial (mtDNA), both encoding proteins involved in oxidative phosphorylation. Because of the extensive interactions, adaptive coevolution of the two genomes must occur to ensure normal mitochondrial function. To investigate whether incompatibilities between these two genomes could contribute to interspecies reproductive barriers, we performed reciprocal mtDNA replacement (MR) in zygotes between widely divergent Mus m. domesticus (B6) and conplastic Mus m. musculus (PWD) mice. Transfer of MR1 cybrid embryos (B6nDNA-PWDmtDNA) supported normal development of F1 offspring with reduced male fertility but unaffected reproductive fitness in females. Furthermore, donor PWD mtDNA was faithfully transmitted through the germline into F2 and F3 generations. In contrast, reciprocal MR2 (PWDnDNA-B6mtDNA) produced high embryonic loss and stillborn rates, suggesting an association between mitochondrial function and infertility. These results strongly suggest that functional incompatibility between nuclear and mitochondrial genomes contributes to interspecies reproductive isolation in mammals.

  18. The complete DNA sequence of the mitochondrial genome of a "living fossil," the coelacanth (Latimeria chalumnae).

    Science.gov (United States)

    Zardoya, R; Meyer, A

    1997-07-01

    The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3' end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNAs, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship.

  19. The mitochondrial genome of Atrijuglans hetaohei Yang (Lepidoptera: Gelechioidea) and related phylogenetic analyses.

    Science.gov (United States)

    Wang, Qiqi; Zhang, Zhengqing; Tang, Guanghui

    2016-04-25

    Complete mitochondrial genome sequences are of great importance for better understanding the genome-level characteristics and phylogenetic relationships among related species. In this study, the complete mitochondrial genome of Atrijuglans hetaohei Yang is sequenced and analyzed, which is 15,379bp in length (GenBank: KT581634) and contains a typical set of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a non-coding region (control region). Except for cox1 gene that is initiated by CGA codon, all protein-coding genes start with ATN codons and end with the stop codon T, TA or TAA. All tRNAs have a typical clover-leaf secondary structure, except for trnS1, of which the DHU arm could not form a stable stem-loop structure. The secondary structure of rrnL and rrnS consists of 49 helices and 33 helices, respectively. Phylogenetic analyses of the complete mitochondrial genome sequences and of the amino acid sequences for 13 mitochondrial protein-coding genes among related species support the view that A. hetaohei is more closely related to the Gelechioidea than Yponomeutoidea. This result is consistent with a previous classification based on morphology.

  20. The complete mitochondrial genome of Paracheirodon axelrodi (Characiformes:Characidae:Paracheirodon).

    Science.gov (United States)

    Zhang, Songhao; Cui, Jun; Xu, Ru; Xu, Peng; Sun, Jinsheng

    2016-01-01

    The complete mitochondrial genome of Paracheirodon axelrodi was obtained by the traditional polymerase chain reaction method. The mitogenome was determined to be a 17,100 bp long circular molecule. It contains the typical complement of 13 protein-coding genes, 2 rRNAs and 22 tRNAs. This is first report on the complete mitogenome sequence of P. axelrodi.

  1. The complete mitochondrial genome and phylogenetic position of the Philippines spurdog, Squalus montalbani.

    Science.gov (United States)

    Kemper, Jenny M; Naylor, Gavin J P

    2016-11-01

    We present the complete mitochondrial genome sequence (16 555 bp) of the Philippines spurdog, Squalus montalbani, currently listed as Vulnerable due to population declines and fishing pressures. A phylogenetic analysis was carried out on S. montalbani and representative shark mitogenomes. Squalus montalbani was placed within the Squaliformes as a sister taxon to Squalus acanthias and Cirrhigaleus australis.

  2. Massively parallel pyrosequencing of the mitochondrial genome with the 454 methodology in forensic genetics

    DEFF Research Database (Denmark)

    Mikkelsen, Martin; Frank-Hansen, Rune; Hansen, Anders Johannes;

    2014-01-01

    RESULTS: of sequencing of whole mitochondrial genome, HV1 and HV2 DNA with the second generation system (SGS) Roche 454 GS Junior were compared with results of Sanger sequencing and SNP typing with SNaPshot single base extension detected with MALDI-TOF and capillary electrophoresis. We investigat...

  3. The mitochondrial genome of the garden pea leafminer Chromatomyia horticola (Goureau, 1851) (Diptera: Agromyzidae).

    Science.gov (United States)

    Wang, You-Zhu; Jin, Gui-Hua; Zhu, Jia-Ying; Wei, Shu-Jun

    2016-07-01

    Here we report the mitochondrial genome sequence of the garden pea leafminer Chromatomyia horticola (Goureau, 1851) (Diptera: Agromyzidae) (GenBank accession no. KR047789). This is the first species with sequenced mitochondrial genome from the genus Chromatomyia. The current length with partial A  +  T-rich region of this mitochondrial genome is 15,320 bp with an A  +  T content of 77.54%. All the 13 protein-coding, two rRNA, and 22 tRNA genes were sequenced, except for the A  +  T-rich region. As in most other sequenced mitochondrial genomes of Diptera, there is no rearrangement compared with the pupative ancestral arrangement of insects. All protein-coding genes start with the ATN start codon except for the gene cox1, which uses abnormal TTG. The A  +  T-rich region is located between rrnS and trnI with a sequenced length of 503 bp. Phylogenetic analysis using the Bayesian method based on the first and second codon positions of the 13 protein-coding genes recovered the monophyly of Agromyzidae with one species of Chromatomyia and four species of Liriomyza in our study. The superfamily Oestroidea (with Agromyzidae in analysis) is sister to the Opomyzoidea.

  4. The complete mitochondrial genome of human parasitic roundworm, Ascaris lumbricoides.

    Science.gov (United States)

    Park, Yung Chul; Kim, Won; Park, Joong-Ki

    2011-08-01

    The genome length of the Ascaris lumbricoides, human parasitic roundworm, is 14,281 bp with a nucleotide composition of 22.1% A, 49.8% T, 7.8% C, and 20.3% G. The genome consists of 12 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region.

  5. Complete mitochondrial DNA sequence of the ark shell Scapharca broughtonii: an ultra-large metazoan mitochondrial genome.

    Science.gov (United States)

    Liu, Yun-Guo; Kurokawa, Tadahide; Sekino, Masashi; Tanabe, Toru; Watanabe, Kazuhito

    2013-03-01

    The complete mitochondrial (mt) genome of the ark shell Scapharca broughtonii was determined using long PCR and a genome walking sequencing strategy with genus-specific primers. The S. broughtonii mt genome (GenBank accession number AB729113) contained 12 protein-coding genes (the atp8 gene is missing, as in most bivalves), 2 ribosomal RNA genes, and 42 transfer tRNA genes, in a length of 46,985 nucleotides for the size of mtDNA with only one copy of the heteroplasmic tandem repeat (HTR) unit. Moreover the S. broughtonii mt genome shows size variation; these genomes ranged in size from about 47 kb to about 50 kb because of variation in the number of repeat sequences in the non-coding region. The mt-genome of S. broughtonii is, to date, the longest reported metazoan mtDNA sequence. Sequence duplication in non-coding region and the formation of HTR arrays were two of the factors responsible for the ultra-large size of this mt genome. All the tRNA genes were found within the S. broughtonii mt genome, unlike the other bivalves usually lacking one or more tRNA genes. Twelve additional specimens were used to analyze the patterns of tandem repeat arrays by PCR amplification and agarose electrophoresis. Each of the 12 specimens displayed extensive heteroplasmy and had 8-10 length variants. The motifs of the HTR arrays are about 353-362 bp and the number of repeats ranges from 1 to 11.

  6. Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore

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    Pilgrim Kristine

    2011-04-01

    Full Text Available Abstract Background Science-based wildlife management relies on genetic information to infer population connectivity and identify conservation units. The most commonly used genetic marker for characterizing animal biodiversity and identifying maternal lineages is the mitochondrial genome. Mitochondrial genotyping figures prominently in conservation and management plans, with much of the attention focused on the non-coding displacement ("D" loop. We used massively parallel multiplexed sequencing to sequence complete mitochondrial genomes from 40 fishers, a threatened carnivore that possesses low mitogenomic diversity. This allowed us to test a key assumption of conservation genetics, specifically, that the D-loop accurately reflects genealogical relationships and variation of the larger mitochondrial genome. Results Overall mitogenomic divergence in fishers is exceedingly low, with 66 segregating sites and an average pairwise distance between genomes of 0.00088 across their aligned length (16,290 bp. Estimates of variation and genealogical relationships from the displacement (D loop region (299 bp are contradicted by the complete mitochondrial genome, as well as the protein coding fraction of the mitochondrial genome. The sources of this contradiction trace primarily to the near-absence of mutations marking the D-loop region of one of the most divergent lineages, and secondarily to independent (recurrent mutations at two nucleotide position in the D-loop amplicon. Conclusions Our study has two important implications. First, inferred genealogical reconstructions based on the fisher D-loop region contradict inferences based on the entire mitogenome to the point that the populations of greatest conservation concern cannot be accurately resolved. Whole-genome analysis identifies Californian haplotypes from the northern-most populations as highly distinctive, with a significant excess of amino acid changes that may be indicative of molecular

  7. Interspecific Comparison and annotation of two complete mitochondrial genome sequences from the plant pathogenic fungus Mycosphaerella graminicola

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    Millenbaugh, Bonnie A; Pangilinan, Jasmyn L.; Torriani, Stefano F.F.; Goodwin, Stephen B.; Kema, Gert H.J.; McDonald, Bruce A.

    2007-12-07

    The mitochondrial genomes of two isolates of the wheat pathogen Mycosphaerella graminicola were sequenced completely and compared to identify polymorphic regions. This organism is of interest because it is phylogenetically distant from other fungi with sequenced mitochondrial genomes and it has shown discordant patterns of nuclear and mitochondrial diversity. The mitochondrial genome of M. graminicola is a circular molecule of approximately 43,960 bp containing the typical genes coding for 14 proteins related to oxidative phosphorylation, one RNA polymerase, two rRNA genes and a set of 27 tRNAs. The mitochondrial DNA of M. graminicola lacks the gene encoding the putative ribosomal protein (rps5-like), commonly found in fungal mitochondrial genomes. Most of the tRNA genes were clustered with a gene order conserved with many other ascomycetes. A sample of thirty-five additional strains representing the known global mt diversity was partially sequenced to measure overall mitochondrial variability within the species. Little variation was found, confirming previous RFLP-based findings of low mitochondrial diversity. The mitochondrial sequence of M. graminicola is the first reported from the family Mycosphaerellaceae or the order Capnodiales. The sequence also provides a tool to better understand the development of fungicide resistance and the conflicting pattern of high nuclear and low mitochondrial diversity in global populations of this fungus.

  8. The Spy VI child: a newly discovered Neandertal infant.

    Science.gov (United States)

    Crevecoeur, Isabelle; Bayle, Priscilla; Rougier, Hélène; Maureille, Bruno; Higham, Thomas; van der Plicht, Johannes; De Clerck, Nora; Semal, Patrick

    2010-12-01

    Spy cave (Jemeppe-sur-Sambre, Belgium) is reputed for the two adult Neandertal individuals discovered in situ in 1886. Recent reassessment of the Spy collections has allowed direct radiocarbon dating of these individuals. The sorting of all of the faunal collections has also led to the discovery of the remains of a Neandertal child, Spy VI. This individual is represented by two mandibular corpus fragments. The left fragment is the most complete and both sides preserve the mental foramen. Four deciduous teeth are associated with these mandibular remains: three incisors and one canine. The lower left canine (Spy 645a) conjoins with the corresponding alveolar socket in the left part of the mandible. Following extant standards, the developmental stage of the preserved teeth indicate an age at death of about one and a half years. In addition to performing a classical morphometric comparative study of the mandible and teeth, we have evaluated the dental tissue proportions using high-resolution microtomographic techniques. Our results show that Spy VI generally falls within the Neandertal range of variation. However, this specimen also exhibits particular traits, notably in the dental internal structural organization, which reveals that variation in the immature Neandertal variation is larger than what was variation currently represented by the available fossil record. These observations demonstrate the need for investigating the frequency and expression of immature Neandertal traits in fossil anterior teeth, as well as their temporal and geographic variation. Direct radiocarbon dating of the Spy VI specimen has been conducted in two different laboratories. The results of Spy VI confirm the age previously determined for the two adults, making the Spy Neandertal remains the youngest ever directly dated in northwest Europe.

  9. Intron Derived Size Polymorphism in the Mitochondrial Genomes of Closely Related Chrysoporthe Species.

    Science.gov (United States)

    Kanzi, Aquillah Mumo; Wingfield, Brenda Diana; Steenkamp, Emma Theodora; Naidoo, Sanushka; van der Merwe, Nicolaas Albertus

    2016-01-01

    In this study, the complete mitochondrial (mt) genomes of Chrysoporthe austroafricana (190,834 bp), C. cubensis (89,084 bp) and C. deuterocubensis (124,412 bp) were determined. Additionally, the mitochondrial genome of another member of the Cryphonectriaceae, namely Cryphonectria parasitica (158,902 bp), was retrieved and annotated for comparative purposes. These genomes showed high levels of synteny, especially in regions including genes involved in oxidative phosphorylation and electron transfer, unique open reading frames (uORFs), ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs), as well as intron positions. Comparative analyses revealed signatures of duplication events, intron number and length variation, and varying intronic ORFs which highlighted the genetic diversity of mt genomes among the Cryphonectriaceae. These mt genomes showed remarkable size polymorphism. The size polymorphism in the mt genomes of these closely related Chrysoporthe species was attributed to the varying number and length of introns, coding sequences and to a lesser extent, intergenic sequences. Compared to publicly available fungal mt genomes, the C. austroafricana mt genome is the second largest in the Ascomycetes thus far.

  10. Complete mitochondrial genome of Nanorana pleskei (Amphibia: Anura: Dicroglossidae) and evolutionary characteristics

    Institute of Scientific and Technical Information of China (English)

    Guiying CHEN; Bin WANG; Jiongyu LIU; Feng XIE; Jianping JIANG

    2011-01-01

    The complete mitochondrial genome of Nanorana pleskei from the Qinghai-Tibet Plateau was sequenced.It includes 17,660 base pairs,containing 13 protein-coding genes,two rRNAs and 23 tRNAs.A tandem duplication of tRNAMet gene was found in this mitochondrial genome,and the similarity between the two tRNAMet genes is 85.8%,being the highest in amphibian mitochondrial genomes sequenced thus far.Based on gene organization,24 types were found from 145 amphibian mitochondrial genomes.Type 1 was present in 108 species,type 11 in 11 species,types 5,16,17,and 20 each in two species,and the others each present in one species.Fifteen types were found in Anura,being the most diversity in three orders of the Lissamphibia.Our phylogenetic results using 11 protein-coding gene sequences of 145 amphibian mitochondrial genomes strongly support the monophyly of the Lissamphibia,as well as its three orders,the Gymnophiona,Caudata,and Anura,among which the relationships were ((Gymnophiona (Caudata,Anura)).Based on the phylogenetic trees,type 1 was recognized as the ancestral type for amphibians,and type 11 was the synapomorphic type for the Neobatrachia.Gene rearrangements among lineages provide meaningful phylogenetic information.The rearrangement of the LTPF tRNA gene cluster and the translocation of the ND5 gene only found in the Neobatrachia support the monophyly of this group; similarly,the tandem duplication of the tRNAMet genes only found in the Dicroglossidae support the monophyly of this family [Current Zoology 57 (6):785-805,2011].

  11. Migration of mitochondrial DNA in the nuclear genome of colorectal adenocarcinoma.

    Science.gov (United States)

    Srinivasainagendra, Vinodh; Sandel, Michael W; Singh, Bhupendra; Sundaresan, Aishwarya; Mooga, Ved P; Bajpai, Prachi; Tiwari, Hemant K; Singh, Keshav K

    2017-03-29

    Colorectal adenocarcinomas are characterized by abnormal mitochondrial DNA (mtDNA) copy number and genomic instability, but a molecular interaction between mitochondrial and nuclear genome remains unknown. Here we report the discovery of increased copies of nuclear mtDNA (NUMT) in colorectal adenocarcinomas, which supports link between mtDNA and genomic instability in the nucleus. We name this phenomenon of nuclear occurrence of mitochondrial component as numtogenesis. We provide a description of NUMT abundance and distribution in tumor versus matched blood-derived normal genomes. Whole-genome sequence data were obtained for colon adenocarcinoma and rectum adenocarcinoma patients participating in The Cancer Genome Atlas, via the Cancer Genomics Hub, using the GeneTorrent file acquisition tool. Data were analyzed to determine NUMT proportion and distribution on a genome-wide scale. A NUMT suppressor gene was identified by comparing numtogenesis in other organisms. Our study reveals that colorectal adenocarcinoma genomes, on average, contains up to 4.2-fold more somatic NUMTs than matched normal genomes. Women colorectal tumors contained more NUMT than men. NUMT abundance in tumor predicted parallel abundance in blood. NUMT abundance positively correlated with GC content and gene density. Increased numtogenesis was observed with higher mortality. We identified YME1L1, a human homolog of yeast YME1 (yeast mitochondrial DNA escape 1) to be frequently mutated in colorectal tumors. YME1L1 was also mutated in tumors derived from other tissues. We show that inactivation of YME1L1 results in increased transfer of mtDNA in the nuclear genome. Our study demonstrates increased somatic transfer of mtDNA in colorectal tumors. Our study also reveals sex-based differences in frequency of NUMT occurrence and that NUMT in blood reflects NUMT in tumors, suggesting NUMT may be used as a biomarker for tumorigenesis. We identify YME1L1 as the first NUMT suppressor gene in human and

  12. The mitochondrial genome of the lycophyte Huperzia squarrosa: the most archaic form in vascular plants.

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    Yang Liu

    Full Text Available Mitochondrial genomes have maintained some bacterial features despite their residence within eukaryotic cells for approximately two billion years. One of these features is the frequent presence of polycistronic operons. In land plants, however, it has been shown that all sequenced vascular plant chondromes lack large polycistronic operons while bryophyte chondromes have many of them. In this study, we provide the completely sequenced mitochondrial genome of a lycophyte, from Huperzia squarrosa, which is a member of the sister group to all other vascular plants. The genome, at a size of 413,530 base pairs, contains 66 genes and 32 group II introns. In addition, it has 69 pseudogene fragments for 24 of the 40 protein- and rRNA-coding genes. It represents the most archaic form of mitochondrial genomes of all vascular plants. In particular, it has one large conserved gene cluster containing up to 10 ribosomal protein genes, which likely represents a polycistronic operon but has been disrupted and greatly reduced in the chondromes of other vascular plants. It also has the least rearranged gene order in comparison to the chondromes of other vascular plants. The genome is ancestral in vascular plants in several other aspects: the gene content resembling those of charophytes and most bryophytes, all introns being cis-spliced, a low level of RNA editing, and lack of foreign DNA of chloroplast or nuclear origin.

  13. Characterization of the mitochondrial genome of Diphyllobothrium latum (Cestoda: Pseudophyllidea) - implications for the phylogeny of eucestodes.

    Science.gov (United States)

    Park, J-K; Kim, K-H; Kang, S; Jeon, H K; Kim, J-H; Littlewood, D T J; Eom, K S

    2007-05-01

    The complete nucleotide sequence of the mitochondrial genome was determined for the fish tapeworm Diphyllobothrium latum. This genome is 13,608 bp in length and encodes 12 protein-coding genes (but lacks the atp8), 22 transfer RNA (tRNA) and 2 ribosomal RNA (rRNA) genes, corresponding to the gene complement found thus far in other flatworm mitochondrial (mt) DNAs. The gene arrangement of this pseudophyllidean cestode is the same as the 6 cyclophyllidean cestodes characterized to date, with only minor variation in structure among these other genomes; the relative position of trnS2 and trnL1 is switched in Hymenolepis diminuta. Phylogenetic analyses of the concatenated amino acid sequences for 12 protein-coding genes of all complete cestode mtDNAs confirmed taxonomic and previous phylogenetic assessments, with D. latum being a sister taxon to the cyclophyllideans. High nodal support and phylogenetic congruence between different methods suggest that mt genomes may be of utility in resolving ordinal relationships within the cestodes. All species of Diphyllobothrium infect fish-eating vertebrates, and D. latum commonly infects humans through the ingestion of raw, poorly cooked or pickled fish. The complete mitochondrial genome provides a wealth of genetic markers which could be useful for identifying different life-cycle stages and for investigating their population genetics, ecology and epidemiology.

  14. The complete mitochondrial genome of European wild boar, Sus scrofa scrofa.

    Science.gov (United States)

    Hu, Xiao-Di; Yang, Xiao-Tian; Yang, En

    2016-09-01

    In this study, we report the complete mitochondrial genome sequence of the European wild boar, Sus scrofa scrofa for the first time. The genome is found to be 16,770 bp in length and has a base composition of A (34.63%), G (13.38%), C (26.21%), and T (25.78%), indicating that the percentage of A + T (60.41%) was higher than G + C (39.59%). Similar to other pigs, it contains a typically conserved structure including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region (D-loop). Most of the genes were located on the H-strand except for the ND6 gene and eight tRNA genes. The complete mitochondrial genome sequence provided here would add a new genetic resource and new study on the evolution of the genus Sus.

  15. Complete mitochondrial genome of the Algerian honeybee, Apis mellifera intermissa (Hymenoptera: Apidae).

    Science.gov (United States)

    Hu, Peng; Lu, Zhi-Xiang; Haddad, Nizar; Noureddine, Adjlane; Loucif-Ayad, Wahida; Wang, Yong-Zhi; Zhao, Ren-Bin; Zhang, Ai-Ling; Guan, Xin; Zhang, Hai-Xi; Niu, Hua

    2016-05-01

    In this study, the complete mitochondrial genome sequence of Algerian honeybee, Apis mellifera intermissa, is analyzed for the first time. The results show that this genome is 16,336 bp in length, and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region (D-loop). The overall base composition is A (43.2%), C (9.8%), G (5.6%), and T (41.4%), so the percentage of A and T (84.6%) is considerably higher than that of G and C. All the genes are encoded on H-strand, except for four subunit genes (ND1, ND4, ND4L, and ND5), two rRNA genes (12S and 16S rRNA), and eight tRNA genes. The complete mitochondrial genome sequence reported here would be useful for further phylogenetic analysis and conservation genetic studies in A. m. intermissa.

  16. The first mitochondrial genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997 (Diptera: Sciomyzoidea: Sepsidae), with mitochondrial genome phylogeny of cyclorrhapha.

    Science.gov (United States)

    Li, Xuankun; Ding, Shuangmei; Cameron, Stephen L; Kang, Zehui; Wang, Yuyu; Yang, Ding

    2015-01-01

    Sepsid flies (Diptera: Sepsidae) are important model insects for sexual selection research. In order to develop mitochondrial (mt) genome data for this significant group, we sequenced the first complete mt genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997. The circular 15,878 bp mt genome is typical of Diptera, containing all 37 genes usually present in bilaterian animals. We discovered inaccurate annotations of fly mt genomes previously deposited on GenBank and thus re-annotated all published mt genomes of Cyclorrhapha. These re-annotations were based on comparative analysis of homologous genes, and provide a statistical analysis of start and stop codon positions. We further detected two 18 bp of conserved intergenic sequences from tRNAGlu-tRNAPhe and ND1-tRNASer(UCN) across Cyclorrhapha, which are the mtTERM binding site motifs. Additionally, we compared automated annotation software MITOS with hand annotation method. Phylogenetic trees based on the mt genome data from Cyclorrhapha were inferred by Maximum-likelihood and Bayesian methods, strongly supported a close relationship between Sepsidae and the Tephritoidea.

  17. The first mitochondrial genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997 (Diptera: Sciomyzoidea: Sepsidae, with mitochondrial genome phylogeny of cyclorrhapha.

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    Xuankun Li

    Full Text Available Sepsid flies (Diptera: Sepsidae are important model insects for sexual selection research. In order to develop mitochondrial (mt genome data for this significant group, we sequenced the first complete mt genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997. The circular 15,878 bp mt genome is typical of Diptera, containing all 37 genes usually present in bilaterian animals. We discovered inaccurate annotations of fly mt genomes previously deposited on GenBank and thus re-annotated all published mt genomes of Cyclorrhapha. These re-annotations were based on comparative analysis of homologous genes, and provide a statistical analysis of start and stop codon positions. We further detected two 18 bp of conserved intergenic sequences from tRNAGlu-tRNAPhe and ND1-tRNASer(UCN across Cyclorrhapha, which are the mtTERM binding site motifs. Additionally, we compared automated annotation software MITOS with hand annotation method. Phylogenetic trees based on the mt genome data from Cyclorrhapha were inferred by Maximum-likelihood and Bayesian methods, strongly supported a close relationship between Sepsidae and the Tephritoidea.

  18. The complete mitochondrial genome of a basal teleost, the Asian arowana (Scleropages formosus, Osteoglossidae

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    Yue Gen

    2006-09-01

    Full Text Available Abstract Background Mitochondrial DNA-derived sequences have become popular markers for evolutionary studies, as their comparison may yield significant insights into the evolution of both the organisms and their genomes. From the more than 24,000 teleost species, only 254 complete mtDNA sequences are available (GenBank status on 06 Sep 2006. In this paper, we report the complete mitochondrial genome sequence of Asian arowana, a basal bonytongue fish species, which belongs to the order of Osteoglossiformes. Results The complete mitochondrial genomic sequence (mtDNA of Asian arowana (Scleropages formosus was determined by using shotgun sequencing method. The length of Asian arowana mtDNA is ca. 16,650 bp (its variation is due to polymorphic repeats in the control region, containing 13 protein-coding genes, 22 tRNA and 2 rRNA genes. Twelve of the thirteen protein coding genes were found to be encoded by the heavy strand in the order typically observed for vertebrate mitochondrial genomes, whereas only nad6 was located on the light strand. An interesting feature of Asian arowana mitogenome is that two different repeat arrays were identified in the control region: a 37 bp tandem repeat at the 5' end and an AT-type dinucleotide microsatellite at the 3' end. Both repeats show polymorphism among the six individuals tested; moreover the former one is present in the mitochondrial genomes of several other teleost groups. The TACAT motif described earlier only from mammals and lungfish was found in the tandem repeat of several osteoglossid and eel species. Phylogenetic analysis of fish species representing Actinopterygii and Sarcopterygii taxa has shown that the Asian arowana is located near the baseline of the teleost tree, confirming its status among the ancestral teleost lineages. Conclusion The mitogenome of Asian arowana is very similar to the typical vertebrate mitochondrial genome in terms of gene arrangements, codon usage and base composition

  19. Complete mitochondrial genome of the Chinese spiny lobster Panulirus stimpsoni (Crustacea: Decapoda): genome characterization and phylogenetic considerations.

    Science.gov (United States)

    Liu, Yuan; Cui, Zhaoxia

    2011-01-01

    The genetics and molecular biology of the commercially important Chinese spiny lobster, Panulirus stimpsoni are little known. Here, we present the complete mitochondrial genome sequence of P. stimpsoni, determined by the long polymerase chain reaction and primer walking sequencing method. The entire genome is 15,677 bp in length, encoding the standard set of 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. The overall A+T content of the genome is 65.6%, lower than most malacostracan species. The gene order is consistent with the pancrustacean ground pattern. Several conserved elements were identified from P. stimpsoni control region, viz. one [TA(A)]n-block, two GA-blocks and three hairpin structures. However, the position of [TA(A)]n-block and number of hairpin structure are different from those in the congeneric P. japonicus and other decapods. Phylogenetic analyses using the concatenated nucleotide and amino acid sequences of 13 protein-coding genes do not support the monophyly of suborder Pleocyemata, which is in contrast to most morphological and molecular results. However, the position of Palinura and Astacidea is unstable, as represented by the basal or sister branches to other Reptantia species. P. stimpsoni, as the second species of Palinura with complete mitochondrial genome available, will provide important information on both genomics and conservation biology of the group.

  20. A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes.

    Science.gov (United States)

    Bonnet, Timothée; Leblois, Raphaël; Rousset, François; Crochet, Pierre-André

    2017-09-01

    Hybridization is increasingly recognized as a significant evolutionary process, in particular because it can lead to introgression of genes from one species to another. A striking pattern of discordance in the amount of introgression between mitochondrial and nuclear markers exists such that substantial mitochondrial introgression is often found in combination with no or little nuclear introgression. Multiple mechanisms have been proposed to explain this discordance, including positive selection for introgressing mitochondrial variants, several types of sex-biases, drift, negative selection against introgression in the nuclear genome, and spatial expansion. Most of these hypotheses are verbal, and have not been quantitatively evaluated so far. We use individual-based, multilocus, computer simulations of secondary contact under a wide range of demographic and genetic scenarios to evaluate the ability of the different mechanisms to produce discordant introgression. Sex-biases and spatial expansions fail to produce substantial mito-nuclear discordance. Drift and nuclear selection can produce strong discordance, but only under a limited range of conditions. In contrast, selection on the mitochondrial genome produces strong discordance, particularly when dispersal rates are low. However, commonly used statistical tests have little power to detect this selection. Altogether, these results dismiss several popular hypotheses, and provide support for adaptive mitochondrial introgression. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  1. Complete mitochondrial genomes reveal phylogeny relationship and evolutionary history of the family Felidae.

    Science.gov (United States)

    Zhang, W Q; Zhang, M H

    2013-09-03

    Many mitochondrial DNA sequences are used to estimate phylogenetic relationships among animal taxa and perform molecular phylogenetic evolution analysis. With the continuous development of sequencing technology, numerous mitochondrial sequences have been released in public databases, especially complete mitochondrial DNA sequences. Using multiple sequences is better than using single sequences for phylogenetic analysis of animals because multiple sequences have sufficient information for evolutionary process reconstruction. Therefore, we performed phylogenetic analyses of 14 species of Felidae based on complete mitochondrial genome sequences, with Canis familiaris as an outgroup, using neighbor joining, maximum likelihood, maximum parsimony, and Bayesian inference methods. The consensus phylogenetic trees supported the monophyly of Felidae, and the family could be divided into 2 subfamilies, Felinae and Pantherinae. The genus Panthera and species tigris were also studied in detail. Meanwhile, the divergence of this family was estimated by phylogenetic analysis using the Bayesian method with a relaxed molecular clock, and the results shown were consistent with previous studies. In summary, the evolution of Felidae was reconstructed by phylogenetic analysis based on mitochondrial genome sequences. The described method may be broadly applicable for phylogenetic analyses of anima taxa.

  2. Involvement of plastid, mitochondrial and nuclear genomes in plant-to-plant horizontal gene transfer

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    Maria Virginia Sanchez-Puerta

    2014-12-01

    Full Text Available This review focuses on plant-to-plant horizontal gene transfer (HGT involving the three DNA-containing cellular compartments. It highlights the great incidence of HGT in the mitochondrial genome (mtDNA of angiosperms, the increasing number of examples in plant nuclear genomes, and the lack of any convincing evidence for HGT in the well-studied plastid genome of land plants. Most of the foreign mitochondrial genes are non-functional, generally found as pseudogenes in the recipient plant mtDNA that maintains its functional native genes. The few exceptions involve chimeric HGT, in which foreign and native copies recombine leading to a functional and single copy of the gene. Maintenance of foreign genes in plant mitochondria is probably the result of genetic drift, but a possible evolutionary advantage may be conferred through the generation of genetic diversity by gene conversion between native and foreign copies. Conversely, a few cases of nuclear HGT in plants involve functional transfers of novel genes that resulted in adaptive evolution. Direct cell-to-cell contact between plants (e.g. host-parasite relationships or natural grafting facilitate the exchange of genetic material, in which HGT has been reported for both nuclear and mitochondrial genomes, and in the form of genomic DNA, instead of RNA. A thorough review of the literature indicates that HGT in mitochondrial and nuclear genomes of angiosperms is much more frequent than previously expected and that the evolutionary impact and mechanisms underlying plant-to-plant HGT remain to be uncovered.

  3. A complete mitochondrial genome sequence from a mesolithic wild aurochs (Bos primigenius.

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    Ceiridwen J Edwards

    Full Text Available BACKGROUND: The derivation of domestic cattle from the extinct wild aurochs (Bos primigenius has been well-documented by archaeological and genetic studies. Genetic studies point towards the Neolithic Near East as the centre of origin for Bos taurus, with some lines of evidence suggesting possible, albeit rare, genetic contributions from locally domesticated wild aurochsen across Eurasia. Inferences from these investigations have been based largely on the analysis of partial mitochondrial DNA sequences generated from modern animals, with limited sequence data from ancient aurochsen samples. Recent developments in DNA sequencing technologies, however, are affording new opportunities for the examination of genetic material retrieved from extinct species, providing new insight into their evolutionary history. Here we present DNA sequence analysis of the first complete mitochondrial genome (16,338 base pairs from an archaeologically-verified and exceptionally-well preserved aurochs bone sample. METHODOLOGY: DNA extracts were generated from an aurochs humerus bone sample recovered from a cave site located in Derbyshire, England and radiocarbon-dated to 6,738+/-68 calibrated years before present. These extracts were prepared for both Sanger and next generation DNA sequencing technologies (Illumina Genome Analyzer. In total, 289.9 megabases (22.48% of the post-filtered DNA sequences generated using the Illumina Genome Analyzer from this sample mapped with confidence to the bovine genome. A consensus B. primigenius mitochondrial genome sequence was constructed and was analysed alongside all available complete bovine mitochondrial genome sequences. CONCLUSIONS: For all nucleotide positions where both Sanger and Illumina Genome Analyzer sequencing methods gave high-confidence calls, no discrepancies were observed. Sequence analysis reveals evidence of heteroplasmy in this sample and places this mitochondrial genome sequence securely within a previously

  4. Complete Sequence and Analysis of the Mitochondrial Genome of Hemiselmis andersenii CCMP644 (Cryptophyceae

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    Bowman Sharen

    2008-05-01

    Full Text Available Abstract Background Cryptophytes are an enigmatic group of unicellular eukaryotes with plastids derived by secondary (i.e., eukaryote-eukaryote endosymbiosis. Cryptophytes are unusual in that they possess four genomes–a host cell-derived nuclear and mitochondrial genome and an endosymbiont-derived plastid and 'nucleomorph' genome. The evolutionary origins of the host and endosymbiont components of cryptophyte algae are at present poorly understood. Thus far, a single complete mitochondrial genome sequence has been determined for the cryptophyte Rhodomonas salina. Here, the second complete mitochondrial genome of the cryptophyte alga Hemiselmis andersenii CCMP644 is presented. Results The H. andersenii mtDNA is 60,553 bp in size and encodes 30 structural RNAs and 36 protein-coding genes, all located on the same strand. A prominent feature of the genome is the presence of a ~20 Kbp long intergenic region comprised of numerous tandem and dispersed repeat units of between 22–336 bp. Adjacent to these repeats are 27 copies of palindromic sequences predicted to form stable DNA stem-loop structures. One such stem-loop is located near a GC-rich and GC-poor region and may have a regulatory function in replication or transcription. The H. andersenii mtDNA shares a number of features in common with the genome of the cryptophyte Rhodomonas salina, including general architecture, gene content, and the presence of a large repeat region. However, the H. andersenii mtDNA is devoid of inverted repeats and introns, which are present in R. salina. Comparative analyses of the suite of tRNAs encoded in the two genomes reveal that the H. andersenii mtDNA has lost or converted its original trnK(uuu gene and possesses a trnS-derived 'trnK(uuu', which appears unable to produce a functional tRNA. Mitochondrial protein coding gene phylogenies strongly support a variety of previously established eukaryotic groups, but fail to resolve the relationships among higher

  5. Complete mitochondrial genome sequence from an endangered Indian snake, Python molurus molurus (Serpentes, Pythonidae).

    Science.gov (United States)

    Dubey, Bhawna; Meganathan, P R; Haque, Ikramul

    2012-07-01

    This paper reports the complete mitochondrial genome sequence of an endangered Indian snake, Python molurus molurus (Indian Rock Python). A typical snake mitochondrial (mt) genome of 17258 bp length comprising of 37 genes including the 13 protein coding genes, 22 tRNA genes, and 2 ribosomal RNA genes along with duplicate control regions is described herein. The P. molurus molurus mt. genome is relatively similar to other snake mt. genomes with respect to gene arrangement, composition, tRNA structures and skews of AT/GC bases. The nucleotide composition of the genome shows that there are more A-C % than T-G% on the positive strand as revealed by positive AT and CG skews. Comparison of individual protein coding genes, with other snake genomes suggests that ATP8 and NADH3 genes have high divergence rates. Codon usage analysis reveals a preference of NNC codons over NNG codons in the mt. genome of P. molurus. Also, the synonymous and non-synonymous substitution rates (ka/ks) suggest that most of the protein coding genes are under purifying selection pressure. The phylogenetic analyses involving the concatenated 13 protein coding genes of P. molurus molurus conformed to the previously established snake phylogeny.

  6. The position of the Hymenoptera within the Holometabola as inferred from the mitochondrial genome of Perga condei (Hymenoptera: Symphyta: Pergidae).

    Science.gov (United States)

    Castro, Lyda Raquel; Dowton, Mark

    2005-03-01

    We sequenced most of the mitochondrial genome of the sawfly Perga condei (Insecta: Hymenoptera: Symphyta: Pergidae) and tested different models of phylogenetic reconstruction in order to resolve the position of the Hymenoptera within the Holometabola, using mitochondrial genomes. The mitochondrial genome sequenced for P. condei had less compositional bias and slower rates of molecular evolution than the honeybee, as well as a less rearranged genome organization. Phylogenetic analyses showed that, when using mitochondrial genomes, both adequate taxon sampling and more realistic models of analysis are necessary to resolve relationships among insect orders. Both parsimony and Bayesian analyses performed better when nucleotide instead of amino acid sequences were used. In particular, this study supports the placement of the Hymenoptera as sister group to the Mecopterida.

  7. Complete mitochondrial genome of Porzana fusca and Porzana pusilla and phylogenetic relationship of 16 Rallidae species.

    Science.gov (United States)

    Chen, Peng; Han, Yuqing; Zhu, Chaoying; Gao, Bin; Ruan, Luzhang

    2017-09-23

    The complete mitochondrial genome sequences of Porzana fusca and Porzana pusilla were determined. The two avian species share a high degree of homology in terms of mitochondrial genome organization and gene arrangement. Their corresponding mitochondrial genomes are 16,935 and 16,978 bp and consist of 37 genes and a control region. Their PCGs were both 11,365 bp long and have similar structure. Their tRNA gene sequences could be folded into canonical cloverleaf secondary structure, except for tRNA(Ser (AGY)), which lost its "DHU" arm. Based on the concatenated nucleotide sequences of the complete mitochondrial DNA genes of 16 Rallidae species, reconstruction of phylogenetic trees and analysis of the molecular clock of P. fusca and P. pusilla indicated that these species from a sister group, which in turn are sister group to Rallina eurizonoides. The genus Gallirallus is a sister group to genus Lewinia, and these groups in turn are sister groups to genus Porphyrio. Moreover, molecular clock analyses suggested that the basal divergence of Rallidae could be traced back to 40.47 (41.46‒39.45) million years ago (Mya), and the divergence of Porzana occurred approximately 5.80 (15.16‒0.79) Mya.

  8. Complex evolutionary patterns revealed by mitochondrial genomes of the domestic horse.

    Science.gov (United States)

    Ning, T; Li, J; Lin, K; Xiao, H; Wylie, S; Hua, S; Li, H; Zhang, Y-P

    2014-01-01

    The domestic horse is the most widely used and important stock and recreational animal, valued for its strength and endurance. The energy required by the domestic horse is mainly supplied by mitochondria via oxidative phosphorylation. Thus, selection may have played an essential role in the evolution of the horse mitochondria. Besides, demographic events also affect the DNA polymorphic pattern on mitochondria. To understand the evolutionary patterns of the mitochondria of the domestic horse, we used a deep sequencing approach to obtain the complete sequences of 15 mitochondrial genomes, and four mitochondrial gene sequences, ND6, ATP8, ATP6 and CYTB, collected from 509, 363, 363 and 409 domestic horses, respectively. Evidence of strong substitution rate heterogeneity was found at nonsynonymous sites across the genomes. Signatures of recent positive selection on mtDNA of domestic horse were detected. Specifically, five amino acids in the four mitochondrial genes were identified as the targets of positive selection. Coalescentbased simulations imply that recent population expansion is the most probable explanation for the matrilineal population history for domestic horse. Our findings reveal a complex pattern of non-neutral evolution of the mitochondrial genome in the domestic horses.

  9. Gene arrangement convergence, diverse intron content, and genetic code modifications in mitochondrial genomes of sphaeropleales (chlorophyta).

    Science.gov (United States)

    Fučíková, Karolina; Lewis, Paul O; González-Halphen, Diego; Lewis, Louise A

    2014-08-08

    The majority of our knowledge about mitochondrial genomes of Viridiplantae comes from land plants, but much less is known about their green algal relatives. In the green algal order Sphaeropleales (Chlorophyta), only one representative mitochondrial genome is currently available-that of Acutodesmus obliquus. Our study adds nine completely sequenced and three partially sequenced mitochondrial genomes spanning the phylogenetic diversity of Sphaeropleales. We show not only a size range of 25-53 kb and variation in intron content (0-11) and gene order but also conservation of 13 core respiratory genes and fragmented ribosomal RNA genes. We also report an unusual case of gene arrangement convergence in Neochloris aquatica, where the two rns fragments were secondarily placed in close proximity. Finally, we report the unprecedented usage of UCG as stop codon in Pseudomuriella schumacherensis. In addition, phylogenetic analyses of the mitochondrial protein-coding genes yield a fully resolved, well-supported phylogeny, showing promise for addressing systematic challenges in green algae. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  10. Plant mitochondrial genome peculiarities evolving in the earliest vascular plant lineages

    Institute of Scientific and Technical Information of China (English)

    Volker KNOOP

    2013-01-01

    In plants,the mitochondrial DNA has evolved in peculiar ways.Simple circular mitochondrial genomes found in most other eukaryotic lineages have expanded tremendously in size.Mitochondrial DNAs in some flowering plants may in fact be larger than genomes of free-living bacteria.Introns,retrotransposons,pseudogene fragments,and promiscuous DNA copied from the chloroplast or nuclear genome contribute to the size expansion but most intergenic DNA remains unaccounted for so far.Additionally,frequent recombination results in heterogeneous pools of coexisting,subgenomic mtDNA molecules in angiosperms.In contrast,the mitochondrial DNAs of bryophytes,the extant representatives of very early splits in plant phylogeny,are more conservative in structural evolution and seem to be devoid of active recombination.However,whereas mitochondrial introns are highly conserved among seed plants (spermatophytes),not a single one of more than 80 different introns in bryophyte mtDNAs is conserved among the three divisions,liverworts,mosses,and hornworts.Lycophytes are now unequivocally identified as living representatives of the earliest vascular plant branch in a crucial phylogenetic position between bryophytes and later diversifying tracheophytes including spermatophytes.Very recently,mtDNAs have become available for the three orders of extant lycophytes-Isoetales,Selaginellales,and Lycopodiales.As I will discuss here,the lycophyte mtDNAs not only show a surprising diversity of features but also previously unseen novelties of plant mitochondrial DNA evolution.The transition from a gametophyte-dominated bryophyte lifestyle to a sporophytedominated vascular plant lifestyle apparently gave rise to several peculiar independent changes in plant chondrome evolution.

  11. The mitochondrial genome of the fission yeast Schizosaccharomyces pombe : 5. Characterization of mitochondrial deletion mutants.

    Science.gov (United States)

    Ahne, F; Merlos-Lange, A M; Lang, B F; Wolf, K

    1984-09-01

    The three mutator strains ana (r)-8, ana (r)-14, and diu (r)-301 were shown to produce respiratory deficient mutants at different rates. The frequency of respiratory deficient mutants in a culture could be increased by adding ethidium bromide. According to their cytochrome spectra and enzymatic activities they form three classes, namely mutants defective in cytochrome oxidase, in cytochrome b, and in both cytochromes. By restriction enzyme analysis of mitochondrial DNA from about 100 mutants, 22 deletion mutants were identified. The deletions, ranging from 50 to 1,500 base pairs were physically mapped. Deletions were localized in the genes coding for subunit 1 of cytochrome oxidase with its two introns, within the cytochrome b gene and its intron, and within the genes for subunits 2 and 3 of cytochrome oxidase. In several cases, where the physical mapping yielded ambiguous results, pairwise genetic crosses ruled out an overlap between two neighbouring deletions.Using these mitochondrial deletion mutants as tester strains, it was shown that only tetrad analysis and chemical haploidization, but not mitotic segregation analysis, allows a decision between chromosomal and mitochondrial inheritance of respiratory deficiency in Schizosaccharomyces pombe.

  12. The massive mitochondrial genome of the angiosperm Silene noctiflora is evolving by gain or loss of entire chromosomes.

    Science.gov (United States)

    Wu, Zhiqiang; Cuthbert, Jocelyn M; Taylor, Douglas R; Sloan, Daniel B

    2015-08-18

    Across eukaryotes, mitochondria exhibit staggering diversity in genomic architecture, including the repeated evolution of multichromosomal structures. Unlike in the nucleus, where mitosis and meiosis ensure faithful transmission of chromosomes, the mechanisms of inheritance in fragmented mitochondrial genomes remain mysterious. Multichromosomal mitochondrial genomes have recently been found in multiple species of flowering plants, including Silene noctiflora, which harbors an unusually large and complex mitochondrial genome with more than 50 circular-mapping chromosomes totaling ∼7 Mb in size. To determine the extent to which such genomes are stably maintained, we analyzed intraspecific variation in the mitochondrial genome of S. noctiflora. Complete genomes from two populations revealed a high degree of similarity in the sequence, structure, and relative abundance of mitochondrial chromosomes. For example, there are no inversions between the genomes, and there are only nine SNPs in 25 kb of protein-coding sequence. Remarkably, however, these genomes differ in the presence or absence of 19 entire chromosomes, all of which lack any identifiable genes or contain only duplicate gene copies. Thus, these mitochondrial genomes retain a full gene complement but carry a highly variable set of chromosomes that are filled with presumably dispensable sequence. In S. noctiflora, conventional mechanisms of mitochondrial sequence divergence are being outstripped by an apparently nonadaptive process of whole-chromosome gain/loss, highlighting the inherent challenge in maintaining a fragmented genome. We discuss the implications of these findings in relation to the question of why mitochondria, more so than plastids and bacterial endosymbionts, are prone to the repeated evolution of multichromosomal genomes.

  13. The First Complete Mitochondrial Genome Sequences for Stomatopod Crustaceans: Implications for Phylogeny

    Energy Technology Data Exchange (ETDEWEB)

    Swinstrom, Kirsten; Caldwell, Roy; Fourcade, H. Matthew; Boore, Jeffrey L.

    2005-09-07

    We report the first complete mitochondrial genome sequences of stomatopods and compare their features to each other and to those of other crustaceans. Phylogenetic analyses of the concatenated mitochondrial protein-coding sequences were used to explore relationships within the Stomatopoda, within the malacostracan crustaceans, and among crustaceans and insects. Although these analyses support the monophyly of both Malacostraca and, within it, Stomatopoda, it also confirms the view of a paraphyletic Crustacea, with Malacostraca being more closely related to insects than to the branchiopod crustaceans.

  14. Organization of the mitochondrial genome of mantis shrimp Pseudosquilla ciliata (Crustacea: Stomatopoda).

    Science.gov (United States)

    Podsiadlowski, Lars; Bartolomaeus, Thomas

    2005-01-01

    We determined the nearly complete mitochondrial genome of Pseudosquilla ciliata (Crustacea, Stomatopoda), including all protein-coding genes and all but one of the transfer RNAs. There were no gene rearrangements relative to the pattern shared by crustaceans and hexapods. Phylogenetic analysis using concatenated amino acid sequences of the mitochondrial protein-coding genes confirmed a basal position of Stomatopoda among Eumalacostraca. Pancrustacean relationships based on mitogenomic data were analyzed and are discussed in relation to crustacean and hexapod monophyly and hexapod affinities to crustacean subtaxa.

  15. Whole mitochondrial genome analysis in South Indian patients with Leber's hereditary optic neuropathy.

    Science.gov (United States)

    Saikia, Bibhuti Ballav; Dubey, Sushil Kumar; Shanmugam, Mahesh Kumar; Sundaresan, Periasamy

    2016-10-28

    Leber's hereditary optic neuropathy (LHON) is a mitochondrial DNA (mtDNA) associated neurodegenerative disorder of retinal ganglion cells. In this study, whole mitochondrial genome sequencing of 75 LHON patients and 40 controls was performed to identify the mutation frequency and haplogroup background of South Indian population. Analysis of mtDNA revealed 559 different variants in LHON patients, including 7 pathogenic mutations, 30 private, and 22 other disease associated variants. A significantly higher (p=0.0008) overall variation load per individual was noted among LHON patients versus controls. We reported for the first time, the association of M haplogroup (p=0.028) with LHON in this cohort.

  16. Mitochondrial Genome Deletion for Detection of Prostate Cancer — EDRN Public Portal

    Science.gov (United States)

    The Prostate Core Mitomic Test™ is based upon a 3.4 kb mitochondrial genome deletion (3.4 mtdelta) that was identified through PCR analysis of frozen prostate cancer samples. In cancer research it has been found that deletions in mitochondrial DNA can correlate with cellular changes that indicate development of cancer. This deletion includes the terminal 22 bases of MT-ND4L, all of MT-ND4, 3 tRNAs (histidine, serine 2, and leucine 2), and all except the terminal 24 bases of MT-ND5.

  17. The initial peopling of the Americas: A growing number of founding mitochondrial genomes from Beringia

    OpenAIRE

    Perego, Ugo A.; Angerhofer, Norman; Pala, Maria; Olivieri, Anna; Lancioni, Hovirag; Hooshiar Kashani, Baharak; Carossa, Valeria; Jayne E Ekins; Gomez-Carballa, Alberto; Huber, Gabriela; Zimmermann, Bettina; Corach, Daniel; Babudri, Nora; Panara, Fausto; Myres, Natalie M

    2010-01-01

    Pan-American mitochondrial DNA (mtDNA) haplogroup C1 has been recently subdivided into three branches, two of which (C1b and C1c) are characterized by ages and geographical distributions that are indicative of an early arrival from Beringia with Paleo-Indians. In contrast, the estimated ages of C1d—the third subset of C1—looked too young to fit the above scenario. To define the origin of this enigmatic C1 branch, we completely sequenced 63 C1d mitochondrial genomes from a wide range of geogra...

  18. The complete mitochondrial genome of Coilia nasus (Clupeiformes: Engraulidae) from Ariake Sea.

    Science.gov (United States)

    Zhang, Nan; Song, Na; Gao, Tianxiang

    2016-01-01

    In this study, the complete mitochondrial genome (mitogenome) sequence of Coilia nasus has been determined by long polymerase chain reaction and primer walking methods. The mitogenome is a circular molecule of 16,900 bp in length and contains 37 mitochondrial genes including 13 protein-coding genes, 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA) and a control region as other bony fishes. Within the control region, we identified the termination-associated sequence domain (TAS), the central conserved sequence block domains (CSB-F, CSB-E and CSB-D), and the conserved sequence block domains (CSB-1, CSB-2 and CSB-3).

  19. Complete mitochondrial genome of a brown frog, Rana kunyuensis (Anura: Ranidae).

    Science.gov (United States)

    Li, Jiao; Yin, Wei; Xia, Rong; Lei, Guangchun; Fu, Cuizhang

    2016-01-01

    The first complete mitochondrial genome (mitogenome) of Rana sensu stricto (sensu Frost, 2013) was determined using Rana kunyuensis as a representative species. The mitogenome was 22,255 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and duplicated control regions. The mitogenome of R. kunyuensis showed novel gene order arrangement with a translocation of tRNA(Leu)((CUN)) and ND5 in comparison with published anuran mitogenomes to date. This mitogenome should contribute to understand the evolution of anuran mitochondrial gene order arrangements.

  20. Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species.

    Science.gov (United States)

    Lassiter, Erica S; Russ, Carsten; Nusbaum, Chad; Zeng, Qiandong; Saville, Amanda C; Olarte, Rodrigo A; Carbone, Ignazio; Hu, Chia-Hui; Seguin-Orlando, Andaine; Samaniego, Jose A; Thorne, Jeffrey L; Ristaino, Jean B

    2015-11-01

    Phytophthora infestans is one of the most destructive plant pathogens of potato and tomato globally. The pathogen is closely related to four other Phytophthora species in the 1c clade including P. phaseoli, P. ipomoeae, P. mirabilis and P. andina that are important pathogens of other wild and domesticated hosts. P. andina is an interspecific hybrid between P. infestans and an unknown Phytophthora species. We have sequenced mitochondrial genomes of the sister species of P. infestans and examined the evolutionary relationships within the clade. Phylogenetic analysis indicates that the P. phaseoli mitochondrial lineage is basal within the clade. P. mirabilis and P. ipomoeae are sister lineages and share a common ancestor with the Ic mitochondrial lineage of P. andina. These lineages in turn are sister to the P. infestans and P. andina Ia mitochondrial lineages. The P. andina Ic lineage diverged much earlier than the P. andina Ia mitochondrial lineage and P. infestans. The presence of two mitochondrial lineages in P. andina supports the hybrid nature of this species. The ancestral state of the P. andina Ic lineage in the tree and its occurrence only in the Andean regions of Ecuador, Colombia and Peru suggests that the origin of this species hybrid in nature may occur there.

  1. Lost region in amyloid precursor protein (APP) through TALEN-mediated genome editing alters mitochondrial morphology.

    Science.gov (United States)

    Wang, Yajie; Wu, Fengyi; Pan, Haining; Zheng, Wenzhong; Feng, Chi; Wang, Yunfu; Deng, Zixin; Wang, Lianrong; Luo, Jie; Chen, Shi

    2016-02-29

    Alzheimer's disease (AD) is characterized by amyloid-β (Aβ) deposition in the brain. Aβ plaques are produced through sequential β/γ cleavage of amyloid precursor protein (APP), of which there are three main APP isoforms: APP695, APP751 and APP770. KPI-APPs (APP751 and APP770) are known to be elevated in AD, but the reason remains unclear. Transcription activator-like (TAL) effector nucleases (TALENs) induce mutations with high efficiency at specific genomic loci, and it is thus possible to knock out specific regions using TALENs. In this study, we designed and expressed TALENs specific for the C-terminus of APP in HeLa cells, in which KPI-APPs are predominantly expressed. The KPI-APP mutants lack a 12-aa region that encompasses a 5-aa trans-membrane (TM) region and 7-aa juxta-membrane (JM) region. The mutated KPI-APPs exhibited decreased mitochondrial localization. In addition, mitochondrial morphology was altered, resulting in an increase in spherical mitochondria in the mutant cells through the disruption of the balance between fission and fusion. Mitochondrial dysfunction, including decreased ATP levels, disrupted mitochondrial membrane potential, increased ROS generation and impaired mitochondrial dehydrogenase activity, was also found. These results suggest that specific regions of KPI-APPs are important for mitochondrial localization and function.

  2. Recombinant mitochondrial genome with standard transmission route from Mediterranean mussel Mytilus galloprovincialis.

    Science.gov (United States)

    Śmietanka, Beata; Filipowicz, Monika; Burzyński, Artur

    2016-01-01

    Several bivalve species, including marine mussels Mytilus are atypical in having two gender-specific and highly divergent mtDNA genomes. This peculiar genetic system allows not only the recombination to occur but also facilitates its detection. Previous reports associated the existence of mosaic recombinant haplotypes with the switch of their transmission route. Here we report nearly complete sequence of a mitochondrial genome isolated from a homoplasmic female individual of Mediterranean Mytilus galloprovincialis. The genome has clear phylogenetic affinity with and organization identical to the M. galloprovincialis female haplotypes, in the coding part. However, the genome is very large, approximately 20,600 bp long, exclusively due to a long and complex control region. It contains an array of repeats, some of which are degenerated. A large part of the control region is derived from the paternal genome. This finding shows that not all haplotypes with recombinant control regions must be paternally inherited in Mytilus.

  3. Organization of the mitochondrial genomes of whiteflies, aphids, and psyllids (Hemiptera, Sternorrhyncha)

    Science.gov (United States)

    Thao, MyLo L; Baumann, Linda; Baumann, Paul

    2004-01-01

    Background With some exceptions, mitochondria within the class Insecta have the same gene content, and generally, a similar gene order allowing the proposal of an ancestral gene order. The principal exceptions are several orders within the Hemipteroid assemblage including the order Thysanoptera, a sister group of the order Hemiptera. Within the Hemiptera, there are available a number of completely sequenced mitochondrial genomes that have a gene order similar to that of the proposed ancestor. None, however, are available from the suborder Sternorryncha that includes whiteflies, psyllids and aphids. Results We have determined the complete nucleotide sequence of the mitochondrial genomes of six species of whiteflies, one psyllid and one aphid. Two species of whiteflies, one psyllid and one aphid have mitochondrial genomes with a gene order very similar to that of the proposed insect ancestor. The remaining four species of whiteflies had variations in the gene order. In all cases, there was the excision of a DNA fragment encoding for cytochrome oxidase subunit III(COIII)-tRNAgly-NADH dehydrogenase subunit 3(ND3)-tRNAala-tRNAarg-tRNAasn from the ancestral position between genes for ATP synthase subunit 6 and NADH dehydrogenase subunit 5. Based on the position in which all or part of this fragment was inserted, the mitochondria could be subdivided into four different gene arrangement types. PCR amplification spanning from COIII to genes outside the inserted region and sequence determination of the resulting fragments, indicated that different whitefly species could be placed into one of these arrangement types. A phylogenetic analysis of 19 whitefly species based on genes for mitochondrial cytochrome b, NADH dehydrogenase subunit 1, and 16S ribosomal DNA as well as cospeciating endosymbiont 16S and 23S ribosomal DNA indicated a clustering of species that corresponded to the gene arrangement types. Conclusions In whiteflies, the region of the mitochondrial genome

  4. Organization of the mitochondrial genomes of whiteflies, aphids, and psyllids (Hemiptera, Sternorrhyncha

    Directory of Open Access Journals (Sweden)

    Baumann Paul

    2004-08-01

    Full Text Available Abstract Background With some exceptions, mitochondria within the class Insecta have the same gene content, and generally, a similar gene order allowing the proposal of an ancestral gene order. The principal exceptions are several orders within the Hemipteroid assemblage including the order Thysanoptera, a sister group of the order Hemiptera. Within the Hemiptera, there are available a number of completely sequenced mitochondrial genomes that have a gene order similar to that of the proposed ancestor. None, however, are available from the suborder Sternorryncha that includes whiteflies, psyllids and aphids. Results We have determined the complete nucleotide sequence of the mitochondrial genomes of six species of whiteflies, one psyllid and one aphid. Two species of whiteflies, one psyllid and one aphid have mitochondrial genomes with a gene order very similar to that of the proposed insect ancestor. The remaining four species of whiteflies had variations in the gene order. In all cases, there was the excision of a DNA fragment encoding for cytochrome oxidase subunit III(COIII-tRNAgly-NADH dehydrogenase subunit 3(ND3-tRNAala-tRNAarg-tRNAasn from the ancestral position between genes for ATP synthase subunit 6 and NADH dehydrogenase subunit 5. Based on the position in which all or part of this fragment was inserted, the mitochondria could be subdivided into four different gene arrangement types. PCR amplification spanning from COIII to genes outside the inserted region and sequence determination of the resulting fragments, indicated that different whitefly species could be placed into one of these arrangement types. A phylogenetic analysis of 19 whitefly species based on genes for mitochondrial cytochrome b, NADH dehydrogenase subunit 1, and 16S ribosomal DNA as well as cospeciating endosymbiont 16S and 23S ribosomal DNA indicated a clustering of species that corresponded to the gene arrangement types. Conclusions In whiteflies, the region of the

  5. The complete mitochondrial genome of Thamnaconus hypargyreus (Tetraodontiformes: Monacanthidae).

    Science.gov (United States)

    Li, Yufang; Chen, Guobao; Li, Min; Yu, Jie; Wu, Shuiqing; Xiong, Dan; Li, Yongzhen

    2016-01-01

    Lesser-spotted leatherjacket Thamnaconus hypargyreus (Tetraodontiformes: Monacanthidae) is an economically important fish species in the South China Sea. In this study, we designed 15 pairs of primers for amplification of the mitochondrial fragments of T. hypargyreus by PCR. The complete mitogenome sequence has 16,438 bp, containing the usual 2 rRNA genes, 13 protein-coding genes, 22 tRNA genes, and 1 control region, the gene composition and order of which are similar to most of other vertebrates. Most mitochondrial genes except ND6 and eight tRNA genes are encoded on the heavy strand. The overall base composition of the heavy strand is 27.5% A, 26.0% T, 17.4% G, 29.1% C with a slight AT bias of 53.5%. There are 12 regions of gene overlaps totaling 32 bp and 11 intergenic spacer regions totaling 68 bp. This mitogenome sequence data of T. hypargyreus would provide the fundamental genetic data for further conservation genetic studies for this important fish species.

  6. Major genomic mitochondrial lineages delineate early human expansions

    Directory of Open Access Journals (Sweden)

    Flores Carlos

    2001-08-01

    Full Text Available Abstract Background The phylogeographic distribution of human mitochondrial DNA variations allows a genetic approach to the study of modern Homo sapiens dispersals throughout the world from a female perspective. As a new contribution to this study we have phylogenetically analysed complete mitochondrial DNA(mtDNA sequences from 42 human lineages, representing major clades with known geographic assignation. Results We show the relative relationships among the 42 lineages and present more accurate temporal calibrations than have been previously possible to give new perspectives as how modern humans spread in the Old World. Conclusions The first detectable expansion occurred around 59,000–69,000 years ago from Africa, independently colonizing western Asia and India and, following this southern route, swiftly reaching east Asia. Within Africa, this expansion did not replace but mixed with older lineages detectable today only in Africa. Around 39,000–52,000 years ago, the western Asian branch spread radially, bringing Caucasians to North Africa and Europe, also reaching India, and expanding to north and east Asia. More recent migrations have entangled but not completely erased these primitive footprints of modern human expansions.

  7. Maintenance and expression of the S. cerevisiae mitochondrial genome--from genetics to evolution and systems biology.

    Science.gov (United States)

    Lipinski, Kamil A; Kaniak-Golik, Aneta; Golik, Pawel

    2010-01-01

    As a legacy of their endosymbiotic eubacterial origin, mitochondria possess a residual genome, encoding only a few proteins and dependent on a variety of factors encoded by the nuclear genome for its maintenance and expression. As a facultative anaerobe with well understood genetics and molecular biology, Saccharomyces cerevisiae is the model system of choice for studying nucleo-mitochondrial genetic interactions. Maintenance of the mitochondrial genome is controlled by a set of nuclear-coded factors forming intricately interconnected circuits responsible for replication, recombination, repair and transmission to buds. Expression of the yeast mitochondrial genome is regulated mostly at the post-transcriptional level, and involves many general and gene-specific factors regulating splicing, RNA processing and stability and translation. A very interesting aspect of the yeast mitochondrial system is the relationship between genome maintenance and gene expression. Deletions of genes involved in many different aspects of mitochondrial gene expression, notably translation, result in an irreversible loss of functional mtDNA. The mitochondrial genetic system viewed from the systems biology perspective is therefore very fragile and lacks robustness compared to the remaining systems of the cell. This lack of robustness could be a legacy of the reductive evolution of the mitochondrial genome, but explanations involving selective advantages of increased evolvability have also been postulated. Copyright © 2009 Elsevier B.V. All rights reserved.

  8. Structural and Expressional Variations of the Mitochondrial Genome Conferring the Wild Abortive Type of Cytoplasmic Male Sterility in Rice

    Institute of Scientific and Technical Information of China (English)

    Zhen-Lan Liu; Hong Xu; Jing-Xin Guo; Yao-Guang Liu

    2007-01-01

    The so-called "wild abortive" (WA) type of cytoplasmic male sterility (CMS) derived from a wild rice species Oryza rufipogon has been extensively used for hybrid rice breeding. However, extensive analysis of the structure of the related mitochondrial genome has not been reported, and the CMS-associated gene(s) remain unknown. In this study, we exploited a mitochondrial genome-wide strategy to examine the structural and expressional variations in the mitochondrial genome conferring the CMS. The entire mitochondrial genomes of a CMS-WA line and two normal fertile rice lines were amplified by Long-polymerase chain reaction into tilling fragments of up to 15.2 kb. Restriction and DNA blotting analyses of these fragments revealed that structural variations occurred in several regions in the WA mitochondrial genome, as compared to those of the fertile lines. All of the amplified fragments covering the entire mitochondrial genome were used as RNA blot probes to examine the mitochondrial expression profile among the CMS-WA and fertile lines. As a result, only two mRNAs were found to be differentially expressed between the CMS-WA and the fertile lines, which were detected by a probe containing the nadS and orf153 genes and the other having the ribosomal protein gene rp15, respectively. These mRNAs are proposed to be the candidates for further identification and functional studies of the CMS gene.

  9. The mitochondrial and plastid genomes of Volvox carteri: bloated molecules rich in repetitive DNA

    Directory of Open Access Journals (Sweden)

    Lee Robert W

    2009-03-01

    Full Text Available Abstract Background The magnitude of noncoding DNA in organelle genomes can vary significantly; it is argued that much of this variation is attributable to the dissemination of selfish DNA. The results of a previous study indicate that the mitochondrial DNA (mtDNA of the green alga Volvox carteri abounds with palindromic repeats, which appear to be selfish elements. We became interested in the evolution and distribution of these repeats when, during a cursory exploration of the V. carteri nuclear DNA (nucDNA and plastid DNA (ptDNA sequences, we found palindromic repeats with similar structural features to those of the mtDNA. Upon this discovery, we decided to investigate the diversity and evolutionary implications of these palindromic elements by sequencing and characterizing large portions of mtDNA and ptDNA and then comparing these data to the V. carteri draft nuclear genome sequence. Results We sequenced 30 and 420 kilobases (kb of the mitochondrial and plastid genomes of V. carteri, respectively – resulting in partial assemblies of these genomes. The mitochondrial genome is the most bloated green-algal mtDNA observed to date: ~61% of the sequence is noncoding, most of which is comprised of short palindromic repeats spread throughout the intergenic and intronic regions. The plastid genome is the largest (>420 kb and most expanded (>80% noncoding ptDNA sequence yet discovered, with a myriad of palindromic repeats in the noncoding regions, which have a similar size and secondary structure to those of the mtDNA. We found that 15 kb (~0.01% of the nuclear genome are homologous to the palindromic elements of the mtDNA, and 50 kb (~0.05% are homologous to those of the ptDNA. Conclusion Selfish elements in the form of short palindromic repeats have propagated in the V. carteri mtDNA and ptDNA, resulting in the distension of these genomes. Copies of these same repeats are also found in a small fraction of the nucDNA, but appear to be inert in this

  10. Functional morphology of the Neandertal scapular glenoid fossa.

    Science.gov (United States)

    Macias, Marisa E; Churchill, Steven E

    2015-01-01

    Neandertals and Homo sapiens are known to differ in scapular glenoid fossa morphology. Functional explanations may be appropriate for certain aspects of glenoid fossa morphology; however, other factors--e.g., allometry, evolutionary development--must be addressed before functional morphology is considered. Using three-dimensional geometric morphometrics, shape of the scapular glenoid fossa was compared among Neandertals, early and recent modern humans, chimpanzees, orangutans, Australopithecus afarensis, and Au. sediba. Permutation analysis revealed that side, sex, and lifestyle did not correlate with shape. Of the features we found to differ between groups, anterior glenoid rim morphology and fossa curvature did not correlate with the aforementioned shape variables; thus, a functional explanation is appropriate for these components of glenoid fossa shape. Shared morphology among recent humans and chimpanzees (to the exclusion of Neandertals and orangutans) suggests independent forces contributing to these morphological configurations. Potential explanations include adaptations to habitual behavior and locomotor adaptations in the scapulae of recent humans and chimpanzees; these explanations are supported by clinical and experimental literature. The absence of these morphological features in Neandertals may support the lack of these selective forces on their scapular glenoid fossa morphology.

  11. The Spy VI child : A newly discovered Neandertal infant

    NARCIS (Netherlands)

    Crevecoeur, Isabelle; Bayle, Priscilla; Rougier, Helene; Maureille, Bruno; Higham, Thomas; van der Plicht, Johannes; De Clerck, Nora; Semal, Patrick

    2010-01-01

    Spy cave (Jemeppe-sur-Sambre Belgium) is reputed for the two adult Neandertal individuals discovered in situ in 1886 Recent reassessment of the Spy collections has allowed direct radiocarbon dating of these individuals The sorting of all of the faunal collections has also led to the discovery of the

  12. The vertebral column of the Regourdou 1 Neandertal.

    Science.gov (United States)

    Gómez-Olivencia, Asier; Couture-Veschambre, Christine; Madelaine, Stéphane; Maureille, Bruno

    2013-06-01

    The Regourdou 1 partial skeleton was found in 1957 in level IV of the eponymous site located in Montignac-sur-Vézère (Dordogne, France) and until now it has been only partially published. The ongoing revision of the faunal remains from the site has yielded additional fossils that pertain to this skeleton. Here we study the vertebral column of this individual, providing for the first time detailed descriptions for all of the fossils and reassessing the anatomical position of all of the fragments. The vertebral column of Regourdou 1 is one of the most complete in the Neandertal fossil record with at least 20 pre-sacral vertebrae (seven cervicals, nine thoracic and four lumbars), a partial sacrum and a fragmentary first coccygeal vertebra. When compared with modern humans, the vertebrae of Regourdou 1 display significant metric differences, and fit well within the range of Neandertal variability. A preliminary analysis of the most complete thoracic vertebrae of this individual indicates that Neandertals displayed significant differences from modern humans in the thoracic spine, which adds to the differences already observed in the cervical and lumbar regions. Finally, we have also observed mild signs of osteoarthrosis, albeit to a lower degree of that present in other Neandertals such as La Chapelle-aux-Saints, La Ferrassie 1 or Shanidar 3. This is consistent with the younger adult age for Regourdou 1.

  13. Localized Retroprocessing as a Model of Intron Loss in the Plant Mitochondrial Genome.

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    Cuenca, Argelia; Ross, T Gregory; Graham, Sean W; Barrett, Craig F; Davis, Jerrold I; Seberg, Ole; Petersen, Gitte

    2016-08-03

    Loss of introns in plant mitochondrial genes is commonly explained by retroprocessing. Under this model, an mRNA is reverse transcribed and integrated back into the genome, simultaneously affecting the contents of introns and edited sites. To evaluate the extent to which retroprocessing explains intron loss, we analyzed patterns of intron content and predicted RNA editing for whole mitochondrial genomes of 30 species in the monocot order Alismatales. In this group, we found an unusually high degree of variation in the intron content, even expanding the hitherto known variation among angiosperms. Some species have lost some two-third of the cis-spliced introns. We found a strong correlation between intron content and editing frequency, and detected 27 events in which intron loss is consistent with the presence of nucleotides in an edited state, supporting retroprocessing. However, we also detected seven cases of intron loss not readily being explained by retroprocession. Our analyses are also not consistent with the entire length of a fully processed cDNA copy being integrated into the genome, but instead indicate that retroprocessing usually occurs for only part of the gene. In some cases, several rounds of retroprocessing may explain intron loss in genes completely devoid of introns. A number of taxa retroprocessing seem to be very common and a possibly ongoing process. It affects the entire mitochondrial genome.

  14. Comparative analysis of mitochondrial genomes of five aphid species (Hemiptera: Aphididae and phylogenetic implications.

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    Yuan Wang

    Full Text Available Insect mitochondrial genomes (mitogenomes are of great interest in exploring molecular evolution, phylogenetics and population genetics. Only two mitogenomes have been previously released in the insect group Aphididae, which consists of about 5,000 known species including some agricultural, forestry and horticultural pests. Here we report the complete 16,317 bp mitogenome of Cavariella salicicola and two nearly complete mitogenomes of Aphis glycines and Pterocomma pilosum. We also present a first comparative analysis of mitochondrial genomes of aphids. Results showed that aphid mitogenomes share conserved genomic organization, nucleotide and amino acid composition, and codon usage features. All 37 genes usually present in animal mitogenomes were sequenced and annotated. The analysis of gene evolutionary rate revealed the lowest and highest rates for COI and ATP8, respectively. A unique repeat region exclusively in aphid mitogenomes, which included variable numbers of tandem repeats in a lineage-specific manner, was highlighted for the first time. This region may have a function as another origin of replication. Phylogenetic reconstructions based on protein-coding genes and the stem-loop structures of control regions confirmed a sister relationship between Cavariella and pterocommatines. Current evidence suggest that pterocommatines could be formally transferred into Macrosiphini. Our paper also offers methodological instructions for obtaining other Aphididae mitochondrial genomes.

  15. The initial peopling of the Americas: a growing number of founding mitochondrial genomes from Beringia.

    Science.gov (United States)

    Perego, Ugo A; Angerhofer, Norman; Pala, Maria; Olivieri, Anna; Lancioni, Hovirag; Hooshiar Kashani, Baharak; Carossa, Valeria; Ekins, Jayne E; Gómez-Carballa, Alberto; Huber, Gabriela; Zimmermann, Bettina; Corach, Daniel; Babudri, Nora; Panara, Fausto; Myres, Natalie M; Parson, Walther; Semino, Ornella; Salas, Antonio; Woodward, Scott R; Achilli, Alessandro; Torroni, Antonio

    2010-09-01

    Pan-American mitochondrial DNA (mtDNA) haplogroup C1 has been recently subdivided into three branches, two of which (C1b and C1c) are characterized by ages and geographical distributions that are indicative of an early arrival from Beringia with Paleo-Indians. In contrast, the estimated ages of C1d--the third subset of C1--looked too young to fit the above scenario. To define the origin of this enigmatic C1 branch, we completely sequenced 63 C1d mitochondrial genomes from a wide range of geographically diverse, mixed, and indigenous American populations. The revised phylogeny not only brings the age of C1d within the range of that of its two sister clades, but reveals that there were two C1d founder genomes for Paleo-Indians. Thus, the recognized maternal founding lineages of Native Americans are at least 15, indicating that the overall number of Beringian or Asian founder mitochondrial genomes will probably increase extensively when all Native American haplogroups reach the same level of phylogenetic and genomic resolution as obtained here for C1d.

  16. The initial peopling of the Americas: A growing number of founding mitochondrial genomes from Beringia

    Science.gov (United States)

    Perego, Ugo A.; Angerhofer, Norman; Pala, Maria; Olivieri, Anna; Lancioni, Hovirag; Kashani, Baharak Hooshiar; Carossa, Valeria; Ekins, Jayne E.; Gómez-Carballa, Alberto; Huber, Gabriela; Zimmermann, Bettina; Corach, Daniel; Babudri, Nora; Panara, Fausto; Myres, Natalie M.; Parson, Walther; Semino, Ornella; Salas, Antonio; Woodward, Scott R.; Achilli, Alessandro; Torroni, Antonio

    2010-01-01

    Pan-American mitochondrial DNA (mtDNA) haplogroup C1 has been recently subdivided into three branches, two of which (C1b and C1c) are characterized by ages and geographical distributions that are indicative of an early arrival from Beringia with Paleo-Indians. In contrast, the estimated ages of C1d—the third subset of C1—looked too young to fit the above scenario. To define the origin of this enigmatic C1 branch, we completely sequenced 63 C1d mitochondrial genomes from a wide range of geographically diverse, mixed, and indigenous American populations. The revised phylogeny not only brings the age of C1d within the range of that of its two sister clades, but reveals that there were two C1d founder genomes for Paleo-Indians. Thus, the recognized maternal founding lineages of Native Americans are at least 15, indicating that the overall number of Beringian or Asian founder mitochondrial genomes will probably increase extensively when all Native American haplogroups reach the same level of phylogenetic and genomic resolution as obtained here for C1d. PMID:20587512

  17. Complete Sequence and Analysis of Coconut Palm (Cocos nucifera) Mitochondrial Genome.

    Science.gov (United States)

    Aljohi, Hasan Awad; Liu, Wanfei; Lin, Qiang; Zhao, Yuhui; Zeng, Jingyao; Alamer, Ali; Alanazi, Ibrahim O; Alawad, Abdullah O; Al-Sadi, Abdullah M; Hu, Songnian; Yu, Jun

    2016-01-01

    Coconut (Cocos nucifera L.), a member of the palm family (Arecaceae), is one of the most economically important crops in tropics, serving as an important source of food, drink, fuel, medicine, and construction material. Here we report an assembly of the coconut (C. nucifera, Oman local Tall cultivar) mitochondrial (mt) genome based on next-generation sequencing data. This genome, 678,653bp in length and 45.5% in GC content, encodes 72 proteins, 9 pseudogenes, 23 tRNAs, and 3 ribosomal RNAs. Within the assembly, we find that the chloroplast (cp) derived regions account for 5.07% of the total assembly length, including 13 proteins, 2 pseudogenes, and 11 tRNAs. The mt genome has a relatively large fraction of repeat content (17.26%), including both forward (tandem) and inverted (palindromic) repeats. Sequence variation analysis shows that the Ti/Tv ratio of the mt genome is lower as compared to that of the nuclear genome and neutral expectation. By combining public RNA-Seq data for coconut, we identify 734 RNA editing sites supported by at least two datasets. In summary, our data provides the second complete mt genome sequence in the family Arecaceae, essential for further investigations on mitochondrial biology of seed plants.

  18. A complete sequence and transcriptomic analyses of date palm (Phoenix dactylifera L. mitochondrial genome.

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    Yongjun Fang

    Full Text Available Based on next-generation sequencing data, we assembled the mitochondrial (mt genome of date palm (Phoenix dactylifera L. into a circular molecule of 715,001 bp in length. The mt genome of P. dactylifera encodes 38 proteins, 30 tRNAs, and 3 ribosomal RNAs, which constitute a gene content of 6.5% (46,770 bp over the full length. The rest, 93.5% of the genome sequence, is comprised of cp (chloroplast-derived (10.3% with respect to the whole genome length and non-coding sequences. In the non-coding regions, there are 0.33% tandem and 2.3% long repeats. Our transcriptomic data from eight tissues (root, seed, bud, fruit, green leaf, yellow leaf, female flower, and male flower showed higher gene expression levels in male flower, root, bud, and female flower, as compared to four other tissues. We identified 120 potential SNPs among three date palm cultivars (Khalas, Fahal, and Sukry, and successfully found seven SNPs in the coding sequences. A phylogenetic analysis, based on 22 conserved genes of 15 representative plant mitochondria, showed that P. dactylifera positions at the root of all sequenced monocot mt genomes. In addition, consistent with previous discoveries, there are three co-transcribed gene clusters-18S-5S rRNA, rps3-rpl16 and nad3-rps12-in P. dactylifera, which are highly conserved among all known mitochondrial genomes of angiosperms.

  19. Complete Sequence and Analysis of Coconut Palm (Cocos nucifera) Mitochondrial Genome

    Science.gov (United States)

    Zhao, Yuhui; Zeng, Jingyao; Alamer, Ali; Alanazi, Ibrahim O.; Alawad, Abdullah O.; Al-Sadi, Abdullah M.; Hu, Songnian; Yu, Jun

    2016-01-01

    Coconut (Cocos nucifera L.), a member of the palm family (Arecaceae), is one of the most economically important crops in tropics, serving as an important source of food, drink, fuel, medicine, and construction material. Here we report an assembly of the coconut (C. nucifera, Oman local Tall cultivar) mitochondrial (mt) genome based on next-generation sequencing data. This genome, 678,653bp in length and 45.5% in GC content, encodes 72 proteins, 9 pseudogenes, 23 tRNAs, and 3 ribosomal RNAs. Within the assembly, we find that the chloroplast (cp) derived regions account for 5.07% of the total assembly length, including 13 proteins, 2 pseudogenes, and 11 tRNAs. The mt genome has a relatively large fraction of repeat content (17.26%), including both forward (tandem) and inverted (palindromic) repeats. Sequence variation analysis shows that the Ti/Tv ratio of the mt genome is lower as compared to that of the nuclear genome and neutral expectation. By combining public RNA-Seq data for coconut, we identify 734 RNA editing sites supported by at least two datasets. In summary, our data provides the second complete mt genome sequence in the family Arecaceae, essential for further investigations on mitochondrial biology of seed plants. PMID:27736909

  20. Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae).

    Science.gov (United States)

    Alverson, Andrew J; Wei, XiaoXin; Rice, Danny W; Stern, David B; Barry, Kerrie; Palmer, Jeffrey D

    2010-06-01

    The mitochondrial genomes of seed plants are unusually large and vary in size by at least an order of magnitude. Much of this variation occurs within a single family, the Cucurbitaceae, whose genomes range from an estimated 390 to 2,900 kb in size. We sequenced the mitochondrial genomes of Citrullus lanatus (watermelon: 379,236 nt) and Cucurbita pepo (zucchini: 982,833 nt)--the two smallest characterized cucurbit mitochondrial genomes--and determined their RNA editing content. The relatively compact Citrullus mitochondrial genome actually contains more and longer genes and introns, longer segmental duplications, and more discernibly nuclear-derived DNA. The large size of the Cucurbita mitochondrial genome reflects the accumulation of unprecedented amounts of both chloroplast sequences (>113 kb) and short repeated sequences (>370 kb). A low mutation rate has been hypothesized to underlie increases in both genome size and RNA editing frequency in plant mitochondria. However, despite its much larger genome, Cucurbita has a significantly higher synonymous substitution rate (and presumably mutation rate) than Citrullus but comparable levels of RNA editing. The evolution of mutation rate, genome size, and RNA editing are apparently decoupled in Cucurbitaceae, reflecting either simple stochastic variation or governance by different factors.

  1. [The application of mitochondrial genomics to forensic investigations based on human mitochondrial DNA testing].

    Science.gov (United States)

    Skonieczna, Katarzyna; Bednarek, Jarosław; Rogalla, Urszula; Woźniak, Marcin; Gorzkiewicz, Marta; Linkowska, Katarzyna; Duleba, Anna; Sliwka, Karol; Grzybowski, Tomasz

    2012-01-01

    In this study we present two forensic cases where mitochondrial DNA HVS I and HVS II haplotypes of evidentiary hairs match reference samples. Based on the information retrieved from mtDNA coding region of reference material, we selected single nucleotide polymorphisms (SNPs) located outside the HVS I and HVS II regions that could increase the informativeness of mtDNA analysis. The SNPs were typed via SNaPshot or dideoxy sequencing technology. In both cases the SNP results allowed for unambiguous exlusion of the evidence and for determining that reference samples originated from the same person.

  2. Complete mitochondrial genome of the jellyfish, Chrysaora quinquecirrha (Cnidaria, Scyphozoa).

    Science.gov (United States)

    Hwang, Dae-Sik; Park, Eunji; Won, Yong-Jin; Lee, Woo-Jin; Shin, Kyoungsoon; Lee, Jae-Seong

    2014-02-01

    We sequenced 16,775 bp of the linear mitochondrial DNA of the jellyfish Chrysaora quinquecirrha and characterized them. C. quinquecirrha has 13 protein-coding genes (PCGs), 16S rRNA and 12S rRNA with 3 tRNAs (tRNA-Leu, tRNA-Ser(TGA), tRNA-Met) as shown in Aurelia sp. nov. Both have another two PCGs such as helicase and orf363 with telomeres at both ends. The PCGs of C. quinquecirrha shows anti-G bias on 2nd and 3rd positions of PCGs as well as anti-C bias on 1st and 3rd positions of PCGs.

  3. The complete mitochondrial genome of Corydoras nattereri (Callichthyidae: Corydoradinae

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    Daniel A. Moreira

    Full Text Available ABSTRACT The complete mitogenome of Corydoras nattereri , a species of mailed catfishes from southeastern Brazil, was reconstructed using next-generation sequencing techniques. The mitogenome was assembled using mitochondrial transcripts from the liver transcriptomes of three individuals, and produced a circular DNA sequence of 16,557 nucleotides encoding 22 tRNA genes, two rRNA genes, 13 protein-coding genes and two noncoding control regions (D-loop, OrigL. Phylogeographic analysis of closely related sequences of Cytochrome Oxydase C subunit I (COI demonstrates high diversity among morphologically similar populations of C. nattereri . Corydoras nattereri is nested within a complex of populations currently assigned to C. paleatus and C. ehrhardti . Analysis of mitogenome structure demonstrated that an insertion of 21 nucleotides between the ATPase subunit-6 and COIII genes may represent a phylogenetically informative character associated with the evolution of the Corydoradinae.

  4. MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease.

    Science.gov (United States)

    Shen, Lishuang; Diroma, Maria Angela; Gonzalez, Michael; Navarro-Gomez, Daniel; Leipzig, Jeremy; Lott, Marie T; van Oven, Mannis; Wallace, Douglas C; Muraresku, Colleen Clarke; Zolkipli-Cunningham, Zarazuela; Chinnery, Patrick F; Attimonelli, Marcella; Zuchner, Stephan; Falk, Marni J; Gai, Xiaowu

    2016-06-01

    MSeqDR is the Mitochondrial Disease Sequence Data Resource, a centralized and comprehensive genome and phenome bioinformatics resource built by the mitochondrial disease community to facilitate clinical diagnosis and research investigations of individual patient phenotypes, genomes, genes, and variants. A central Web portal (https://mseqdr.org) integrates community knowledge from expert-curated databases with genomic and phenotype data shared by clinicians and researchers. MSeqDR also functions as a centralized application server for Web-based tools to analyze data across both mitochondrial and nuclear DNA, including investigator-driven whole exome or genome dataset analyses through MSeqDR-Genesis. MSeqDR-GBrowse genome browser supports interactive genomic data exploration and visualization with custom tracks relevant to mtDNA variation and mitochondrial disease. MSeqDR-LSDB is a locus-specific database that currently manages 178 mitochondrial diseases, 1,363 genes associated with mitochondrial biology or disease, and 3,711 pathogenic variants in those genes. MSeqDR Disease Portal allows hierarchical tree-style disease exploration to evaluate their unique descriptions, phenotypes, and causative variants. Automated genomic data submission tools are provided that capture ClinVar compliant variant annotations. PhenoTips will be used for phenotypic data submission on deidentified patients using human phenotype ontology terminology. The development of a dynamic informed patient consent process to guide data access is underway to realize the full potential of these resources.

  5. Complete mitochondrial genomes reveal neolithic expansion into Europe.

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    Qiaomei Fu

    Full Text Available The Neolithic transition from hunting and gathering to farming and cattle breeding marks one of the most drastic cultural changes in European prehistory. Short stretches of ancient mitochondrial DNA (mtDNA from skeletons of pre-Neolithic hunter-gatherers as well as early Neolithic farmers support the demic diffusion model where a migration of early farmers from the Near East and a replacement of pre-Neolithic hunter-gatherers are largely responsible for cultural innovation and changes in subsistence strategies during the Neolithic revolution in Europe. In order to test if a signal of population expansion is still present in modern European mitochondrial DNA, we analyzed a comprehensive dataset of 1,151 complete mtDNAs from present-day Europeans. Relying upon ancient DNA data from previous investigations, we identified mtDNA haplogroups that are typical for early farmers and hunter-gatherers, namely H and U respectively. Bayesian skyline coalescence estimates were then used on subsets of complete mtDNAs from modern populations to look for signals of past population expansions. Our analyses revealed a population expansion between 15,000 and 10,000 years before present (YBP in mtDNAs typical for hunters and gatherers, with a decline between 10,000 and 5,000 YBP. These corresponded to an analogous population increase approximately 9,000 YBP for mtDNAs typical of early farmers. The observed changes over time suggest that the spread of agriculture in Europe involved the expansion of farming populations into Europe followed by the eventual assimilation of resident hunter-gatherers. Our data show that contemporary mtDNA datasets can be used to study ancient population history if only limited ancient genetic data is available.

  6. The Complete Mitochondrial Genome of Aleurocanthus camelliae: Insights into Gene Arrangement and Genome Organization within the Family Aleyrodidae.

    Science.gov (United States)

    Chen, Shi-Chun; Wang, Xiao-Qing; Li, Pin-Wu; Hu, Xiang; Wang, Jin-Jun; Peng, Ping

    2016-11-07

    There are numerous gene rearrangements and transfer RNA gene absences existing in mitochondrial (mt) genomes of Aleyrodidae species. To understand how mt genomes evolved in the family Aleyrodidae, we have sequenced the complete mt genome of Aleurocanthus camelliae and comparatively analyzed all reported whitefly mt genomes. The mt genome of A. camelliae is 15,188 bp long, and consists of 13 protein-coding genes, two rRNA genes, 21 tRNA genes and a putative control region (GenBank: KU761949). The tRNA gene, trnI, has not been observed in this genome. The mt genome has a unique gene order and shares most gene boundaries with Tetraleurodes acaciae. Nineteen of 21 tRNA genes have the conventional cloverleaf shaped secondary structure and two (trnS₁ and trnS₂) lack the dihydrouridine (DHU) arm. Using ARWEN and homologous sequence alignment, we have identified five tRNA genes and revised the annotation for three whitefly mt genomes. This result suggests that most absent genes exist in the genomes and have not been identified, due to be lack of technology and inference sequence. The phylogenetic relationships among 11 whiteflies and Drosophila melanogaster were inferred by maximum likelihood and Bayesian inference methods. Aleurocanthus camelliae and T. acaciae form a sister group, and all three Bemisia tabaci and two Bemisia afer strains gather together. These results are identical to the relationships inferred from gene order. We inferred that gene rearrangement plays an important role in the mt genome evolved from whiteflies.

  7. Seventeen new complete mtDNA sequences reveal extensive mitochondrial genome evolution within the Demospongiae.

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    Xiujuan Wang

    Full Text Available Two major transitions in animal evolution--the origins of multicellularity and bilaterality--correlate with major changes in mitochondrial DNA (mtDNA organization. Demosponges, the largest class in the phylum Porifera, underwent only the first of these transitions and their mitochondrial genomes display a peculiar combination of ancestral and animal-specific features. To get an insight into the evolution of mitochondrial genomes within the Demospongiae, we determined 17 new mtDNA sequences from this group and analyzing them with five previously published sequences. Our analysis revealed that all demosponge mtDNAs are 16- to 25-kbp circular molecules, containing 13-15 protein genes, 2 rRNA genes, and 2-27 tRNA genes. All but four pairs of sampled genomes had unique gene orders, with the number of shared gene boundaries ranging from 1 to 41. Although most demosponge species displayed low rates of mitochondrial sequence evolution, a significant acceleration in evolutionary rates occurred in the G1 group (orders Dendroceratida, Dictyoceratida, and Verticillitida. Large variation in mtDNA organization was also observed within the G0 group (order Homosclerophorida including gene rearrangements, loss of tRNA genes, and the presence of two introns in Plakortis angulospiculatus. While introns are rare in modern-day demosponge mtDNA, we inferred that at least one intron was present in cox1 of the common ancestor of all demosponges. Our study uncovered an extensive mitochondrial genomic diversity within the Demospongiae. Although all sampled mitochondrial genomes retained some ancestral features, including a minimally modified genetic code, conserved structures of tRNA genes, and presence of multiple non-coding regions, they vary considerably in their size, gene content, gene order, and the rates of sequence evolution. Some of the changes in demosponge mtDNA, such as the loss of tRNA genes and the appearance of hairpin-containing repetitive elements

  8. Seventeen New Complete mtDNA Sequences Reveal Extensive Mitochondrial Genome Evolution within the Demospongiae

    Science.gov (United States)

    Wang, Xiujuan; Lavrov, Dennis V.

    2008-01-01

    Two major transitions in animal evolution–the origins of multicellularity and bilaterality–correlate with major changes in mitochondrial DNA (mtDNA) organization. Demosponges, the largest class in the phylum Porifera, underwent only the first of these transitions and their mitochondrial genomes display a peculiar combination of ancestral and animal-specific features. To get an insight into the evolution of mitochondrial genomes within the Demospongiae, we determined 17 new mtDNA sequences from this group and analyzing them with five previously published sequences. Our analysis revealed that all demosponge mtDNAs are 16- to 25-kbp circular molecules, containing 13–15 protein genes, 2 rRNA genes, and 2–27 tRNA genes. All but four pairs of sampled genomes had unique gene orders, with the number of shared gene boundaries ranging from 1 to 41. Although most demosponge species displayed low rates of mitochondrial sequence evolution, a significant acceleration in evolutionary rates occurred in the G1 group (orders Dendroceratida, Dictyoceratida, and Verticillitida). Large variation in mtDNA organization was also observed within the G0 group (order Homosclerophorida) including gene rearrangements, loss of tRNA genes, and the presence of two introns in Plakortis angulospiculatus. While introns are rare in modern-day demosponge mtDNA, we inferred that at least one intron was present in cox1 of the common ancestor of all demosponges. Our study uncovered an extensive mitochondrial genomic diversity within the Demospongiae. Although all sampled mitochondrial genomes retained some ancestral features, including a minimally modified genetic code, conserved structures of tRNA genes, and presence of multiple non-coding regions, they vary considerably in their size, gene content, gene order, and the rates of sequence evolution. Some of the changes in demosponge mtDNA, such as the loss of tRNA genes and the appearance of hairpin-containing repetitive elements, occurred in

  9. The complete mitochondrial genome of the house dust mite Dermatophagoides pteronyssinus (Trouessart: a novel gene arrangement among arthropods

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    Vanholme Bartel

    2009-03-01

    Full Text Available Abstract Background The apparent scarcity of available sequence data has greatly impeded evolutionary studies in Acari (mites and ticks. This subclass encompasses over 48,000 species and forms the largest group within the Arachnida. Although mitochondrial genomes are widely utilised for phylogenetic and population genetic studies, only 20 mitochondrial genomes of Acari have been determined, of which only one belongs to the diverse order of the Sarcoptiformes. In this study, we describe the mitochondrial genome of the European house dust mite Dermatophagoides pteronyssinus, the most important member of this largely neglected group. Results The mitochondrial genome of D. pteronyssinus is a circular DNA molecule of 14,203 bp. It contains the complete set of 37 genes (13 protein coding genes, 2 rRNA genes and 22 tRNA genes, usually present in metazoan mitochondrial genomes. The mitochondrial gene order differs considerably from that of other Acari mitochondrial genomes. Compared to the mitochondrial genome of Limulus polyphemus, considered as the ancestral arthropod pattern, only 11 of the 38 gene boundaries are conserved. The majority strand has a 72.6% AT-content but a GC-skew of 0.194. This skew is the reverse of that normally observed for typical animal mitochondrial genomes. A microsatellite was detected in a large non-coding region (286 bp, which probably functions as the control region. Almost all tRNA genes lack a T-arm, provoking the formation of canonical cloverleaf tRNA-structures, and both rRNA genes are considerably reduced in size. Finally, the genomic sequence was used to perform a phylogenetic study. Both maximum likelihood and Bayesian inference analysis clustered D. pteronyssinus with Steganacarus magnus, forming a sistergroup of the Trombidiformes. Conclusion Although the mitochondrial genome of D. pteronyssinus shares different features with previously characterised Acari mitochondrial genomes, it is unique in many ways. Gene

  10. The assembly and annotation of the complete Rufous-bellied thrush mitochondrial genome.

    Science.gov (United States)

    Gomes de Sá, Pablo; Veras, Adonney; Fontana, Carla Suertegaray; Aleixo, Alexandre; Burlamaqui, Tibério; Mello, Claudio Vianna; de Vasconcelos, Ana Tereza Ribeiro; Prosdocimi, Francisco; Ramos, Rommel; Schneider, Maria; Silva, Artur

    2017-03-01

    Among known bird species, oscines are one of the few groups that produce complex vocalizations due to vocal learning. One of the most conspicuous oscine passerines in southeastern South America is the Rufous-bellied Thrush, Turdus rufiventris. The complete mitochondrial genome of this species was sequenced with the Illumina HiSeq platform (Illumina Inc., San Diego, CA), assembled using MITObim software and annotated by MITOS web server and Artemis software. This mitogenome contained 16 669 bases, organized as 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and a control region (d-loop). The sequencing of the Rufous-bellied Thrush mitochondrial genome is of particular interest for better understanding of population genetics and phylogeography of the Turdidae family.

  11. Complete mitochondrial genome of the Eurasian siskin, Spinus spinus (Passeriformes: Fringillidae).

    Science.gov (United States)

    Kan, Xianzhao; Ren, Qiongqiong; Wang, Ping; Jiang, Lan; Zhang, Liqin; Wang, Ying; Zhang, Qin

    2016-05-01

    The Eurasian siskin (Spinus spinus), also called the European siskin, common siskin or just siskin, is found throughout Europe and Asia. In this study, the complete mitochondrial genome of S. spinus was determined to be 16,828 bp. The size of protein-coding genes (PCGs) in the S. spinus mitochondrial genome was 11,400 bp. The longest PCG of S. spinus mtDNA was nad5 (1818 bp), whereas the shortest is atp8 (168 bp). The nad6 gene of S. spinus mitogenome had strong skews of T versus A (-0.54), and G versus C (0.64). According to the distribution of the conserved motifs in other avian CRs, the CR of S. spinus can be divided into three domains: ETAS domain I, central conserved domain II, and CSB domain III.

  12. Complete mitochondrial genome of the Antarctic amphipod Gondogeneia antarctica (Crustacea, amphipod).

    Science.gov (United States)

    Shin, Seung Chul; Cho, Jin; Lee, Jong Kyu; Ahn, Do Hwan; Lee, Hyoungseok; Park, Hyun

    2012-02-01

    The complete sequence of the mitochondrial genome of the Antarctic amphipod Gondogeneia antarctica was determined to be 18,424 bp in length, and to contain 13 protein-coding genes (PCGs), 22 tRNA genes, and large (rrnL) and small (rrnS) rRNA genes. Its total A+T content is 70.1%. The G. antarctica mitogenome is the largest known among those of crustaceans, due to the existence of two relatively large intergenic non-coding sequences. The PCG arrangement of G. antarctica is identical to that of the ancestral pancrustacean ground pattern, although the tRNA arrangement differs somewhat. The complete mitogenome sequences of 68 species of pancrustacea have been added to the NCBI database, only 4 of which represent complete mitogenome sequences from amphipods. This is the first report of a mitogenome sequence of an Antarctic amphipod, and provides insights into the evolution of crustacean mitochondrial genomes, particularly in amphipods.

  13. The mitochondrial genome sequence of the scorpion Centruroides limpidus (Karsch 1879) (Chelicerata; Arachnida).

    Science.gov (United States)

    Dávila, Sonia; Piñero, Daniel; Bustos, Patricia; Cevallos, Miguel A; Dávila, Guillermo

    2005-11-07

    The mitochondrial genome of the scorpion Centruroides limpidus (Chelicerata; Arachnida) has been completely sequenced and is 14519 bp long. The genome contains 13 protein-encoding genes, two ribosomal RNA genes, 21 transfer RNA genes and a large non-coding region related to the control region. The overall A+T composition is the lowest among the complete mitochondrial sequences published within the Chelicerata subphylum. Gene order and gene content differ slightly from that of Limulus polyphemus (Chelicerata: Xiphosura): i.e., the lack of the trnD gene, and the translocation-inversion of the trnI gene. Preliminary phylogenetic analysis of some Chelicerata shows that scorpions (C. limpidus and Mesobuthus gibbosus) make a tight cluster with the spiders (Arachnida; Araneae). Our analysis does not support that Scorpiones order is the sister group to all Arachnida Class, since it is closer to Araneae than to Acari orders.

  14. Illumina based whole mitochondrial genome of Junonia iphita reveals minor intraspecific variation

    Directory of Open Access Journals (Sweden)

    Catherine Vanlalruati

    2015-12-01

    Full Text Available In the present study, the near complete mitochondrial genome (mitogenome of Junonia iphita (Lepidoptera: Nymphalidae: Nymphalinae was determined to be 14,892 bp. The gene order and orientation are identical to those in other butterfly species. The phylogenetic tree constructed from the whole mitogenomes using the 13 protein coding genes (PCGs defines the genetic relatedness of the two J. iphita species collected from two different regions. All the Junonia species clustered together, and were further subdivided into clade one consisting of J. almana and J. orithya and clade two comprising of the two J. iphita which were collected from Indo and Indochinese subregions separated by river barrier. Comparison between the two J. iphita sequences revealed minor variations and Single Nucleotide Polymorphisms were identified at 51 sites amounting to 0.4% of the entire mitochondrial genome.

  15. Complete mitochondrial genome sequence of the Chinese scrub vole (Neodon irene).

    Science.gov (United States)

    Fan, Longqing; Fan, Zhenxin; Yue, Hao; Zhang, Xiuyue; Liu, Yang; Sun, Zhiyu; Liu, Shaoying; Yue, Bisong

    2011-06-01

    The Chinese scrub vole (Neodon irene) belongs to the subfamily Arvicolinae, which is restricted to mountain areas at high altitudes (2800-4000). In this study, we sequenced the complete mitochondrial genome of N. irene. It was determined to be 16,367 bases. The nucleotide sequence data of 12 heavy-strand protein-coding genes of N. irene and other 22 rodents were used for phylogenetic analysis. Bayesian inference (BI) and maximum likelihood (ML) were used. Both the BI and ML trees demonstrated that Microtus rossiaemeridionalis and Microtus kikuchii did not cluster together with each other. On the contrary, M. rossiaemeridionalis showed close relationship with N. irene. In the present study, only one sequence from Neodon and two sequences from Microtus were included in the phylogenetic analysis which should contribute to the unusual relationship. Therefore, in order to better understand the phylogenetic relationship within Rodentia, more rodents' complete mitochondrial genomes are required.

  16. The complete mitochondrial genome of the Xuefeng black-boned chicken.

    Science.gov (United States)

    Liu, Li-Li; Xie, Hong-Bing; Yang, Yong-Sheng; Yu, Qi-Fang; He, Jian-Hua

    2016-01-01

    Xuefeng black-boned chicken is one of the famous native breeds in China. In this work, we reported the complete mitochondrial genome sequence of the Xuefeng black-boned chicken for the first time, which was determined through PCR-based method. The total length of the mitogenome was 16,783 bp, with the base composition of 30.24% for A, 23.72% for T, 32.52% for C, 13.53% for G, in the order C > A > T > G feature occurring in the Xuefeng black-boned chicken. It contained the typical structure, including 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). It was similar to the gene arrangement in Silky chicken. The complete mitochondrial genome sequence of the Xuefeng black-boned chicken provided an important data for further study on the genetic mechanism.

  17. The complete mitochondrial genomes of Opisthoplatia orientalis and Blaptica dubia (Blattodea: Blaberidae).

    Science.gov (United States)

    Tian, Xiaoxuan; Ma, Guangyin; Cui, Ying; Dong, Pengzhi; Zhu, Yan; Gao, Xiumei

    2017-01-01

    The first complete mitochondrial genome in Blaberidae has been reported in this research. Opisthoplatia orientalis (Blaberidae, Epilamprinae) known as ground cockroach with golden edge is distributed in East and South Asia and widely used for thrombolytic therapy in China. Meanwhile, Blaptica dubia (Blaberidae, Blaberinae) has been adopted as feeder insect for various kinds of pets all over the world. In the present study, we investigated the complete mitochondrial genome of O. orientalis and B. dubia, and the mitogenome is 18 724  and 17 340 bp in length, respectively. The circular molecule consists of 13 protein coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a non-coding control region, with an AT content of 75.7% for O. orientalis and 72.8% for B. dubia. A preliminary phylogenetic analysis has been carried out with 11 related species and the status of these two species is further confirmed.

  18. Ancient mitochondrial genome reveals trace of prehistoric migration in the east Pamir by pastoralists.

    Science.gov (United States)

    Ning, Chao; Gao, Shizhu; Deng, Boping; Zheng, Hongxiang; Wei, Dong; Lv, Haoze; Li, Hongjie; Song, Li; Wu, Yong; Zhou, Hui; Cui, Yinqiu

    2016-02-01

    The complete mitochondrial genome of one 700-year-old individual found in Tashkurgan, Xinjiang was target enriched and sequenced in order to shed light on the population history of Tashkurgan and determine the phylogenetic relationship of haplogroup U5a. The ancient sample was assigned to a subclade of haplogroup U5a2a1, which is defined by two rare and stable transversions at 16114A and 13928C. Phylogenetic analysis shows a distribution pattern for U5a2a that is indicative of an origin in the Volga-Ural region and exhibits a clear eastward geographical expansion that correlates with the pastoral culture also entering the Eurasian steppe. The haplogroup U5a2a present in the ancient Tashkurgan individual reveals prehistoric migration in the East Pamir by pastoralists. This study shows that studying an ancient mitochondrial genome is a useful approach for studying the evolutionary process and population history of Eastern Pamir.

  19. Complete mitochondrial genome of the European Grapevine moth (EGVM) Lobesia botrana (Lepidoptera: Tortricidae).

    Science.gov (United States)

    Piper, Melissa Claire; van Helden, Maarten; Court, Leon N; Tay, Wee Tek

    2016-09-01

    The Lobesia botrana larvae feed on grapevine (Vitis vinifera L.), thereby reducing crop yield and increasing crop susceptibility to fungal and bacterial attacks. We determined the circular mitochondrial genome of L. botrana as 15 229 bp (GenBank KP677508) and contained 13 protein coding genes (PCG's), 22 transfer RNAs (tRNA), and two ribosomal RNAs. All tRNAs have the "clover-shaped" 2-D structures, while the tRNA-Ile which has the TψC-stem but lacked the TψC-loop. Knowledge of L. botrana mitochondrial genome represents a valuable molecular resource for developing effective DNA identification tools for biosecurity purposes and will contribute to better understanding of its evolutionary and population genetics.

  20. Next-generation sequencing of human mitochondrial reference genomes uncovers high heteroplasmy frequency.

    Directory of Open Access Journals (Sweden)

    Maria Ximena Sosa

    Full Text Available We describe methods for rapid sequencing of the entire human mitochondrial genome (mtgenome, which involve long-range PCR for specific amplification of the mtgenome, pyrosequencing, quantitative mapping of sequence reads to identify sequence variants and heteroplasmy, as well as de novo sequence assembly. These methods have been used to study 40 publicly available HapMap samples of European (CEU and African (YRI ancestry to demonstrate a sequencing error rate <5.63×10(-4, nucleotide diversity of 1.6×10(-3 for CEU and 3.7×10(-3 for YRI, patterns of sequence variation consistent with earlier studies, but a higher rate of heteroplasmy varying between 10% and 50%. These results demonstrate that next-generation sequencing technologies allow interrogation of the mitochondrial genome in greater depth than previously possible which may be of value in biology and medicine.

  1. A mitochondrial genome sequence of a hominin from Sima de los Huesos.

    Science.gov (United States)

    Meyer, Matthias; Fu, Qiaomei; Aximu-Petri, Ayinuer; Glocke, Isabelle; Nickel, Birgit; Arsuaga, Juan-Luis; Martínez, Ignacio; Gracia, Ana; de Castro, José María Bermúdez; Carbonell, Eudald; Pääbo, Svante

    2014-01-16

    Excavations of a complex of caves in the Sierra de Atapuerca in northern Spain have unearthed hominin fossils that range in age from the early Pleistocene to the Holocene. One of these sites, the 'Sima de los Huesos' ('pit of bones'), has yielded the world's largest assemblage of Middle Pleistocene hominin fossils, consisting of at least 28 individuals dated to over 300,000 years ago. The skeletal remains share a number of morphological features with fossils classified as Homo heidelbergensis and also display distinct Neanderthal-derived traits. Here we determine an almost complete mitochondrial genome sequence of a hominin from Sima de los Huesos and show that it is closely related to the lineage leading to mitochondrial genomes of Denisovans, an eastern Eurasian sister group to Neanderthals. Our results pave the way for DNA research on hominins from the Middle Pleistocene.

  2. Complete mitochondrial genome of the striped sandgoby Acentrogobius pflaumii (Perciformes, gobiidae).

    Science.gov (United States)

    Jin, Xiaoxiao; Wang, Rixin; Zhao, Shenglong; Xu, Tianjun; Shi, Ge

    2012-12-01

    The striped sandgoby, Acentrogobius pflaumii (Perciformes, Gobiidae), is a widespread goby inhabiting shallow sandy-muddy bottoms in temperate riverine estuaries and inner bays. In this study, the complete mitochondrial genome of A. pflaumii was firstly determined. The genome is 16,515 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 2 main non-coding regions (the control region and the origin of the light-strand replication). The overall base composition of A. pflaumii is 25.8% for T, 29.3% for C, 26.6% for A, and 18.3% for G, with a slight A+T bias of 52.4%. It has the typical vertebrate mitochondrial gene arrangement.

  3. Mitochondrial genome analyses suggest multiple Trichuris species in humans, baboons, and pigs from different geographical regions

    DEFF Research Database (Denmark)

    Hawash, Mohamed B. F.; Andersen, Lee O.; Gasser, Robin B.;

    2015-01-01

    BACKGROUND: The whipworms Trichuris trichiura and Trichuris suis are two parasitic nematodes of humans and pigs, respectively. Although whipworms in human and non-human primates historically have been referred to as T. trichiura, recent reports suggest that several Trichuris spp. are found...... in primates. METHODS AND FINDINGS: We sequenced and annotated complete mitochondrial genomes of Trichuris recovered from a human in Uganda, an olive baboon in the US, a hamadryas baboon in Denmark, and two pigs from Denmark and Uganda. Comparative analyses using other published mitochondrial genomes...... of Trichuris recovered from a human and a porcine host in China and from a françois' leaf-monkey (China) were performed, including phylogenetic analyses and pairwise genetic and amino acid distances. Genetic and protein distances between human Trichuris in Uganda and China were high (~19% and 15%, respectively...

  4. Mitochondrial genome sequence of Egyptian swift Rock Pigeon (Columba livia breed Egyptian swift).

    Science.gov (United States)

    Li, Chun-Hong; Shi, Wei; Shi, Wan-Yu

    2015-06-01

    The Egyptian swift Rock Pigeon is a breed of fancy pigeon developed over many years of selective breeding. In this work, we report the complete mitochondrial genome sequence of Egyptian swift Rock Pigeon. The total length of the mitogenome was 17,239 bp and its overall base composition was estimated to be 30.2% for A, 24.0% for T, 31.9% for C and 13.9% for G, indicating an A-T (54.2%)-rich feature in the mitogenome. It contained the typical structure of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a non-coding control region (D-loop region). The complete mitochondrial genome sequence of Egyptian swift Rock Pigeon would serve as an important data set of the germplasm resources for further study.

  5. Mitochondrial genome of the black flying fox, Pteropus alecto (Chiroptera: Megachiroptera: Pteropodidae).

    Science.gov (United States)

    Gao, Cheng-Wen; Wang, Shuo; Gao, Li-Zhi

    2016-01-01

    In this article we report the complete mitochondrial genome of black flying fox, Pteropus alecto, with the sequence length of 16,739 bp for the first time. The mitogenome contained a total of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region. The base composition was A (33.1%), G (14.5%), C (27.2%) and T (25.2%), indicating that the percentage of A and T (58.3%) was higher than that of G and C. Most of these genes were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes. The mitochondrial genome analyzed here will provide new genetic information to study the evolution of bats.

  6. The complete mitochondrial genome of Neobenedenia melleni (Platyhelminthes: Monogenea): mitochondrial gene content, arrangement and composition compared with two Benedenia species.

    Science.gov (United States)

    Zhang, Juan; Wu, Xiangyun; Li, Yanwei; Zhao, Mengwei; Xie, Mingquan; Li, Anxing

    2014-10-01

    The complete mitochondrial (mt) genome sequences of Neobenedenia melleni were determined and compared with those of Benedenia seriolae and B. hoshinai. This circular genome comprises 13,270 bp and includes all 36 typical mt genes found in flatworms. Total AT content of N. melleni is 75.9 %. ATG is the most common start codon, while nad4L is initiated by GTG. All protein-coding genes are predicted to terminate with TAG and TAA. N. melleni has the trnR with a TCG anticodon, which is the same to B. seriolae but different from B. hoshinai (ACG). The mt gene arrangement of N. melleni is similar to that of B. seriolae and B. hoshinai with the exception of three translocations (trnF, trnT and trnG). The overlapped region between nad4L and nad4 was found in the N. melleni mt genome, which was also reported for the published Gyrodactylus species, but it was not found in those of B. seriolae and B. hoshinai, which are non-coding regions instead. The present study provides useful molecular characters for species or strain identification and systematic studies of this parasite.

  7. The complete mitochondrial genome of the citrus red mite Panonychus citri (Acari: Tetranychidae): high genome rearrangement and extremely truncated tRNAs.

    Science.gov (United States)

    Yuan, Ming-Long; Wei, Dan-Dan; Wang, Bao-Jun; Dou, Wei; Wang, Jin-Jun

    2010-10-23

    The family Tetranychidae (Chelicerata: Acari) includes ~1200 species, many of which are of agronomic importance. To date, mitochondrial genomes of only two Tetranychidae species have been sequenced, and it has been found that these two mitochondrial genomes are characterized by many unusual features in genome organization and structure such as gene order and nucleotide frequency. The scarcity of available sequence data has greatly impeded evolutionary studies in Acari (mites and ticks). Information on Tetranychidae mitochondrial genomes is quite important for phylogenetic evaluation and population genetics, as well as the molecular evolution of functional genes such as acaricide-resistance genes. In this study, we sequenced the complete mitochondrial genome of Panonychus citri (Family Tetranychidae), a worldwide citrus pest, and provide a comparison to other Acari. The mitochondrial genome of P. citri is a typical circular molecule of 13,077 bp, and contains the complete set of 37 genes that are usually found in metazoans. This is the smallest mitochondrial genome within all sequenced Acari and other Chelicerata, primarily due to the significant size reduction of protein coding genes (PCGs), a large rRNA gene, and the A + T-rich region. The mitochondrial gene order for P. citri is the same as those for P. ulmi and Tetranychus urticae, but distinctly different from other Acari by a series of gene translocations and/or inversions. The majority of the P. citri mitochondrial genome has a high A + T content (85.28%), which is also reflected by AT-rich codons being used more frequently, but exhibits a positive GC-skew (0.03). The Acari mitochondrial nad1 exhibits a faster amino acid substitution rate than other genes, and the variation of nucleotide substitution patterns of PCGs is significantly correlated with the G + C content. Most tRNA genes of P. citri are extremely truncated and atypical (44-65, 54.1 ± 4.1 bp), lacking either the T- or D-arm, as found in P. ulmi

  8. The complete mitochondrial genome of the citrus red mite Panonychus citri (Acari: Tetranychidae: high genome rearrangement and extremely truncated tRNAs

    Directory of Open Access Journals (Sweden)

    Dou Wei

    2010-10-01

    Full Text Available Abstract Background The family Tetranychidae (Chelicerata: Acari includes ~1200 species, many of which are of agronomic importance. To date, mitochondrial genomes of only two Tetranychidae species have been sequenced, and it has been found that these two mitochondrial genomes are characterized by many unusual features in genome organization and structure such as gene order and nucleotide frequency. The scarcity of available sequence data has greatly impeded evolutionary studies in Acari (mites and ticks. Information on Tetranychidae mitochondrial genomes is quite important for phylogenetic evaluation and population genetics, as well as the molecular evolution of functional genes such as acaricide-resistance genes. In this study, we sequenced the complete mitochondrial genome of Panonychus citri (Family Tetranychidae, a worldwide citrus pest, and provide a comparison to other Acari. Results The mitochondrial genome of P. citri is a typical circular molecule of 13,077 bp, and contains the complete set of 37 genes that are usually found in metazoans. This is the smallest mitochondrial genome within all sequenced Acari and other Chelicerata, primarily due to the significant size reduction of protein coding genes (PCGs, a large rRNA gene, and the A + T-rich region. The mitochondrial gene order for P. citri is the same as those for P. ulmi and Tetranychus urticae, but distinctly different from other Acari by a series of gene translocations and/or inversions. The majority of the P. citri mitochondrial genome has a high A + T content (85.28%, which is also reflected by AT-rich codons being used more frequently, but exhibits a positive GC-skew (0.03. The Acari mitochondrial nad1 exhibits a faster amino acid substitution rate than other genes, and the variation of nucleotide substitution patterns of PCGs is significantly correlated with the G + C content. Most tRNA genes of P. citri are extremely truncated and atypical (44-65, 54.1 ± 4.1 bp, lacking

  9. Molecular analyses of mitochondrial pseudogenes within the nuclear genome of arvicoline rodents.

    Science.gov (United States)

    Triant, Deborah A; DeWoody, J Andrew

    2008-01-01

    Nuclear sequences of mitochondrial origin (numts) are common among animals and plants. The mechanism(s) by which numts transfer from the mitochondrion to the nucleus is uncertain, but their insertions may be mediated in part by chromosomal repair mechanisms. If so, then lineages where chromosomal rearrangements are common should be good models for the study of numt evolution. Arvicoline rodents are known for their karyotypic plasticity and numt pseudogenes have been discovered in this group. Here, we characterize a 4 kb numt pseudogene in the arvicoline vole Microtus rossiaemeridionalis. This sequence is among the largest numts described for a mammal lacking a completely sequenced genome. It encompasses three protein-coding and six tRNA pseudogenes that span approximately 25% of the entire mammalian mitochondrial genome. It is bordered by a dinucleotide microsatellite repeat and contains four transposable elements within its sequence and flanking regions. To determine the phylogenetic distribution of this numt among the arvicolines, we characterized one of the mitochondrial pseudogenes (cytochrome b) in 21 additional arvicoline species. Average rates of nucleotide substitution in this arvicoline pseudogene are estimated as 2.3 x 10(-8) substitutions/per site/per year. Furthermore, we performed comparative analyses among all species to estimate the age of this mitochondrial transfer at nearly 4 MYA, predating the origin of most arvicolines.

  10. Frequency and pattern of heteroplasmy in the complete human mitochondrial genome.

    Directory of Open Access Journals (Sweden)

    Amanda Ramos

    Full Text Available Determining the levels of human mitochondrial heteroplasmy is of utmost importance in several fields. In spite of this, there are currently few published works that have focused on this issue. In order to increase the knowledge of mitochondrial DNA (mtDNA heteroplasmy, the main goal of this work is to investigate the frequency and the mutational spectrum of heteroplasmy in the human mtDNA genome. To address this, a set of nine primer pairs designed to avoid co-amplification of nuclear DNA (nDNA sequences of mitochondrial origin (NUMTs was used to amplify the mitochondrial genome in 101 individuals. The analysed individuals represent a collection with a balanced representation of genders and mtDNA haplogroup distribution, similar to that of a Western European population. The results show that the frequency of heteroplasmic individuals exceeds 61%. The frequency of point heteroplasmy is 28.7%, with a widespread distribution across the entire mtDNA. In addition, an excess of transitions in heteroplasmy were detected, suggesting that genetic drift and/or selection may be acting to reduce its frequency at population level. In fact, heteroplasmy at highly stable positions might have a greater impact on the viability of mitochondria, suggesting that purifying selection must be operating to prevent their fixation within individuals. This study analyses the frequency of heteroplasmy in a healthy population, carrying out an evolutionary analysis of the detected changes and providing a new perspective with important consequences in medical, evolutionary and forensic fields.

  11. Complete mitochondrial genome sequence of the Eastern gorilla (Gorilla beringei) and implications for african ape biogeography.

    Science.gov (United States)

    Das, Ranajit; Hergenrother, Scott D; Soto-Calderón, Iván D; Dew, J Larry; Anthony, Nicola M; Jensen-Seaman, Michael I

    2014-01-01

    The Western and Eastern species of gorillas (Gorilla gorilla and Gorilla beringei) began diverging in the mid-Pleistocene, but in a complex pattern with ongoing gene flow following their initial split. We sequenced the complete mitochondrial genomes of 1 Eastern and 1 Western gorilla to provide the most accurate date for their mitochondrial divergence, and to analyze patterns of nucleotide substitutions. The most recent common ancestor of these genomes existed about 1.9 million years ago, slightly more recent than that of chimpanzee and bonobo. We in turn use this date as a calibration to reanalyze sequences from the Eastern lowland and mountain gorilla subspecies to estimate their mitochondrial divergence at approximately 380000 years ago. These dates help frame a hypothesis whereby populations became isolated nearly 2 million years ago with restricted maternal gene flow, followed by ongoing male migration until the recent past. This process of divergence with prolonged hybridization occurred against the backdrop of the African Pleistocene, characterized by intense fluctuations in temperature and aridity, while at the same time experiencing tectonic uplifting and consequent shifts in the drainage of major river systems. Interestingly, this same pattern of introgression following divergence and discrepancies between mitochondrial and nuclear loci is seen in fossil hominins from Eurasia, suggesting that such processes may be common in hominids and that living gorillas may provide a useful model for understanding isolation and migration in our extinct relatives.

  12. Massively convergent evolution for ribosomal protein gene content in plastid and mitochondrial genomes.

    Science.gov (United States)

    Maier, Uwe-G; Zauner, Stefan; Woehle, Christian; Bolte, Kathrin; Hempel, Franziska; Allen, John F; Martin, William F

    2013-01-01

    Plastid and mitochondrial genomes have undergone parallel evolution to encode the same functional set of genes. These encode conserved protein components of the electron transport chain in their respective bioenergetic membranes and genes for the ribosomes that express them. This highly convergent aspect of organelle genome evolution is partly explained by the redox regulation hypothesis, which predicts a separate plastid or mitochondrial location for genes encoding bioenergetic membrane proteins of either photosynthesis or respiration. Here we show that convergence in organelle genome evolution is far stronger than previously recognized, because the same set of genes for ribosomal proteins is independently retained by both plastid and mitochondrial genomes. A hitherto unrecognized selective pressure retains genes for the same ribosomal proteins in both organelles. On the Escherichia coli ribosome assembly map, the retained proteins are implicated in 30S and 50S ribosomal subunit assembly and initial rRNA binding. We suggest that ribosomal assembly imposes functional constraints that govern the retention of ribosomal protein coding genes in organelles. These constraints are subordinate to redox regulation for electron transport chain components, which anchor the ribosome to the organelle genome in the first place. As organelle genomes undergo reduction, the rRNAs also become smaller. Below size thresholds of approximately 1,300 nucleotides (16S rRNA) and 2,100 nucleotides (26S rRNA), all ribosomal protein coding genes are lost from organelles, while electron transport chain components remain organelle encoded as long as the organelles use redox chemistry to generate a proton motive force.

  13. A comparison of the mitochondrial genomes from two families of Solifugae (Arthropoda: Chelicerata): Eremobatidae and Ammotrechidae.

    Science.gov (United States)

    Masta, Susan E; Klann, Anja E; Podsiadlowski, Lars

    2008-07-01

    Arachnids are an ancient and diverse group of arthropods, yet few representative mitochondrial genomes have been published for most of the 11 orders. Here, we present and compare sequence and genomic data from two complete mitochondrial genomes from the arachnid order Solifugae (the camel spiders or wind scorpions), representing two families, Ammotrechidae and Eremobatidae. We also make genome-level and sequence comparisons between these taxa and the horseshoe crab, a chelicerate from the sister group to arachnids. In their organization, the two solifuge mitochondrial genomes are similar to that of the horseshoe crab, although both of the solifuges possess a region of repeated sequence. All 13 protein-coding genes and the two ribosomal RNA genes are of similar sizes to those found in the horseshoe crab. The ammotrechid and the eremobatid each have one tRNA gene that differs in location from those of other chelicerates, suggesting that these translocations occurred after the divergence of Solifugae from other arachnid lineages. All 22 tRNA genes in both solifuges are inferred to form secondary structures that are typical of those found in other metazoan mt genomes. However, in the eremobatid, the tRNA(Ser(UCN)) gene in the repeat region appears to have undergone partial duplication and loss of function, and a new tRNA(Ser(UCN)) gene has been created de novo. Our divergence data, in conjunction with the fossil record, indicate that these two solifuge families diverged more than 230 million years ago. Thus, despite several gene rearrangements and duplications, these data indicate a remarkable degree of evolutionary stasis.

  14. Quantitative Proteomic Analysis of Mitochondrial Proteins Reveals Pro-Survival Mechanisms in the Perpetuation of Radiation-Induced Genomic Instability

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, Stefani N.; Waters, Katrina M.; Morgan, William F.; Yang, Austin; Baulch, Janet E.

    2012-07-26

    Radiation induced genomic instability is a well-studied phenomenon that is measured as mitotically heritable genetic alterations observed in the progeny of an irradiated cell. The mechanisms that perpetuate this instability are unclear, however, a role for chronic oxidative stress has consistently been demonstrated. In the chromosomally unstable LS12 cell line, oxidative stress and genomic instability were correlated with mitochondrial dysfunction. To clarify this mitochondrial dysfunction and gain insight into the mechanisms underlying radiation induced genomic instability we have evaluated the mitochondrial sub-proteome and performed quantitative mass spectrometry (MS) analysis of LS12 cells. Of 98 quantified mitochondrial proteins, 17 met criteria for fold changes and reproducibility; and 11 were statistically significant in comparison with the stable parental GM10115 cell line. Previous observations implicated defects in the electron transport chain (ETC) in the LS12 cell mitochondrial dysfunction. Proteomic analysis supports these observations, demonstrating significantly reduced levels of mitochondrial cytochrome c, the intermediary between complexes III and IV of the ETC. Results also suggest that LS12 cells compensate for ETC dysfunction and oxidative stress through increased levels of tricarboxylic acid cycle enzymes and up-regulation of proteins that protect against oxidative stress and apoptosis. More than one cellular defect is likely to contribute to the genomic instability phenotype. These data suggest that LS12 cells have adapted mechanisms that allow survival under sub-optimal conditions of oxidative stress and compromised mitochondrial function to perpetuate genomic instability.

  15. Phylogenetic approaches for the analysis of mitochondrial genome sequence data in the Hymenoptera--a lineage with both rapidly and slowly evolving mitochondrial genomes.

    Science.gov (United States)

    Dowton, Mark; Cameron, Stephen L; Austin, Andy D; Whiting, Michael F

    2009-08-01

    We entirely sequenced two new hymenopteran mitochondrial genomes (Cephus cinctus and Orussus occidentalis), and a substantial portion of another three hymenopterans (Schlettererius cinctipes, Venturia canescens, and Enicospilus). We analyze them together with nine others reported in the literature. We establish that the rate of genetic divergence is two to three times higher among some Hymenoptera when compared with others, making this a group with both long and short phylogenetic branches. We then assessed the ability of a range of phylogenetic approaches to recover seven uncontroversial relationships, when lineages show markedly different rates of molecular evolution. This range encompassed maximum parsimony and Bayesian analysis of (i) amino acid data, (ii) nucleotide data, and (iii) nucleotide data excluding third codon positions. Unpartitioned analyses were compared with partitioned analyses, with the data partitioned by codon position (ribosomal genes were placed in a separate partition). These analyses indicated that partitioned, Bayesian analysis of nucleotide data, excluding 3rd codon positions, recovered more of the uncontroversial relationships than any other approach. These results suggest that the analysis of complete mitochondrial genome sequences holds promise for the resolution of hymenopteran superfamily relationships.

  16. The complete mitochondrial genome of Haliotis laevigata (Gastropoda: Haliotidae) using MiSeq and HiSeq sequencing.

    Science.gov (United States)

    Robinson, Nick A; Hall, Nathan E; Ross, Elizabeth M; Cooke, Ira R; Shiel, Brett P; Robinson, Andrew J; Strugnell, Jan M

    2016-01-01

    The mitochondrial genome of greenlip abalone, Haliotis laevigata, is reported. MiSeq and HiSeq sequencing of one individual was assembled to yield a single 16,545 bp contig. The sequence shares 92% identity to the H. rubra mitochondrial genome (a closely related species that hybridize with H. laevigata in the wild). The sequence will be useful for determining the maternal contribution to hybrid populations, for investigating population structure and stock-enhancement effectiveness.

  17. The mitochondrial genomes of the iguana (Iguana iguana) and the caiman (Caiman crocodylus): implications for amniote phylogeny

    OpenAIRE

    Janke, Axel; Erpenbeck, Dirk; Nilsson, Malin; Arnason, Ulfur

    2001-01-01

    The complete mitochondrial genomes of two reptiles, the common iguana (Iguana iguana) and the caiman (Caiman crocodylus), were sequenced in order to investigate phylogenetic questions of tetrapod evolution. The addition of the two species allows analysis of reptilian relationships using data sets other than those including only fast-evolving species. The crocodilian mitochondrial genomes seem to have evolved generally at a higher rate than those of other vertebrates. Phylogenetic analyses of ...

  18. Characterization of the complete mitochondrial genome of the hybrid Epinephelus moara♀ × Epinephelus lanceolatus♂, and phylogenetic analysis in subfamily epinephelinae

    Science.gov (United States)

    Gao, Fengtao; Wei, Min; Zhu, Ying; Guo, Hua; Chen, Songlin; Yang, Guanpin

    2017-06-01

    This study presents the complete mitochondrial genome of the hybrid Epinephelus moara♀× Epinephelus lanceolatus♂. The genome is 16886 bp in length, and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, a light-strand replication origin and a control region. Additionally, phylogenetic analysis based on the nucleotide sequences of 13 conserved protein-coding genes using the maximum likelihood method indicated that the mitochondrial genome is maternally inherited. This study presents genomic data for studying phylogenetic relationships and breeding of hybrid Epinephelinae.

  19. Extensive mitochondrial genome rearrangements between Cerithioidea and Hypsogastropoda (Mollusca; Caenogastropoda) as determined from the partial nucleotide sequences of the mitochondrial DNA of Cerithidea djadjariensis and Batillaria cumingi.

    Science.gov (United States)

    Kojima, Shigeaki

    2010-06-01

    Partial nucleotide sequences ( approximately 8000 bp) of the mitochondrial DNA of two cerithioidean gastropod species-Cerithidea djadjariensis and Batillaria cumingi-were determined. The order of mitochondrial genes (eight protein genes, two ribosomal RNA genes, and nine transfer RNA genes) was identical between these two species. and remarkably different from the previously reported order in other gastropods. The results indicate that the genome structure of the common ancestor of Cerithioidea and its sister group, Hypsogastropoda, is almost identical to that of the common ancestor of Gastropoda; moreover, independent mitochondrial genome rearrangements were identified between the lineages of Cerithioidea and Hypsogastropoda. The rearrangements within Cerithioidea can be explained by the inversion of a single tRNA gene, two translocations of a single tRNA gene, and three translocations of a genome fragment containing a tRNA gene and protein-coding gene(s).

  20. The complete mitochondrial genome of the marbled rockfish Sebastiscus marmoratus (Scorpaeniformes, Scorpaenidae) from Japan.

    Science.gov (United States)

    Sun, Dianrong; Zhang, Hui; Yanagimoto, Takashi; Yin, Lina; Gao, Tianxiang

    2015-01-01

    The complete mitochondrial genome of marbled rockfish Sebastiscus marmoratus collected from Japan was determined by next-generation sequencing. The mitogenome is a circular molecule 17,301 bp in length, including the typical structure of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a control region. The ETAS, central CSB and CSB were detected in the control region. The gene contents of the mitogenome are identical to those observed in most bony fishes.

  1. Capturing the Phylogeny of Holometabola with Mitochondrial Genome Data and Bayesian Site-Heterogeneous Mixture Models.

    Science.gov (United States)

    Song, Fan; Li, Hu; Jiang, Pei; Zhou, Xuguo; Liu, Jinpeng; Sun, Changhai; Vogler, Alfried P; Cai, Wanzhi

    2016-05-22

    After decades of debate, a mostly satisfactory resolution of relationships among the 11 recognized holometabolan orders of insects has been reached based on nuclear genes, resolving one of the most substantial branches of the tree-of-life, but the relationships are still not well established with mitochondrial genome data. The main reasons have been the absence of sufficient data in several orders and lack of appropriate phylogenetic methods that avoid the systematic errors from compositional and mutational biases in insect mitochondrial genomes. In this study, we assembled the richest taxon sampling of Holometabola to date (199 species in 11 orders), and analyzed both nucleotide and amino acid data sets using several methods. We find the standard Bayesian inference and maximum-likelihood analyses were strongly affected by systematic biases, but the site-heterogeneous mixture model implemented in PhyloBayes avoided the false grouping of unrelated taxa exhibiting similar base composition and accelerated evolutionary rate. The inclusion of rRNA genes and removal of fast-evolving sites with the observed variability sorting method for identifying sites deviating from the mean rates improved the phylogenetic inferences under a site-heterogeneous model, correctly recovering most deep branches of the Holometabola phylogeny. We suggest that the use of mitochondrial genome data for resolving deep phylogenetic relationships requires an assessment of the potential impact of substitutional saturation and compositional biases through data deletion strategies and by using site-heterogeneous mixture models. Our study suggests a practical approach for how to use densely sampled mitochondrial genome data in phylogenetic analyses. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  2. Dynamic nucleotide mutation gradients and control region usage in squamate reptile mitochondrial genomes.

    Science.gov (United States)

    Castoe, T A; Gu, W; de Koning, A P J; Daza, J M; Jiang, Z J; Parkinson, C L; Pollock, D D

    2009-01-01

    Gradients of nucleotide bias and substitution rates occur in vertebrate mitochondrial genomes due to the asymmetric nature of the replication process. The evolution of these gradients has previously been studied in detail in primates, but not in other vertebrate groups. From the primate study, the strengths of these gradients are known to evolve in ways that can substantially alter the substitution process, but it is unclear how rapidly they evolve over evolutionary time or how different they may be in different lineages or groups of vertebrates. Given the importance of mitochondrial genomes in phylogenetics and molecular evolutionary research, a better understanding of how asymmetric mitochondrial substitution gradients evolve would contribute key insights into how this gradient evolution may mislead evolutionary inferences, and how it may also be incorporated into new evolutionary models. Most snake mitochondrial genomes have an additional interesting feature, 2 nearly identical control regions, which vary among different species in the extent that they are used as origins of replication. Given the expanded sampling of complete snake genomes currently available, together with 2 additional snakes sequenced in this study, we reexamined gradient strength and CR usage in alethinophidian snakes as well as several lizards that possess dual CRs. Our results suggest that nucleotide substitution gradients (and corresponding nucleotide bias) and CR usage is highly labile over the approximately 200 m.y. of squamate evolution, and demonstrates greater overall variability than previously shown in primates. The evidence for the existence of such gradients, and their ability to evolve rapidly and converge among unrelated species suggests that gradient dynamics could easily mislead phylogenetic and molecular evolutionary inferences, and argues strongly that these dynamics should be incorporated into phylogenetic models.

  3. Mitochondrial Genomes Provide Insights into the Phylogeny of Lauxanioidea (Diptera: Cyclorrhapha).

    Science.gov (United States)

    Li, Xuankun; Li, Wenliang; Ding, Shuangmei; Cameron, Stephen L; Mao, Meng; Shi, Li; Yang, Ding

    2017-04-14

    The superfamily Lauxanioidea is a significant dipteran clade including over 2500 known species in three families: Lauxaniidae, Celyphidae and Chamaemyiidae. We sequenced the first five (three complete and two partial) lauxanioid mitochondrial (mt) genomes, and used them to reconstruct the phylogeny of this group. The lauxanioid mt genomes are typical of the Diptera, containing all 37 genes usually present in bilaterian animals. A total of three conserved intergenic sequences have been reported across the Cyclorrhapha. The inferred secondary structure of 22 tRNAs suggested five substitution patterns among the Cyclorrhapha. The control region in the Lauxanioidea has apparently evolved very fast, but four conserved structural elements were detected in all three complete mt genome sequences. Phylogenetic relationships based on the mt genome data were inferred by Maximum Likelihood and Bayesian methods. The traditional relationships between families within the Lauxanioidea, (Chamaemyiidae + (Lauxaniidae + Celyphidae)), were corroborated; however, the higher-level relationships between cyclorrhaphan superfamilies are mostly poorly supported.

  4. The full mitochondrial genome sequence of Raillietina tetragona from chicken (Cestoda: Davaineidae).

    Science.gov (United States)

    Liang, Jian-Ying; Lin, Rui-Qing

    2016-11-01

    In the present study, the complete mitochondrial DNA (mtDNA) sequence of Raillietina tetragona was sequenced and its gene contents and genome organizations was compared with that of other tapeworm. The complete mt genome sequence of R. tetragona is 14,444 bp in length. It contains 12 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and two non-coding region. All genes are transcribed in the same direction and have a nucleotide composition high in A and T. The contents of A + T of the complete mt genome are 71.4% for R. tetragona. The R. tetragona mt genome sequence provides novel mtDNA marker for studying the molecular epidemiology and population genetics of Raillietina and has implications for the molecular diagnosis of chicken cestodosis caused by Raillietina.

  5. Mitochondrial genome evolution in Alismatales: Size reduction and extensive loss of ribosomal protein genes

    DEFF Research Database (Denmark)

    Petersen, Gitte; Cuenca, Argelia; Zervas, Athanasios

    2017-01-01

    The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes ...... mitogenome from a non-parasitic plant. Using a broad sample of the Alismatales, the evolutionary history of ribosomal protein gene loss is analyzed. In Zostera almost all ribosomal protein genes are lost from the mitogenome, but only some can be found in the nucleus....

  6. Complete genome sequence of the mitochondrial DNA of the river lamprey, Lethenteron japonicum.

    Science.gov (United States)

    Kawai, Yuri L; Yura, Kei; Shindo, Miyuki; Kusakabe, Rie; Hayashi, Keiko; Hata, Kenichiro; Nakabayashi, Kazuhiko; Okamura, Kohji

    2015-01-01

    Lampreys are eel-like jawless fishes evolutionarily positioned between invertebrates and vertebrates, and have been used as model organisms to explore vertebrate evolution. In this study we determined the complete genome sequence of the mitochondrial DNA of the Japanese river lamprey, Lethenteron japonicum, using next-generation sequencers. The sequence was 16,272 bp in length. The gene content and order were identical to those of the sea lamprey, Petromyzon marinus, which has been the reference among lamprey species. However, the sequence similarity was less than 90%, suggesting the need for the whole-genome sequencing of L. japonicum.

  7. The complete mitochondrial genome of the North Chinese Leopard (Panthera pardus japonensis).

    Science.gov (United States)

    Dou, Hailong; Feng, Limin; Xiao, Wenhong; Wang, Tianming

    2016-01-01

    The North Chinese Leopard (Panthera pardus japonensis) is an endemic subspecies of Panthera pardus to China, living in small and isolated populations with a severely fragmented distribution. Here we first sequenced and annotated its complete mitochondrial genome. The total length of the North Chinese Leopard is of 16,966 base pairs that consist of 2 rRNA gene, 22 tRNA genes, 13 protein-coding genes, 1 OLR and 1 control region (CR). The structures of the genomes were highly similar to other Felidae.

  8. Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda revealed from complete mitochondrial genomes

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    Lin Feng-Jiau

    2012-11-01

    Full Text Available Abstract Background The evolutionary history and relationships of the mud shrimps (Crustacea: Decapoda: Gebiidea and Axiidea are contentious, with previous attempts revealing mixed results. The mud shrimps were once classified in the infraorder Thalassinidea. Recent molecular phylogenetic analyses, however, suggest separation of the group into two individual infraorders, Gebiidea and Axiidea. Mitochondrial (mt genome sequence and structure can be especially powerful in resolving higher systematic relationships that may offer new insights into the phylogeny of the mud shrimps and the other decapod infraorders, and test the hypothesis of dividing the mud shrimps into two infraorders. Results We present the complete mitochondrial genome sequences of five mud shrimps, Austinogebia edulis, Upogebia major, Thalassina kelanang (Gebiidea, Nihonotrypaea thermophilus and Neaxius glyptocercus (Axiidea. All five genomes encode a standard set of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a putative control region. Except for T. kelanang, mud shrimp mitochondrial genomes exhibited rearrangements and novel patterns compared to the pancrustacean ground pattern. Each of the two Gebiidea species (A. edulis and U. major and two Axiidea species (N. glyptocercus and N. thermophiles share unique gene order specific to their infraorders and analyses further suggest these two derived gene orders have evolved independently. Phylogenetic analyses based on the concatenated nucleotide and amino acid sequences of 13 protein-coding genes indicate the possible polyphyly of mud shrimps, supporting the division of the group into two infraorders. However, the infraordinal relationships among the Gebiidea and Axiidea, and other reptants are poorly resolved. The inclusion of mt genome from more taxa, in particular the reptant infraorders Polychelida and Glypheidea is required in further analysis. Conclusions Phylogenetic analyses on the mt genome

  9. The complete mitochondrial genome of a spiraling whitefly, Aleurodicus dispersus Russell (Hemiptera: Aleyrodidae).

    Science.gov (United States)

    Ming-Xing, Lu; Zhi-Teng, Chen; Wei-Wei, Yu; Yu-Zhou, Du

    2017-03-01

    We report the complete mitochondrial genome (mitogenome) of a spiraling whitefly, Aleurodicus dispersus (Hemiptera: Aleyrodidae). The 16 170 bp long genome consists of 13 protein-coding genes, 20 transfer RNAs, 2 ribosomal RNAs, and a control region. The A. dispersus mitogenome also includes a cytb-like non-coding region and shows several variations relative to the typical insect mitogenome. A phylogenetic tree has been constructed using the 13 protein-coding genes of 12 related species from Hemiptera. Our results would contribute to further study of phylogeny in Aleyrodidae and Hemiptera.

  10. Analysis of the Complete Mitochondrial Genome Sequence of the Diploid Cotton Gossypium raimondii by Comparative Genomics Approaches

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    Changwei Bi

    2016-01-01

    Full Text Available Cotton is one of the most important economic crops and the primary source of natural fiber and is an important protein source for animal feed. The complete nuclear and chloroplast (cp genome sequences of G. raimondii are already available but not mitochondria. Here, we assembled the complete mitochondrial (mt DNA sequence of G. raimondii into a circular genome of length of 676,078 bp and performed comparative analyses with other higher plants. The genome contains 39 protein-coding genes, 6 rRNA genes, and 25 tRNA genes. We also identified four larger repeats (63.9 kb, 10.6 kb, 9.1 kb, and 2.5 kb in this mt genome, which may be active in intramolecular recombination in the evolution of cotton. Strikingly, nearly all of the G. raimondii mt genome has been transferred to nucleus on Chr1, and the transfer event must be very recent. Phylogenetic analysis reveals that G. raimondii, as a member of Malvaceae, is much closer to another cotton (G. barbadense than other rosids, and the clade formed by two Gossypium species is sister to Brassicales. The G. raimondii mt genome may provide a crucial foundation for evolutionary analysis, molecular biology, and cytoplasmic male sterility in cotton and other higher plants.

  11. Human REV3 DNA Polymerase Zeta Localizes to Mitochondria and Protects the Mitochondrial Genome.

    Science.gov (United States)

    Singh, Bhupendra; Li, Xiurong; Owens, Kjerstin M; Vanniarajan, Ayyasamy; Liang, Ping; Singh, Keshav K

    2015-01-01

    To date, mitochondrial DNA polymerase γ (POLG) is the only polymerase known to be present in mammalian mitochondria. A dogma in the mitochondria field is that there is no other polymerase present in the mitochondria of mammalian cells. Here we demonstrate localization of REV3 DNA polymerase in the mammalian mitochondria. We demonstrate localization of REV3 in the mitochondria of mammalian tissue as well as cell lines. REV3 associates with POLG and mitochondrial DNA and protects the mitochondrial genome from DNA damage. Inactivation of Rev3 leads to reduced mitochondrial membrane potential, reduced OXPHOS activity, and increased glucose consumption. Conversely, inhibition of the OXPHOS increases expression of Rev3. Rev3 expression is increased in human primary breast tumors and breast cancer cell lines. Inactivation of Rev3 decreases cell migration and invasion, and localization of Rev3 in mitochondria increases survival and the invasive potential of cancer cells. Taken together, we demonstrate that REV3 functions in mammalian mitochondria and that mitochondrial REV3 is associated with the tumorigenic potential of cells.

  12. The large (134.9 kb) mitochondrial genome of the glomeromycete Funneliformis mosseae.

    Science.gov (United States)

    Nadimi, Maryam; Stefani, Franck O P; Hijri, Mohamed

    2016-10-01

    Funneliformis mosseae is among the most ecologically and economically important glomeromycete species and occurs both in natural and disturbed areas in a wide range of habitats and climates. In this study, we report the sequencing of the complete mitochondrial (mt) genome of F. mosseae isolate FL299 using 454 pyrosequencing and Illumina HiSeq technologies. This mt genome is a full-length circular chromosome of 134,925 bp, placing it among the largest mitochondrial DNAs (mtDNAs) in the fungal kingdom. A comparative analysis with publically available arbuscular mycorrhizal fungal mtDNAs revealed that the mtDNA of F. mosseae FL299 contained a very large number of insertions contributing to its expansion. The gene synteny was completely reshuffled compared to previously published glomeromycotan mtDNAs and several genes were oriented in an anti-sense direction. Furthermore, the presence of different types of introns and insertions in rnl (14 introns) made this gene very distinctive in Glomeromycota. The presence of alternative genetic codes in both initiation (GUG) and termination (UGA) codons was another new feature in this mtDNA compared to previously published glomeromycotan mt genomes. The phylogenetic analysis inferred from the analysis of 14 protein mt genes confirmed the position of the Glomeromycota clade as a sister group of Mortierellomycotina. This mt genome is the largest observed so far in Glomeromycota and the first mt genome within the Funneliformis clade, providing new opportunities to better understand their evolution and to develop molecular markers.

  13. The complete mitochondrial genome of Plodia interpunctella (Lepidoptera: Pyralidae) and comparison with other Pyraloidea insects.

    Science.gov (United States)

    Liu, Qiu-Ning; Chai, Xin-Yue; Bian, Dan-Dan; Zhou, Chun-Lin; Tang, Bo-Ping

    2016-01-01

    The mitochondrial (mt) genome can provide important information for the understanding of phylogenetic relationships. The complete mt genome of Plodia interpunctella (Lepidoptera: Pyralidae) has been sequenced. The circular genome is 15 287 bp in size, encoding 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a control region. The AT skew of this mt genome is slightly negative, and the nucleotide composition is biased toward A+T nucleotides (80.15%). All PCGs start with the typical ATN (ATA, ATC, ATG, and ATT) codons, except for the cox1 gene which may start with the CGA codon. Four of the 13 PCGs harbor the incomplete termination codon T or TA. All the tRNA genes are folded into the typical clover-leaf structure of mitochondrial tRNA, except for trnS1 (AGN) in which the DHU arm fails to form a stable stem-loop structure. The overlapping sequences are 35 bp in total and are found in seven different locations. A total of 240 bp of intergenic spacers are scattered in 16 regions. The control region of the mt genome is 327 bp in length and consisted of several features common to the sequenced lepidopteran insects. Phylogenetic analysis based on 13 PCGs using the Maximum Likelihood method shows that the placement of P. interpunctella was within the Pyralidae.

  14. The Nuclear and Mitochondrial Genomes of the Facultatively Eusocial Orchid Bee Euglossa dilemma.

    Science.gov (United States)

    Brand, Philipp; Saleh, Nicholas; Pan, Hailin; Li, Cai; Kapheim, Karen M; Ramírez, Santiago R

    2017-09-07

    Bees provide indispensable pollination services to both agricultural crops and wild plant populations, and several species of bees have become important models for the study of learning and memory, plant-insect interactions, and social behavior. Orchid bees (Apidae: Euglossini) are especially important to the fields of pollination ecology, evolution, and species conservation. Here we report the nuclear and mitochondrial genome sequences of the orchid bee Euglossa dilemma Bembé & Eltz. E. dilemma was selected because it is widely distributed, highly abundant, and it was recently naturalized in the southeastern United States. We provide a high-quality assembly of the 3.3 Gb genome, and an official gene set of 15,904 gene annotations. We find high conservation of gene synteny with the honey bee throughout 80 MY of divergence time. This genomic resource represents the first draft genome of the orchid bee genus Euglossa, and the first draft orchid bee mitochondrial genome, thus representing a valuable resource to the research community. Copyright © 2017 Brand et al.

  15. Mitochondrial Genome Analysis of Wild Rice (Oryza minuta) and Its Comparison with Other Related Species

    Science.gov (United States)

    Asaf, Sajjad; Khan, Abdul Latif; Khan, Abdur Rahim; Waqas, Muhammad; Kang, Sang-Mo; Khan, Muhammad Aaqil; Shahzad, Raheem; Seo, Chang-Woo; Shin, Jae-Ho; Lee, In-Jung

    2016-01-01

    Oryza minuta (Poaceae family) is a tetraploid wild relative of cultivated rice with a BBCC genome. O. minuta has the potential to resist against various pathogenic diseases such as bacterial blight (BB), white backed planthopper (WBPH) and brown plant hopper (BPH). Here, we sequenced and annotated the complete mitochondrial genome of O. minuta. The mtDNA genome is 515,022 bp, containing 60 protein coding genes, 31 tRNA genes and two rRNA genes. The mitochondrial genome organization and the gene content at the nucleotide level are highly similar (89%) to that of O. rufipogon. Comparison with other related species revealed that most of the genes with known function are conserved among the Poaceae members. Similarly, O. minuta mt genome shared 24 protein-coding genes, 15 tRNA genes and 1 ribosomal RNA gene with other rice species (indica and japonica). The evolutionary relationship and phylogenetic analysis revealed that O. minuta is more closely related to O. rufipogon than to any other related species. Such studies are essential to understand the evolutionary divergence among species and analyze common gene pools to combat risks in the current scenario of a changing environment. PMID:27045847

  16. The Complete Mitochondrial Genome of Delia antiqua and Its Implications in Dipteran Phylogenetics.

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    Nai-Xin Zhang

    Full Text Available Delia antiqua is a major underground agricultural pest widely distributed in Asia, Europe and North America. In this study, we sequenced and annotated the complete mitochondrial genome of this species, which is the first report of complete mitochondrial genome in the family Anthomyiidae. This genome is a double-stranded circular molecule with a length of 16,141 bp and an A+T content of 78.5%. It contains 37 genes (13 protein-coding genes, 22 tRNAs and 2 rRNAs and a non-coding A+T rich region or control region. The mitochondrial genome of Delia antiqua presents a clear bias in nucleotide composition with a positive AT-skew and a negative GC-skew. All of the 13 protein-coding genes use ATN as an initiation codon except for the COI gene that starts with ATCA. Most protein-coding genes have complete termination codons but COII and ND5 that have the incomplete termination codon T. This bias is reflected in both codon usage and amino acid composition. The protein-coding genes in the D. antiqua mitochondrial genome prefer to use the codon UUA (Leu. All of the tRNAs have the typical clover-leaf structure, except for tRNASer(AGN that does not contain the dihydrouridine (DHU arm like in many other insects. There are 7 mismatches with U-U in the tRNAs. The location and structure of the two rRNAs are conservative and stable when compared with other insects. The control region between 12S rRNA and tRNAIle has the highest A+T content of 93.7% in the D. antiqua mitochondrial genome. The control region includes three kinds of special regions, two highly conserved poly-T stretches, a (TAn stretch and several G(AnT structures considered important elements related to replication and transcription. The nucleotide sequences of 13 protein-coding genes are used to construct the phylogenetics of 26 representative Dipteran species. Both maximum likelihood and Bayesian inference analyses suggest a closer relationship of D. antiqua in Anthomyiidae with Calliphoridae

  17. The Complete Mitochondrial Genome of Delia antiqua and Its Implications in Dipteran Phylogenetics.

    Science.gov (United States)

    Zhang, Nai-Xin; Yu, Guo; Li, Ting-Jing; He, Qi-Yi; Zhou, Yong; Si, Feng-Ling; Ren, Shuang; Chen, Bin

    2015-01-01

    Delia antiqua is a major underground agricultural pest widely distributed in Asia, Europe and North America. In this study, we sequenced and annotated the complete mitochondrial genome of this species, which is the first report of complete mitochondrial genome in the family Anthomyiidae. This genome is a double-stranded circular molecule with a length of 16,141 bp and an A+T content of 78.5%. It contains 37 genes (13 protein-coding genes, 22 tRNAs and 2 rRNAs) and a non-coding A+T rich region or control region. The mitochondrial genome of Delia antiqua presents a clear bias in nucleotide composition with a positive AT-skew and a negative GC-skew. All of the 13 protein-coding genes use ATN as an initiation codon except for the COI gene that starts with ATCA. Most protein-coding genes have complete termination codons but COII and ND5 that have the incomplete termination codon T. This bias is reflected in both codon usage and amino acid composition. The protein-coding genes in the D. antiqua mitochondrial genome prefer to use the codon UUA (Leu). All of the tRNAs have the typical clover-leaf structure, except for tRNASer(AGN) that does not contain the dihydrouridine (DHU) arm like in many other insects. There are 7 mismatches with U-U in the tRNAs. The location and structure of the two rRNAs are conservative and stable when compared with other insects. The control region between 12S rRNA and tRNAIle has the highest A+T content of 93.7% in the D. antiqua mitochondrial genome. The control region includes three kinds of special regions, two highly conserved poly-T stretches, a (TA)n stretch and several G(A)nT structures considered important elements related to replication and transcription. The nucleotide sequences of 13 protein-coding genes are used to construct the phylogenetics of 26 representative Dipteran species. Both maximum likelihood and Bayesian inference analyses suggest a closer relationship of D. antiqua in Anthomyiidae with Calliphoridae, Calliphoridae is a

  18. Functional Genomic Analysis of Human Mitochondrial RNA Processing

    Directory of Open Access Journals (Sweden)

    Ashley R. Wolf

    2014-05-01

    Full Text Available Both strands of human mtDNA are transcribed in continuous, multigenic units that are cleaved into the mature rRNAs, tRNAs, and mRNAs required for respiratory chain biogenesis. We sought to systematically identify nuclear-encoded proteins that contribute to processing of mtRNAs within the organelle. First, we devised and validated a multiplex MitoString assay that quantitates 27 mature and precursor mtDNA transcripts. Second, we applied MitoString profiling to evaluate the impact of silencing each of 107 mitochondrial-localized, predicted RNA-binding proteins. With the resulting data set, we rediscovered the roles of recently identified RNA-processing enzymes, detected unanticipated roles of known disease genes in RNA processing, and identified new regulatory factors. We demonstrate that one such factor, FASTKD4, modulates the half-lives of a subset of mt-mRNAs and associates with mtRNAs in vivo. MitoString profiling may be useful for diagnosing and deciphering the pathogenesis of mtDNA disorders.

  19. A molecular phylogeny of Hemiptera inferred from mitochondrial genome sequences.

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    Nan Song

    Full Text Available Classically, Hemiptera is comprised of two suborders: Homoptera and Heteroptera. Homoptera includes Cicadomorpha, Fulgoromorpha and Sternorrhyncha. However, according to previous molecular phylogenetic studies based on 18S rDNA, Fulgoromorpha has a closer relationship to Heteroptera than to other hemipterans, leaving Homoptera as paraphyletic. Therefore, the position of Fulgoromorpha is important for studying phylogenetic structure of Hemiptera. We inferred the evolutionary affiliations of twenty-five superfamilies of Hemiptera using mitochondrial protein-coding genes and rRNAs. We sequenced three mitogenomes, from Pyrops candelaria, Lycorma delicatula and Ricania marginalis, representing two additional families in Fulgoromorpha. Pyrops and Lycorma are representatives of an additional major family Fulgoridae in Fulgoromorpha, whereas Ricania is a second representative of the highly derived clade Ricaniidae. The organization and size of these mitogenomes are similar to those of the sequenced fulgoroid species. Our consensus phylogeny of Hemiptera largely supported the relationships (((Fulgoromorpha,Sternorrhyncha,Cicadomorpha,Heteroptera, and thus supported the classic phylogeny of Hemiptera. Selection of optimal evolutionary models (exclusion and inclusion of two rRNA genes or of third codon positions of protein-coding genes demonstrated that rapidly evolving and saturated sites should be removed from the analyses.

  20. The mitochondrial genome of the entomophagous endoparasite Xenosvesparum (Insecta: Strepsiptera)

    Energy Technology Data Exchange (ETDEWEB)

    Carapelli, Antonio; Vannini, Laura; Nardi, Francesco; Boore,Jeffrey L.; Beani, Laura; Dallai, Romano; Frati, Francesco

    2005-12-01

    In this study, the nearly complete sequence (14,519 bp) of the mitochondrial DNA (mtDNA) of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera) is described. All protein coding genes (PCGs) are in the arrangement known to be ancestral for insects, but three tRNA genes (trnA, trnS(gcu), and trnL(uag)) have transposed to derived positions and there are three tandem copies of trnH, each of which is potentially functional. All of these rearrangements except for that of trnL(uag) is within the short span between nad3 and nad4 and there are numerous blocks of unassignable sequence in this region, perhaps as remnants of larger scale predisposing rearrangements. X. vesparum mtDNA nucleotide composition is strongly biased toward As and Ts, as is typical for insect mtDNAs. There is also significant strand skew in the distribution of these nucleotides, with the J-strand being richer in A than T and in C than G, and the N-strand showing an opposite skew for complementary pairs of nucleotides. The hypothetical secondary structure of the 16S rRNA has also been reconstructed, obtaining a structural model similar to that of other insects.

  1. Mutation and selection cause codon usage and bias in mitochondrial genomes of ribbon worms (Nemertea).

    Science.gov (United States)

    Chen, Haixia; Sun, Shichun; Norenburg, Jon L; Sundberg, Per

    2014-01-01

    The phenomenon of codon usage bias is known to exist in many genomes and it is mainly determined by mutation and selection. To understand the patterns of codon usage in nemertean mitochondrial genomes, we use bioinformatic approaches to analyze the protein-coding sequences of eight nemertean species. Neutrality analysis did not find a significant correlation between GC12 and GC3. ENc-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENc values are below it. ENc-plot suggested that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally and we propose that codons containing A or U at third position are used preferentially in nemertean species, regardless of whether corresponding tRNAs are encoded in the mitochondrial DNA. Context-dependent analysis indicated that the nucleotide at the second codon position slightly affects synonymous codon choices. These results suggested that mutational and selection forces are probably acting to codon usage bias in nemertean mitochondrial genomes.

  2. Mutation and selection cause codon usage and bias in mitochondrial genomes of ribbon worms (Nemertea.

    Directory of Open Access Journals (Sweden)

    Haixia Chen

    Full Text Available The phenomenon of codon usage bias is known to exist in many genomes and it is mainly determined by mutation and selection. To understand the patterns of codon usage in nemertean mitochondrial genomes, we use bioinformatic approaches to analyze the protein-coding sequences of eight nemertean species. Neutrality analysis did not find a significant correlation between GC12 and GC3. ENc-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENc values are below it. ENc-plot suggested that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2 analysis showed that GC and AT were not used proportionally and we propose that codons containing A or U at third position are used preferentially in nemertean species, regardless of whether corresponding tRNAs are encoded in the mitochondrial DNA. Context-dependent analysis indicated that the nucleotide at the second codon position slightly affects synonymous codon choices. These results suggested that mutational and selection forces are probably acting to codon usage bias in nemertean mitochondrial genomes.

  3. Mitochondrial genome sequences of Artemia tibetiana and Artemia urmiana: assessing molecular changes for high plateau adaptation.

    Science.gov (United States)

    Zhang, Hangxiao; Luo, Qibin; Sun, Jing; Liu, Fei; Wu, Gang; Yu, Jun; Wang, Weiwei

    2013-05-01

    Brine shrimps, Artemia (Crustacea, Anostraca), inhabit hypersaline environments and have a broad geographical distribution from sea level to high plateaus. Artemia therefore possess significant genetic diversity, which gives them their outstanding adaptability. To understand this remarkable plasticity, we sequenced the mitochondrial genomes of two Artemia tibetiana isolates from the Tibetan Plateau in China and one Artemia urmiana isolate from Lake Urmia in Iran and compared them with the genome of a low-altitude Artemia, A. franciscana. We compared the ratio of the rate of nonsynonymous (Ka) and synonymous (Ks) substitutions (Ka/Ks ratio) in the mitochondrial protein-coding gene sequences and found that atp8 had the highest Ka/Ks ratios in comparisons of A. franciscana with either A. tibetiana or A. urmiana and that atp6 had the highest Ka/Ks ratio between A. tibetiana and A. urmiana. Atp6 may have experienced strong selective pressure for high-altitude adaptation because although A. tibetiana and A. urmiana are closely related they live at different altitudes. We identified two extended termination-associated sequences and three conserved sequence blocks in the D-loop region of the mitochondrial genomes. We propose that sequence variations in the D-loop region and in the subunits of the respiratory chain complexes independently or collectively contribute to the adaptation of Artemia to different altitudes.

  4. [Sequencing and analysis of the complete mitochondrial genome of the King Cobra, Ophiophagus hannah (Serpents: Elapidae)].

    Science.gov (United States)

    Chen, Nian; Lai, Xiao-Ping

    2010-07-01

    We obtained the complete mitochondrial genome of King Cobra(GenBank accession number: EU_921899) by Ex Taq-PCR, TA-cloning and primer-walking methods. This genome is very similar to other vertebrate, which is 17 267 bp in length and encodes 38 genes (including 13 protein-coding, 2 ribosomal RNA and 23 transfer RNA genes) and two long non-coding regions. The duplication of tRNA-Ile gene forms a new mitochondrial gene rearrangement model. Eight tRNA genes and one protein genes were transcribed from L strand, and the other genes were transcribed genes from H strand. Genes on the H strand show a fairly similar content of Adenosine and Thymine respectively, whereas those on the L strand have higher proportion of A than T. Combined rDNA sequence data (12S+16S rRNA) were used to reconstruct the phylogeny of 21 snake species for which complete mitochondrial genome sequences were available in the public databases. This large data set and an appropriate range of outgroup taxa demonstrated that Elapidae is more closely related to colubridae than viperidae, which supports the traditional viewpoints.

  5. The first complete mitochondrial genome sequences of Amblypygi (Chelicerata: Arachnida) reveal conservation of the ancestral arthropod gene order.

    Science.gov (United States)

    Fahrein, Kathrin; Masta, Susan E; Podsiadlowski, Lars

    2009-05-01

    Amblypygi (whip spiders) are terrestrial chelicerates inhabiting the subtropics and tropics. In morphological and rRNA-based phylogenetic analyses, Amblypygi cluster with Uropygi (whip scorpions) and Araneae (spiders) to form the taxon Tetrapulmonata, but there is controversy regarding the interrelationship of these three taxa. Mitochondrial genomes provide an additional large data set of phylogenetic information (sequences, gene order, RNA secondary structure), but in arachnids, mitochondrial genome data are missing for some of the major orders. In the course of an ongoing project concerning arachnid mitochondrial genomics, we present the first two complete mitochondrial genomes from Amblypygi. Both genomes were found to be typical circular duplex DNA molecules with all 37 genes usually present in bilaterian mitochondrial genomes. In both species, gene order is identical to that of Limulus polyphemus (Xiphosura), which is assumed to reflect the putative arthropod ground pattern. All tRNA gene sequences have the potential to fold into structures that are typical of metazoan mitochondrial tRNAs, except for tRNA-Ala, which lacks the D arm in both amblypygids, suggesting the loss of this feature early in amblypygid evolution. Phylogenetic analysis resulted in weak support for Uropygi being the sister group of Amblypygi.

  6. Complex repeat structures and novel features in the mitochondrial genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana.

    Science.gov (United States)

    Oudot-Le Secq, Marie-Pierre; Green, Beverley R

    2011-05-01

    The mitochondrial genome of the raphid pennate diatom Phaeodactylum tricornutum has several novel features compared with the mitochondrial genomes of the centric diatom Thalassiosira pseudonana and the araphid pennate diatom Synedra acus. It is almost double the size (77,356 bp) due to a 35,454 bp sequence block consisting of an elaborate combination of direct repeats, making it the largest stramenopile (heterokont) mitochondrial genome known. In addition, the cox1 gene has a +1 translational frameshift involving Pro codons CCC and CCT, the first translational frameshift to be detected in an algal mitochondrial genome. The nad9 and rps14 genes are fused by the insertion of an in-frame sequence and cotranscribed. The nad11 gene is split into two parts corresponding to the FeS and molybdate-binding domains, but both parts are still on the mitochondrial genome, in contrast to the brown algae where the second domain appears to have been transferred to the nucleus. In contrast to P. tricornutum, the repeat region of T. pseudonana consists of a much smaller 4790 bp string of almost identical double-hairpin elements, evidence of slipped-strand mispairing and active gene conversion. The diatom mitochondrial genomes have undergone considerable gene rearrangement since the three lineages of diatoms diverged, but all three have kept their repeat regions segregated from their relatively compact coding regions.

  7. Heteroplasmy in the mitochondrial genomes of human lice and ticks revealed by high throughput sequencing.

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    Haoyu Xiong

    Full Text Available The typical mitochondrial (mt genomes of bilateral animals consist of 37 genes on a single circular chromosome. The mt genomes of the human body louse, Pediculus humanus, and the human head louse, Pediculus capitis, however, are extensively fragmented and contain 20 minichromosomes, with one to three genes on each minichromosome. Heteroplasmy, i.e. nucleotide polymorphisms in the mt genome within individuals, has been shown to be significantly higher in the mt cox1 gene of human lice than in humans and other animals that have the typical mt genomes. To understand whether the extent of heteroplasmy in human lice is associated with mt genome fragmentation, we sequenced the entire coding regions of all of the mt minichromosomes of six human body lice and six human head lice from Ethiopia, China and France with an Illumina HiSeq platform. For comparison, we also sequenced the entire coding regions of the mt genomes of seven species of ticks, which have the typical mitochondrial genome organization of bilateral animals. We found that the level of heteroplasmy varies significantly both among the human lice and among the ticks. The human lice from Ethiopia have significantly higher level of heteroplasmy than those from China and France (Pt<0.05. The tick, Amblyomma cajennense, has significantly higher level of heteroplasmy than other ticks (Pt<0.05. Our results indicate that heteroplasmy level can be substantially variable within a species and among closely related species, and does not appear to be determined by single factors such as genome fragmentation.

  8. Complete genomes of Hairstreak butterflies, their speciation, and nucleo-mitochondrial incongruence.

    Science.gov (United States)

    Cong, Qian; Shen, Jinhui; Borek, Dominika; Robbins, Robert K; Otwinowski, Zbyszek; Grishin, Nick V

    2016-04-28

    Comparison of complete genomes of closely related species enables research on speciation and how phenotype is determined by genotype. Lepidoptera, an insect order of 150,000 species with diverse phenotypes, is well-suited for such comparative genomics studies if new genomes, which cover additional Lepidoptera families are acquired. We report a 729 Mbp genome assembly of the Calycopis cecrops, the first genome from the family Lycaenidae and the largest available Lepidoptera genome. As detritivore, Calycopis shows expansion in detoxification and digestion enzymes. We further obtained complete genomes of 8 Calycopis specimens: 3 C. cecrops and 5 C. isobeon, including a dry specimen stored in the museum for 30 years. The two species differ subtly in phenotype and cannot be differentiated by mitochondrial DNA. However, nuclear genomes revealed a deep split between them. Genes that can clearly separate the two species (speciation hotspots) mostly pertain to circadian clock, mating behavior, transcription regulation, development and cytoskeleton. The speciation hotspots and their function significantly overlap with those we previously found in Pterourus, suggesting common speciation mechanisms in these butterflies.

  9. Identification of the most informative regions of the mitochondrial genome for phylogenetic and coalescent analyses.

    Science.gov (United States)

    Non, A L; Kitchen, A; Mulligan, C J

    2007-09-01

    Analysis of complete mitochondrial genome sequences is becoming increasingly common in genetic studies. The availability of full genome datasets enables an analysis of the information content distributed throughout the mitochondrial genome in order to optimize the research design of future evolutionary studies. The goal of our study was to identify informative regions of the human mitochondrial genome using two criteria: (1) accurate reconstruction of a phylogeny and (2) consistent estimates of time to most recent common ancestor (TMRCA). We created two series of datasets by deleting individual genes of varied length and by deleting 10 equal-size fragments throughout the coding region. Phylogenies were statistically compared to the full-coding-region tree, while coalescent methods were used to estimate the TMRCA and associated credible intervals. Individual fragments important for maintaining a phylogeny similar to the full-coding-region tree encompassed bp 577-2122 and 11,399-16,023, including all or part of 12S rRNA, 16S rRNA, ND4, ND5, ND6, and cytb. The control region only tree was the most poorly resolved with the majority of the tree manifest as an unresolved polytomy. Coalescent estimates of TMRCA were less sensitive to removal of any particular fragment(s) than reconstruction of a consistent phylogeny. Overall, we discovered that half the genome, i.e., bp 3669-11,398, could be removed with no significant change in the phylogeny (p(AU)=0.077) while still maintaining overlap of TMRCA 95% credible intervals. Thus, sequencing a contiguous fragment from bp 11,399 through the control region to bp 3668 would create a dataset that optimizes the information necessary for phylogenetic and coalescent analyses and also takes advantage of the wealth of data already available on the control region.

  10. The Complete Sequence of the Mitochondrial Genome of the Chamberednautilus (Mollusca: Cephalopoda)

    Energy Technology Data Exchange (ETDEWEB)

    Boore, Jeffrey L.

    2005-12-01

    Background: Mitochondria contain small genomes that arephysically separate from those of nuclei. Their comparison serves as amodel system for understanding the processes of genome evolution.Although complete mitochondrial genome sequences have been reported formore than 600 animals, the taxonomic sampling is highly biased towardvertebrates and arthropods, leaving much of the diversity yetuncharacterized. Results: The mitochondrial genome of a cephalopodmollusk, the Chambered Nautilus, is 16,258 nts in length and 59.5 percentA+T, both values that are typical of animal mitochondrial genomes. Itcontains the 37 genes that are typical for animal mtDNAs, with 15 on oneDNA strand and 22 on the other. The arrangement of these genes can bederived from that of the distantly related Katharina tunicata (Mollusca:Polyplacophora) by a switch in position of two large blocks of genes andtranspositions of four tRNA genes. There is strong skew in thedistribution of nucleotides between the two strands. There are an unusualnumber of non-coding regions and their function, if any, is not known;however, several of these demark abrupt shifts in nucleotide skew,suggesting that they may play roles in transcription and/or replication.One of the non-coding regions contains multiple repeats of a tRNA-likesequence. Some of the tRNA genes appear to overlap on the same strand,but this could be resolved if the polycistron were cleaved at thebeginning of the downstream gene, followed by polyadenylation of theproduct of the upstream gene to form a fully paired structure.Conclusions: Nautilus sp. mtDNA contains an expected gene content thathas experienced few rearrangements since the evolutionary split betweencephalopods and polyplacophorans. It contains an unusual number ofnon-coding regions, especially considering that these otherwise often aregenerated by the same processes that produce gene rearrangements. Thisappears to be yet another case where polyadenylation of mitochondrialtRNAs restores

  11. The complete mitochondrial genome of Channa argus, Channa maculata and hybrid snakehead fish [Channa maculata (♀) × Channa argus (♂)].

    Science.gov (United States)

    Zhu, Shu-Ren; Ma, Ke-Yi; Xing, Zhi-Jun; Xie, Nan; Wang, Yu-Xi; Wang, Qun; Li, Jia-Le

    2013-06-01

    We sequenced and characterized the complete mitochondrial genome of Channa argus, Channa maculata and their hybrid [C. maculata (♀) and C. argus (♂)]. All the three mitochondrial genomes contained the typical complement of 13 protein-coding genes, 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs) and 1 control region. The entire mitochondrial DNA (mtDNA) molecule of C. maculata was 16,559 bp long while the complete mtDNA molecule of C. argus and hybrid snakehead fish was 16,558 bp long. This is the first report on the complete mitogenome sequence of C. maculata and hybrid snakehead fish.

  12. The mitochondrial genome of Iberobaenia (Coleoptera: Iberobaeniidae): first rearrangement of protein-coding genes in the beetles.

    Science.gov (United States)

    Andujar, Carmelo; Arribas, Paula; Linard, Benjamin; Kundrata, Robin; Bocak, Ladislav; Vogler, Alfried P

    2017-03-01

    The complete mitochondrial genome of the recently discovered beetle family Iberobaeniidae is described and compared with known coleopteran mitogenomes. The mitochondrial sequence was obtained by shotgun metagenomic sequencing using the Illumina Miseq technology and resulted in an average coverage of 130 × and a minimum coverage of 35×. The mitochondrial genome of Iberobaeniidae includes 13 protein-coding genes, 2 rRNAs, 22 tRNAs genes, and 1 putative control region, and showed a unique rearrangement of protein-coding genes. This is the first rearrangement affecting the relative position of protein-coding and ribosomal genes reported for the order Coleoptera.

  13. Octocoral mitochondrial genomes provide insights into the phylogenetic history of gene order rearrangements, order reversals, and cnidarian phylogenetics.

    Science.gov (United States)

    Figueroa, Diego F; Baco, Amy R

    2014-12-24

    We use full mitochondrial genomes to test the robustness of the phylogeny of the Octocorallia, to determine the evolutionary pathway for the five known mitochondrial gene rearrangements in octocorals, and to test the suitability of using mitochondrial genomes for higher taxonomic-level phylogenetic reconstructions. Our phylogeny supports three major divisions within the Octocorallia and show that Paragorgiidae is paraphyletic, with Sibogagorgia forming a sister branch to the Coralliidae. Furthermore, Sibogagorgia cauliflora has what is presumed to be the ancestral gene order in octocorals, but the presence of a pair of inverted repeat sequences suggest that this gene order was not conserved but rather evolved back to this apparent ancestral state. Based on this we recommend the resurrection of the family Sibogagorgiidae to fix the paraphyly of the Paragorgiidae. This is the first study to show that in the Octocorallia, mitochondrial gene orders have evolved back to an ancestral state after going through a gene rearrangement, with at least one of the gene orders evolving independently in different lineages. A number of studies have used gene boundaries to determine the type of mitochondrial gene arrangement present. However, our findings suggest that this method known as gene junction screening may miss evolutionary reversals. Additionally, substitution saturation analysis demonstrates that while whole mitochondrial genomes can be used effectively for phylogenetic analyses within Octocorallia, their utility at higher taxonomic levels within Cnidaria is inadequate. Therefore for phylogenetic reconstruction at taxonomic levels higher than subclass within the Cnidaria, nuclear genes will be required, even when whole mitochondrial genomes are available.

  14. Strikingly Bacteria-Like and Gene-Rich Mitochondrial Genomes throughout Jakobid Protists

    Science.gov (United States)

    Burger, Gertraud; Gray, Michael W.; Forget, Lise; Lang, B. Franz

    2013-01-01

    The most bacteria-like mitochondrial genome known is that of the jakobid flagellate Reclinomonas americana NZ. This genome also encodes the largest known gene set among mitochondrial DNAs (mtDNAs), including the RNA subunit of RNase P (transfer RNA processing), a reduced form of transfer–messenger RNA (translational control), and a four-subunit bacteria-like RNA polymerase, which in other eukaryotes is substituted by a nucleus-encoded, single-subunit, phage-like enzyme. Further, protein-coding genes are preceded by potential Shine–Dalgarno translation initiation motifs. Whether similarly ancestral mitochondrial characters also exist in relatives of R. americana NZ is unknown. Here, we report a comparative analysis of nine mtDNAs from five distant jakobid genera: Andalucia, Histiona, Jakoba, Reclinomonas, and Seculamonas. We find that Andalucia godoyi has an even larger mtDNA gene complement than R. americana NZ. The extra genes are rpl35 (a large subunit mitoribosomal protein) and cox15 (involved in cytochrome oxidase assembly), which are nucleus encoded throughout other eukaryotes. Andalucia cox15 is strikingly similar to its homolog in the free-living α-proteobacterium Tistrella mobilis. Similarly, a long, highly conserved gene cluster in jakobid mtDNAs, which is a clear vestige of prokaryotic operons, displays a gene order more closely resembling that in free-living α-proteobacteria than in Rickettsiales species. Although jakobid mtDNAs, overall, are characterized by bacteria-like features, they also display a few remarkably divergent characters, such as 3′-tRNA editing in Seculamonas ecuadoriensis and genome linearization in Jakoba libera. Phylogenetic analysis with mtDNA-encoded proteins strongly supports monophyly of jakobids with Andalucia as the deepest divergence. However, it remains unclear which α-proteobacterial group is the closest mitochondrial relative. PMID:23335123

  15. The mitochondrial genome of the pufferfish, Fugu rubripes, and ordinal teleostean relationships.

    Science.gov (United States)

    Elmerot, Christian; Arnason, Ulfur; Gojobori, Takashi; Janke, Axel

    2002-08-07

    The small nuclear genome of the pufferfish, Fugu rubripes (order Tetraodontiformes), makes this species highly interesting for genome research. In order to establish the phylogenetic position of the Tetraodontiformes relative to other teleostean orders that might also have a reduced nuclear genome size, we have sequenced the mitochondrial (mt) genome of the pufferfish. The gene order, nucleotide composition and evolutionary rate of the mt genome of the fugu correspond to those of other teleosts. This suggests that the evolution of this genome has not been affected by the processes that led to the dramatic reduction of the size of the nuclear genome of the fugu. The phylogenetic analyses, which were based on the concatenated amino acid sequences of twelve protein-coding mt genes, placed the fugu among the percomorphs. The affinities between the Tetraodontiformes and either the Perciformes or the Zeiformes were limited, however. The common notion of a separate euteleostean clade remained unsupported. The analyses did not support the traditional systematic understanding that the Clupeiformes constitute a basal teleostean lineage. In addition the findings strongly suggest that three teleostean orders, the Perciformes, Zeiformes and Scorpaeniformes, are paraphyletic.

  16. The complete mitochondrial genome of the enigmatic bigheadedturtle (Platysternon): description of unusual genomic features and thereconciliation of phylogenetic hypotheses based on mitochondrial andnuclear DNA

    Energy Technology Data Exchange (ETDEWEB)

    Parham, James F.; Feldman, Chris R.; Boore, Jeffrey L.

    2005-12-28

    The big-headed turtle (Platysternon megacephalum) from east Asia is the sole living representative of a poorly-studied turtle lineage (Platysternidae). It has no close living relatives, and its phylogenetic position within turtles is one of the outstanding controversies in turtle systematics. Platysternon was traditionally considered to be close to snapping turtles (Chelydridae) based on some studies of its morphology and mitochondrial (mt) DNA, however, other studies of morphology and nuclear (nu) DNA do not support that hypothesis. We sequenced the complete mt genome of Platysternon and the nearly complete mt genomes of two other relevant turtles and compared them to turtle mt genomes from the literature to form the largest molecular dataset used to date to address this issue. The resulting phylogeny robustly rejects the placement of Platysternon with Chelydridae, but instead shows that it is a member of the Testudinoidea, a diverse, nearly globally-distributed group that includes pond turtles and tortoises. We also discovered that Platysternon mtDNA has large-scale gene rearrangements and possesses two, nearly identical, control regions, features that distinguish it from all other studied turtles. Our study robustly determines the phylogenetic placement of Platysternon and provides a well-resolved outline of major turtle lineages, while demonstrating the significantly greater resolving power of comparing large amounts of mt sequence over that of short fragments. Earlier phylogenies placing Platysternon with chelydrids required a temporal gap in the fossil record that is now unnecessary. The duplicated control regions and gene rearrangements of the Platysternon mt DNA probably resulted from the duplication of part of the genome and then the subsequent loss of redundant genes. Although it is possible that having two control regions may provide some advantage, explaining why the control regions would be maintained while some of the duplicated genes were eroded

  17. Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda)

    Science.gov (United States)

    Minton, Russell L.; Cruz, Marco A. Martinez; Farman, Mark L.; Perez, Kathryn E.

    2016-01-01

    Abstract Helicoidea is a diverse group of land snails with a global distribution. While much is known regarding the relationships of helicoid taxa, comparatively little is known about the evolution of the mitochondrial genome in the superfamily. We sequenced two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 representing the first such data from the helicoid family Polygyridae, and used them in an evolutionary analysis of mitogenomic gene order. We found the mitochondrial genome of Praticolella mexicana to be 14,008 bp in size, possessing the typical 37 metazoan genes. Multiple alternate stop codons are used, as are incomplete stop codons. Mitogenome size and nucleotide content is consistent with other helicoid species. Our analysis of gene order suggested that Helicoidea has undergone four mitochondrial rearrangements in the past. Two rearrangements were limited to tRNA genes only, and two involved protein coding genes. PMID:27833437

  18. Complete mitochondrial genome of the Nigeria-Cameroon chimpanzee, Pan troglodytes ellioti (Primates: Hominidae).

    Science.gov (United States)

    Wang, Bao-Hua; Wang, Yin-Hua; Tang, Ming-Gui; Chai, Hai-Xia; Xuan, Xing-Wei; Guo, Wei-Yan; Yang, Mu; Pu, Jian-Yi

    2016-05-01

    Chimpanzees are especially suited to teach us about ourselves, both in terms of their similarities and differences with human, and such important similarities and differences have also been noted for the incidence and severity of several major human diseases. In the present work, we report the entire mitochondrial genome of the Nigeria-Cameroon chimpanzee (Pan troglodytes ellioti) for the first time. Results shows that this mitogenome is 16,559 bp long and consists of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 putative non-coding region (D-loop region). The genomic organization and gene order are the same as other Chimpanzees. The whole nucleotide base composition is 31.1% of A, 30.7% of C, 12.9% G, and 25.3% T, with a slight A+T bias of 56.4%. Most of the genes are encoded on H-strand, except for the ND6 subunit gene and 8 tRNA genes. The complete mitochondrial genome sequence reported here provides useful genetic information for P. t. ellioti, and will further contribute to the comparative genomics studies in primates.

  19. The complete sequence and gene organization of the mitochondrial genome of the gadilid scaphopod Siphonondentalium lobatum (Mollusca).

    Science.gov (United States)

    Dreyer, Hermann; Steiner, Gerhard

    2004-05-01

    Comparisons of mitochondrial gene sequences and gene arrangements can be informative for reconstructing high-level phylogenetic relationships. We determined the complete sequence of the mitochondrial genome of Siphonodentalium lobatum, (Mollusca, Scaphopoda). With only 13,932 bases, it is the shortest molluscan mitochondrial genome reported so far. The genome contains the usual 13 protein-coding genes, two rRNA and 22 tRNA genes. The ATPase subunit 8 gene is exceptionally short. Several transfer RNAs show truncated TpsiC arms or DHU arms. The gene arrangement of S. lobatum is markedly different from all other known molluscan mitochondrial genomes and shows low similarity even to an unpublished gene order of a dentaliid scaphopod. Phylogenetic analyses of all available complete molluscan mitochondrial genomes based on amino acid sequences of 11 protein-coding genes yield trees with low support for the basal branches. None of the traditionally accepted molluscan taxa and phylogenies are recovered in all analyses, except for the euthyneuran Gastropoda. S. lobatum appears as the sister taxon to two of the three bivalve species. We conclude that the deep molluscan phylogeny is probably beyond the resolution of mitochondrial protein sequences. Moreover, assessing the phylogenetic signal in gene order data requires a much larger taxon sample than is currently available, given the exceptional diversity of this character set in the Mollusca.

  20. The complete mitochondrial genome and novel gene arrangement of the unique-headed bug Stenopirates sp. (Hemiptera: Enicocephalidae.

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    Hu Li

    Full Text Available Many of true bugs are important insect pests to cultivated crops and some are important vectors of human diseases, but few cladistic analyses have addressed relationships among the seven infraorders of Heteroptera. The Enicocephalomorpha and Nepomorpha are consider the basal groups of Heteroptera, but the basal-most lineage remains unresolved. Here we report the mitochondrial genome of the unique-headed bug Stenopirates sp., the first mitochondrial genome sequenced from Enicocephalomorpha. The Stenopirates sp. mitochondrial genome is a typical circular DNA molecule of 15, 384 bp in length, and contains 37 genes and a large non-coding fragment. The gene order differs substantially from other known insect mitochondrial genomes, with rearrangements of both tRNA genes and protein-coding genes. The overall AT content (82.5% of Stenopirates sp. is the highest among all the known heteropteran mitochondrial genomes. The strand bias is consistent with other true bugs with negative GC-skew and positive AT-skew for the J-strand. The heteropteran mitochondrial atp8 exhibits the highest evolutionary rate, whereas cox1 appears to have the lowest rate. Furthermore, a negative correlation was observed between the variation of nucleotide substitutions and the GC content of each protein-coding gene. A microsatellite was identified in the putative control region. Finally, phylogenetic reconstruction suggests that Enicocephalomorpha is the sister group to all the remaining Heteroptera.

  1. Selective enrichment and sequencing of whole mitochondrial genomes in the presence of nuclear encoded mitochondrial pseudogenes (numts.

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    Jonci N Wolff

    Full Text Available Numts are an integral component of many eukaryote genomes offering a snapshot of the evolutionary process that led from the incorporation of an α-proteobacterium into a larger eukaryotic cell some 1.8 billion years ago. Although numt sequence can be harnessed as molecular marker, these sequences often remain unidentified and are mistaken for genuine mtDNA leading to erroneous interpretation of mtDNA data sets. It is therefore indispensable that during the process of amplifying and sequencing mitochondrial genes, preventive measures are taken to ensure the exclusion of numts to guarantee the recovery of genuine mtDNA. This applies to mtDNA analyses in general but especially to studies where mtDNAs are sequenced de novo as the launch pad for subsequent mtDNA-based research. By using a combination of dilution series and nested rolling circle amplification (RCA, we present a novel strategy to selectively amplify mtDNA and exclude the amplification of numt sequence. We have successfully applied this strategy to de novo sequence the mtDNA of the Black Field Cricket Teleogryllus commodus, a species known to contain numts. Aligning our assembled sequence to the reference genome of Teleogryllus emma (GenBank EU557269.1 led to the identification of a numt sequence in the reference sequence. This unexpected result further highlights the need of a reliable and accessible strategy to eliminate this source of error.

  2. The complete sequence of the mitochondrial genome of Nautilus macromphalus (Mollusca: Cephalopoda

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    Boore Jeffrey L

    2006-07-01

    Full Text Available Abstract Background Mitochondria contain small genomes that are physically separate from those of nuclei. Their comparison serves as a model system for understanding the processes of genome evolution. Although complete mitochondrial genome sequences have been reported for more than 600 animals, the taxonomic sampling is highly biased toward vertebrates and arthropods, leaving much of the diversity yet uncharacterized. Results The mitochondrial genome of the bellybutton nautilus, Nautilus macromphalus, a cephalopod mollusk, is 16,258 nts in length and 59.5% A+T, both values that are typical of animal mitochondrial genomes. It contains the 37 genes that are almost universally found in animal mtDNAs, with 15 on one DNA strand and 22 on the other. The arrangement of these genes can be derived from that of the distantly related Katharina tunicata (Mollusca: Polyplacophora by a switch in position of two large blocks of genes and transpositions of four tRNA genes. There is strong skew in the distribution of nucleotides between the two strands, and analysis of this yields insight into modes of transcription and replication. There is an unusual number of non-coding regions and their function, if any, is not known; however, several of these demark abrupt shifts in nucleotide skew, and there are several identical sequence elements at these junctions, suggesting that they may play roles in transcription and/or replication. One of the non-coding regions contains multiple repeats of a tRNA-like sequence. Some of the tRNA genes appear to overlap on the same strand, but this could be resolved if the polycistron were cleaved at the beginning of the downstream gene, followed by polyadenylation of the product of the upstream gene to form a fully paired structure. Conclusion Nautilus macromphalus mtDNA contains an expected gene content that has experienced few rearrangements since the evolutionary split between cephalopods and polyplacophorans. It contains an

  3. The complete mitochondrial genome of the sexual oribatid mite Steganacarus magnus: genome rearrangements and loss of tRNAs

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    Cameron Stephen L

    2008-11-01

    Full Text Available Abstract Background Complete mitochondrial (mt genomes and the gene rearrangements therein are increasingly used as molecular markers for investigating phylogenetic relationships, especially for elucidating deep splits. Contributing to the complete mt genomes of arthropods, especially Arachnida, available so far, we provide the first complete mt genome of a sarcoptiform mite species, the sexually reproducing oribatid mite Steganacarus magnus (Acari, Oribatida which was determined by sequencing of long PCR products. Results The mt genome of S. magnus lacks 16 tRNAs, only those for leucine, histidine, proline, tryptophan, glutamine and serine are present. Within those tRNAs only tRNA-His and tRNA-Pro have kept their original position, the others are translocated. Furthermore, the mt genome of S. magnus consists of 13,818 bp and it is composed of 13 protein-coding genes and two genes for the ribosomal RNA subunits that are typically found in metazoan mt genomes. The gene order in S. magnus differs from the hypothetical ancestral chelicerate arrangement as conserved in Limulus polyphemus: instead of nad1-rrnL-rrnS-LNR-nad2 (tRNAs excluded S. magnus is nad2-rrnL-nad1-rrnS-LNR. Phylogenetic analyses of a concatenated amino acid dataset of all mt protein-coding genes of 28 arthropod species suggest a sister-group relationship of sarcoptiform and prostigmatid mites (S. magnus and Leptotrombidium. Conclusion The mt gene arrangement of S. magnus differs from the hypothetical ground plan of arthropods and from that of other mites further contributing to the variety of mt gene arrangements found in Arachnida. The unexpected lack of tRNAs is enigmatic, probably showing that the loss of mt genes is an ongoing evolutionary process. For solving phylogenetic relationships of oribatid mite lineages and their position within Acari further complete mt genomes are needed.

  4. The complete sequence of the mitochondrial genome of Butomus umbellatus--a member of an early branching lineage of monocotyledons.

    Science.gov (United States)

    Cuenca, Argelia; Petersen, Gitte; Seberg, Ole

    2013-01-01

    In order to study the evolution of mitochondrial genomes in the early branching lineages of the monocotyledons, i.e., the Acorales and Alismatales, we are sequencing complete genomes from a suite of key taxa. As a starting point the present paper describes the mitochondrial genome of Butomus umbellatus (Butomaceae) based on next-generation sequencing data. The genome was assembled into a circular molecule, 450,826 bp in length. Coding sequences cover only 8.2% of the genome and include 28 protein coding genes, four rRNA genes, and 12 tRNA genes. Some of the tRNA genes and a 16S rRNA gene are transferred from the plastid genome. However, the total amount of recognized plastid sequences in the mitochondrial genome is only 1.5% and the amount of DNA transferred from the nucleus is also low. RNA editing is abundant and a total of 557 edited sites are predicted in the protein coding genes. Compared to the 40 angiosperm mitochondrial genomes sequenced to date, the GC content of the Butomus genome is uniquely high (49.1%). The overall similarity between the mitochondrial genomes of Butomus and Spirodela (Araceae), the closest relative yet sequenced, is low (less than 20%), and the two genomes differ in size by a factor 2. Gene order is also largely unconserved. However, based on its phylogenetic position within the core alismatids Butomus will serve as a good reference point for subsequent studies in the early branching lineages of the monocotyledons.

  5. Complete mitochondrial genome of the nerippe fritillary butterfly, Argynnis nerippe (Lepidoptera: Nymphalidae).

    Science.gov (United States)

    Kim, Min Jee; Jeong, Heon Cheon; Kim, Seong Ryeol; Kim, Iksoo

    2011-08-01

    The complete mitochondrial genome sequence of the nerippe fritillary butterfly, Argynnis nerippe, which is listed as an endangered species in Korea, is described with an emphasis on the A+T-rich region. The 15,140-bp long circular molecule consisted of 13 protein-coding genes, two rRNA genes, 22 tRNA genes and 1 control region, known in insect as the A+T-rich region, as found in typical metazoans. The 329-bp long A+T-rich region located between srRNA and tRNA(Met) possessed the highest A/T content (95.7%) than any other region of the genome. Along with the several conserved sequences found typically in the lepidopteran insects the genome contained one tRNA(Met)-like and tRNA(Leu)(UUR)-like sequence in the A+T-rich region.

  6. Description of the mitochondrial genome of the tree coral Dendrophyllia arbuscula (Anthozoa, Scleractinia).

    Science.gov (United States)

    Luz, Bruna Louise Pereira; Capel, Kátia Cristina Cruz; Stampar, Sérgio Nascimento; Kitahara, Marcelo Visentini

    2016-07-01

    Dendrophylliidae is one of the few monophyletic families within the Scleractinia that embraces zooxanthellate and azooxanthellate species represented by both solitary and colonial forms. Among the exclusively azooxanthellate genera, Dendrophyllia is reported worldwide from 1 to 1200 m deep. To date, although three complete mitochondrial (mt) genomes from representatives of the family are available, only that from Turbinaria peltata has been formally published. Here we describe the complete nucleotide sequence of the mt genome from Dendrophyllia arbuscula that is 19 069 bp in length and comprises two rDNAs, two tRNAs, and 13 protein-coding genes arranged in the canonical scleractinian mt gene order. No genes overlap, resulting in the presence of 18 intergenic spacers and one of the longest scleractinian mt genome sequenced to date.

  7. Characterization of complete mitochondrial genome of Dezhou donkey (Equus asinus) and evolutionary analysis.

    Science.gov (United States)

    Sun, Yan; Jiang, Qiang; Yang, Chunhong; Wang, Xiuge; Tian, Fang; Wang, Yinchao; Ma, Yong; Ju, Zhihua; Huang, Jinming; Zhou, Xiangshan; Zhong, Jifeng; Wang, Changfa

    2016-05-01

    Mitochondrial DNA (mtDNA) has been widely used in species identification and genetic diversification. Comparisons among mtDNAs of closely related species are valuable for phylogenetic studies. However, only the partial mtDNA Cytb gene and the D-loop sequences were used to analysis the phylogenetic relationship between donkey breeds due to lack of complete mitochondrial genome. Dezhou donkey, as a bigger somatotype ass, is one of Chinese domestic donkey breeds, and used by many places as breeding stock. To further investigate the phylogenetic relationship of Dezhou donkey with other breeds, the complete mtDNA was firstly sequenced and de novo assembled using next generation sequence data from total genomic DNA. The genome was 16,813 bp in length (NCBI submission number: KT182635) and contained 13 protein coding genes, 2 ribosomal RNA genes, 25 transfer RNA genes, and 1 control region. Based on the novel complete mtDNA sequence, the sequences of 13 protein coding genes and 2 ribosomal RNA genes were amplifying in other 2 Dezhou donkeys and 3 Yunnan donkeys, respectively. The pattern of genetic variation in horse, wild ass and domestic donkeys among these 15 genes indicated the sequence polymorphisms. The more accurate phylogenetic relationships of donkey species (Dezhou donkey, Yunnan donkey and previously published donkeys) were first obtained using the combined sequences of 12S rRNA+16S rRNA+13 protein-coding genes. Molecular-based phylogeny supported the hypothesis that Chinese domestic donkey breeds may have originated from Somali wild ass, not from Asian wild ass by analyzing mitochondrial genomes.

  8. Hybridization and mitochondrial genome introgression between Rana chensinensis and R. kukunoris.

    Science.gov (United States)

    Qi, Yin; Lu, Bin; Gao, Haiyan; Hu, Ping; Fu, Jinzhong

    2014-11-01

    Mitochondrial genome (mito-genome) introgression among metazoans is commonplace, and several biological processes may promote such introgression. We examined two proposed processes for the mito-genome introgression between Rana chensinensis and R. kukunoris: natural hybridization and sex-biased dispersal. We sampled 477 individuals from 28 sites in the potential hybrid zone in the western Tsinling Mountains. Mitochondrial gene (cyt-b) trees were used to examine the introgression events. Microsatellite DNA loci, cyt-b and morphological data were used to identify hybrids and to examine the extent of natural hybridization. We detected rampant bidirectional introgressions, both ancient and recent, between the two species. Furthermore, we found a wide hybrid zone, and frequent and asymmetric hybridization. The hybrid zone cline analysis revealed a clear mitochondrial-nuclear discordance; while most nuclear markers displayed similar and steep clines, cyt-b had a displaced cline centre and a more gradual and wider cline. We also detected strong and asymmetric historical maternal gene flow across the hybrid zone. This widespread hybridization and detected low mito-nuclear conflicts may, at least partially, explain the high frequency of introgression. Lastly, microsatellite data and population genetic methods were used to assess sex-biased dispersal. A weak pattern of female-biased dispersal was detected in both species, suggesting it may not play an important role in the observed introgression. Our data are consistent with the hybridization hypothesis, but support for the sex-biased dispersal hypothesis is weak. We further suggest that selective advantages of the R. kukunoris-type mito-genome in thermal adaptation may also contribute to the introgression between the two species. © 2014 John Wiley & Sons Ltd.

  9. Inheritance and organisation of the mitochondrial genome differ between two Saccharomyces yeasts

    DEFF Research Database (Denmark)

    Petersen, Randi Føns; Langkjær, Rikke Breinhold; Hvidtfeldt, J.;

    2002-01-01

    Petite-positive Saccharomyces yeasts can be roughly divided into the sensu stricto, including Saccharomyces cerevisiae, and sensu lato group, including Saccharomyces castellii; the latter was recently studied for transmission and the organisation of its mitochondrial genome. S. castellii mitochon......Petite-positive Saccharomyces yeasts can be roughly divided into the sensu stricto, including Saccharomyces cerevisiae, and sensu lato group, including Saccharomyces castellii; the latter was recently studied for transmission and the organisation of its mitochondrial genome. S. castellii...... mitochondrial molecules (mtDNA) carrying point mutations, which confer antibiotic resistance, behaved in genetic crosses as the corresponding point mutants of S. cerevisiae. While S. castellii generated spontaneous petite mutants in a similar way as S. cerevisiae, the petites exhibited a different inheritance...... pattern. In crosses with the wild type strains a majority of S. castellii petites was neutral, and the suppressivity in suppressive petites was never over 50%. The two yeasts also differ in organisation of their mtDNA molecules. The 25,753 bp sequence of S. castellii mtDNA was determined and the coding...

  10. Phylogenetic analyses of complete mitochondrial genome sequences suggest a basal divergence of the enigmatic rodent Anomalurus

    Directory of Open Access Journals (Sweden)

    Gissi Carmela

    2007-02-01

    Full Text Available Abstract Background Phylogenetic relationships between Lagomorpha, Rodentia and Primates and their allies (Euarchontoglires have long been debated. While it is now generally agreed that Rodentia constitutes a monophyletic sister-group of Lagomorpha and that this clade (Glires is sister to Primates and Dermoptera, higher-level relationships within Rodentia remain contentious. Results We have sequenced and performed extensive evolutionary analyses on the mitochondrial genome of the scaly-tailed flying squirrel Anomalurus sp., an enigmatic rodent whose phylogenetic affinities have been obscure and extensively debated. Our phylogenetic analyses of the coding regions of available complete mitochondrial genome sequences from Euarchontoglires suggest that Anomalurus is a sister taxon to the Hystricognathi, and that this clade represents the most basal divergence among sampled Rodentia. Bayesian dating methods incorporating a relaxed molecular clock provide divergence-time estimates which are consistently in agreement with the fossil record and which indicate a rapid radiation within Glires around 60 million years ago. Conclusion Taken together, the data presented provide a working hypothesis as to the phylogenetic placement of Anomalurus, underline the utility of mitochondrial sequences in the resolution of even relatively deep divergences and go some way to explaining the difficulty of conclusively resolving higher-level relationships within Glires with available data and methodologies.

  11. Differentiating sibling species of Zeugodacus caudatus (Insecta: Tephritidae) by complete