Genome duplication and mutations in ACE2 cause multicellular, fast-sedimenting phenotypes in evolved Saccharomyces cerevisiae.

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Oud, Bart; Guadalupe-Medina, Victor; Nijkamp, Jurgen F; de Ridder, Dick; Pronk, Jack T; van Maris, Antonius J A; Daran, Jean-Marc

2013-11-05

Laboratory evolution of the yeast Saccharomyces cerevisiae in bioreactor batch cultures yielded variants that grow as multicellular, fast-sedimenting clusters. Knowledge of the molecular basis of this phenomenon may contribute to the understanding of natural evolution of multicellularity and to manipulating cell sedimentation in laboratory and industrial applications of S. cerevisiae. Multicellular, fast-sedimenting lineages obtained from a haploid S. cerevisiae strain in two independent evolution experiments were analyzed by whole genome resequencing. The two evolved cell lines showed different frameshift mutations in a stretch of eight adenosines in ACE2, which encodes a transcriptional regulator involved in cell cycle control and mother-daughter cell separation. Introduction of the two ace2 mutant alleles into the haploid parental strain led to slow-sedimenting cell clusters that consisted of just a few cells, thus representing only a partial reconstruction of the evolved phenotype. In addition to single-nucleotide mutations, a whole-genome duplication event had occurred in both evolved multicellular strains. Construction of a diploid reference strain with two mutant ace2 alleles led to complete reconstruction of the multicellular-fast sedimenting phenotype. This study shows that whole-genome duplication and a frameshift mutation in ACE2 are sufficient to generate a fast-sedimenting, multicellular phenotype in S. cerevisiae. The nature of the ace2 mutations and their occurrence in two independent evolution experiments encompassing fewer than 500 generations of selective growth suggest that switching between unicellular and multicellular phenotypes may be relevant for competitiveness of S. cerevisiae in natural environments.

Network Analysis of Earth's Co-Evolving Geosphere and Biosphere

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Hazen, R. M.; Eleish, A.; Liu, C.; Morrison, S. M.; Meyer, M.; Consortium, K. D.

2017-12-01

A fundamental goal of Earth science is the deep understanding of Earth's dynamic, co-evolving geosphere and biosphere through deep time. Network analysis of geo- and bio- `big data' provides an interactive, quantitative, and predictive visualization framework to explore complex and otherwise hidden high-dimension features of diversity, distribution, and change in the evolution of Earth's geochemistry, mineralogy, paleobiology, and biochemistry [1]. Networks also facilitate quantitative comparison of different geological time periods, tectonic settings, and geographical regions, as well as different planets and moons, through network metrics, including density, centralization, diameter, and transitivity.We render networks by employing data related to geographical, paragenetic, environmental, or structural relationships among minerals, fossils, proteins, and microbial taxa. An important recent finding is that the topography of many networks reflects parameters not explicitly incorporated in constructing the network. For example, networks for minerals, fossils, and protein structures reveal embedded qualitative time axes, with additional network geometries possibly related to extinction and/or other punctuation events (see Figure). Other axes related to chemical activities and volatile fugacities, as well as pressure and/or depth of formation, may also emerge from network analysis. These patterns provide new insights into the way planets evolve, especially Earth's co-evolving geosphere and biosphere. 1. Morrison, S.M. et al. (2017) Network analysis of mineralogical systems. American Mineralogist 102, in press. Figure Caption: A network of Phanerozoic Era fossil animals from the past 540 million years includes blue, red, and black circles (nodes) representing family-level taxa and grey lines (links) between coexisting families. Age information was not used in the construction of this network; nevertheless an intrinsic timeline is embedded in the network topology. In

New genes expressed in human brains: implications for annotating evolving genomes.

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Zhang, Yong E; Landback, Patrick; Vibranovski, Maria; Long, Manyuan

2012-11-01

New genes have frequently formed and spread to fixation in a wide variety of organisms, constituting abundant sets of lineage-specific genes. It was recently reported that an excess of primate-specific and human-specific genes were upregulated in the brains of fetuses and infants, and especially in the prefrontal cortex, which is involved in cognition. These findings reveal the prevalent addition of new genetic components to the transcriptome of the human brain. More generally, these findings suggest that genomes are continually evolving in both sequence and content, eroding the conservation endowed by common ancestry. Despite increasing recognition of the importance of new genes, we highlight here that these genes are still seriously under-characterized in functional studies and that new gene annotation is inconsistent in current practice. We propose an integrative approach to annotate new genes, taking advantage of functional and evolutionary genomic methods. We finally discuss how the refinement of new gene annotation will be important for the detection of evolutionary forces governing new gene origination. Copyright © 2012 WILEY Periodicals, Inc.

COGNAT: a web server for comparative analysis of genomic neighborhoods.

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Klimchuk, Olesya I; Konovalov, Kirill A; Perekhvatov, Vadim V; Skulachev, Konstantin V; Dibrova, Daria V; Mulkidjanian, Armen Y

2017-11-22

In prokaryotic genomes, functionally coupled genes can be organized in conserved gene clusters enabling their coordinated regulation. Such clusters could contain one or several operons, which are groups of co-transcribed genes. Those genes that evolved from a common ancestral gene by speciation (i.e. orthologs) are expected to have similar genomic neighborhoods in different organisms, whereas those copies of the gene that are responsible for dissimilar functions (i.e. paralogs) could be found in dissimilar genomic contexts. Comparative analysis of genomic neighborhoods facilitates the prediction of co-regulated genes and helps to discern different functions in large protein families. We intended, building on the attribution of gene sequences to the clusters of orthologous groups of proteins (COGs), to provide a method for visualization and comparative analysis of genomic neighborhoods of evolutionary related genes, as well as a respective web server. Here we introduce the COmparative Gene Neighborhoods Analysis Tool (COGNAT), a web server for comparative analysis of genomic neighborhoods. The tool is based on the COG database, as well as the Pfam protein families database. As an example, we show the utility of COGNAT in identifying a new type of membrane protein complex that is formed by paralog(s) of one of the membrane subunits of the NADH:quinone oxidoreductase of type 1 (COG1009) and a cytoplasmic protein of unknown function (COG3002). This article was reviewed by Drs. Igor Zhulin, Uri Gophna and Igor Rogozin.

Variability among the Most Rapidly Evolving Plastid Genomic Regions is Lineage-Specific: Implications of Pairwise Genome Comparisons in Pyrus (Rosaceae) and Other Angiosperms for Marker Choice

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Ter-Voskanyan, Hasmik; Allgaier, Martin; Borsch, Thomas

2014-01-01

Plastid genomes exhibit different levels of variability in their sequences, depending on the respective kinds of genomic regions. Genes are usually more conserved while noncoding introns and spacers evolve at a faster pace. While a set of about thirty maximum variable noncoding genomic regions has been suggested to provide universally promising phylogenetic markers throughout angiosperms, applications often require several regions to be sequenced for many individuals. Our project aims to illuminate evolutionary relationships and species-limits in the genus Pyrus (Rosaceae)—a typical case with very low genetic distances between taxa. In this study, we have sequenced the plastid genome of Pyrus spinosa and aligned it to the already available P. pyrifolia sequence. The overall p-distance of the two Pyrus genomes was 0.00145. The intergenic spacers between ndhC–trnV, trnR–atpA, ndhF–rpl32, psbM–trnD, and trnQ–rps16 were the most variable regions, also comprising the highest total numbers of substitutions, indels and inversions (potentially informative characters). Our comparative analysis of further plastid genome pairs with similar low p-distances from Oenothera (representing another rosid), Olea (asterids) and Cymbidium (monocots) showed in each case a different ranking of genomic regions in terms of variability and potentially informative characters. Only two intergenic spacers (ndhF–rpl32 and trnK–rps16) were consistently found among the 30 top-ranked regions. We have mapped the occurrence of substitutions and microstructural mutations in the four genome pairs. High AT content in specific sequence elements seems to foster frequent mutations. We conclude that the variability among the fastest evolving plastid genomic regions is lineage-specific and thus cannot be precisely predicted across angiosperms. The often lineage-specific occurrence of stem-loop elements in the sequences of introns and spacers also governs lineage-specific mutations

Variability among the most rapidly evolving plastid genomic regions is lineage-specific: implications of pairwise genome comparisons in Pyrus (Rosaceae and other angiosperms for marker choice.

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Nadja Korotkova

Full Text Available Plastid genomes exhibit different levels of variability in their sequences, depending on the respective kinds of genomic regions. Genes are usually more conserved while noncoding introns and spacers evolve at a faster pace. While a set of about thirty maximum variable noncoding genomic regions has been suggested to provide universally promising phylogenetic markers throughout angiosperms, applications often require several regions to be sequenced for many individuals. Our project aims to illuminate evolutionary relationships and species-limits in the genus Pyrus (Rosaceae-a typical case with very low genetic distances between taxa. In this study, we have sequenced the plastid genome of Pyrus spinosa and aligned it to the already available P. pyrifolia sequence. The overall p-distance of the two Pyrus genomes was 0.00145. The intergenic spacers between ndhC-trnV, trnR-atpA, ndhF-rpl32, psbM-trnD, and trnQ-rps16 were the most variable regions, also comprising the highest total numbers of substitutions, indels and inversions (potentially informative characters. Our comparative analysis of further plastid genome pairs with similar low p-distances from Oenothera (representing another rosid, Olea (asterids and Cymbidium (monocots showed in each case a different ranking of genomic regions in terms of variability and potentially informative characters. Only two intergenic spacers (ndhF-rpl32 and trnK-rps16 were consistently found among the 30 top-ranked regions. We have mapped the occurrence of substitutions and microstructural mutations in the four genome pairs. High AT content in specific sequence elements seems to foster frequent mutations. We conclude that the variability among the fastest evolving plastid genomic regions is lineage-specific and thus cannot be precisely predicted across angiosperms. The often lineage-specific occurrence of stem-loop elements in the sequences of introns and spacers also governs lineage-specific mutations. Sequencing

Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC

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Engelen Stefan

2012-02-01

Full Text Available Abstract Background Bacterial genomes displaying a strong bias between the leading and the lagging strand of DNA replication encode two DNA polymerases III, DnaE and PolC, rather than a single one. Replication is a highly unsymmetrical process, and the presence of two polymerases is therefore not unexpected. Using comparative genomics, we explored whether other processes have evolved in parallel with each polymerase. Results Extending previous in silico heuristics for the analysis of gene co-evolution, we analyzed the function of genes clustering with dnaE and polC. Clusters were highly informative. DnaE co-evolves with the ribosome, the transcription machinery, the core of intermediary metabolism enzymes. It is also connected to the energy-saving enzyme necessary for RNA degradation, polynucleotide phosphorylase. Most of the proteins of this co-evolving set belong to the persistent set in bacterial proteomes, that is fairly ubiquitously distributed. In contrast, PolC co-evolves with RNA degradation enzymes that are present only in the A+T-rich Firmicutes clade, suggesting at least two origins for the degradosome. Conclusion DNA replication involves two machineries, DnaE and PolC. DnaE co-evolves with the core functions of bacterial life. In contrast PolC co-evolves with a set of RNA degradation enzymes that does not derive from the degradosome identified in gamma-Proteobacteria. This suggests that at least two independent RNA degradation pathways existed in the progenote community at the end of the RNA genome world.

Genome shuffling of Saccharomyces cerevisiae through recursive population mating to evolve tolerance to inhibitors of Spent Sulfite Liquor

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Martin, V.J.J.; Pinel, D.J.; D' aoust, F. [Concordia Univ., Montreal, PQ (Canada). Dept. of Biological Sciences; Bajwa, P.K.; Trevors, J.T.; Lee, H. [Guelph Univ., ON (Canada). Dept. of Environmental Biology

2009-07-01

The biochemical steps in the conversion of cellulosics to biofuels include the pretreatment, hydrolysis and fermentation of substrates into a final product. Fermentation of lignocellulosic substrates derived from waste biomass requires metabolic engineering. A biochemical flow chart from the Tembec Biorefinery plant was presented in which Spent Sulfite Liquor (SSL) was used to add value to the pulp and paper industry. The sugars contained in this carbohydrate-rich effluent from sulfite pulping were used to produce ethanol. A robust, ethanologenic microorganism that can withstand the substrate toxicity was needed. Saccharomyces cerevisiae is currently used for the production of ethanol from SSL. This yeast will succumb to toxicity and inhibition, particularly in the most inhibitor rich forms of SSL such as hardwood SSL (HWSSL). A genome shuffling method was therefore developed to create a better SSL fermenting strain. This method was designed to improve polygenic traits by generating pools of mutants with improved phenotypes, followed by iterative recombination between their genomes. Through 5 rounds of recursive mating and screening, 3 strains that could survive and grow in undiluted HWSSL were obtained. The study demonstrated that the tolerance of these strains to SSL translates into an increased capacity to produce ethanol over time using this substrate, due to continued viability of the yeast population. Phenotypic analysis of the three strains revealed that the genome shuffling approach successfully co-evolved tolerance to acetic acid, NaCl (osmotic) and HMF. A systems biology analysis of strain R57 was initiated in order to establish the genetic basis for HWSSL tolerance. tabs., figs.

The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes.

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Marion Ouedraogo

Full Text Available BACKGROUND: There has been a surge in studies linking genome structure and gene expression, with special focus on duplicated genes. Although initially duplicated from the same sequence, duplicated genes can diverge strongly over evolution and take on different functions or regulated expression. However, information on the function and expression of duplicated genes remains sparse. Identifying groups of duplicated genes in different genomes and characterizing their expression and function would therefore be of great interest to the research community. The 'Duplicated Genes Database' (DGD was developed for this purpose. METHODOLOGY: Nine species were included in the DGD. For each species, BLAST analyses were conducted on peptide sequences corresponding to the genes mapped on a same chromosome. Groups of duplicated genes were defined based on these pairwise BLAST comparisons and the genomic location of the genes. For each group, Pearson correlations between gene expression data and semantic similarities between functional GO annotations were also computed when the relevant information was available. CONCLUSIONS: The Duplicated Gene Database provides a list of co-localised and duplicated genes for several species with the available gene co-expression level and semantic similarity value of functional annotation. Adding these data to the groups of duplicated genes provides biological information that can prove useful to gene expression analyses. The Duplicated Gene Database can be freely accessed through the DGD website at http://dgd.genouest.org.

Group normalization for genomic data.

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Ghandi, Mahmoud; Beer, Michael A

2012-01-01

Data normalization is a crucial preliminary step in analyzing genomic datasets. The goal of normalization is to remove global variation to make readings across different experiments comparable. In addition, most genomic loci have non-uniform sensitivity to any given assay because of variation in local sequence properties. In microarray experiments, this non-uniform sensitivity is due to different DNA hybridization and cross-hybridization efficiencies, known as the probe effect. In this paper we introduce a new scheme, called Group Normalization (GN), to remove both global and local biases in one integrated step, whereby we determine the normalized probe signal by finding a set of reference probes with similar responses. Compared to conventional normalization methods such as Quantile normalization and physically motivated probe effect models, our proposed method is general in the sense that it does not require the assumption that the underlying signal distribution be identical for the treatment and control, and is flexible enough to correct for nonlinear and higher order probe effects. The Group Normalization algorithm is computationally efficient and easy to implement. We also describe a variant of the Group Normalization algorithm, called Cross Normalization, which efficiently amplifies biologically relevant differences between any two genomic datasets.

A genomic insight into diversity among tribal and nontribal population groups of Manipur, India.

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Saraswathy, K N; Kiranmala, Naorem; Murry, Benrithung; Sinha, Ekata; Saksena, Deepti; Kaur, Harpreet; Sachdeva, M P; Kalla, A K

2009-10-01

Twenty autosomal markers, including linked markers at two gene markers, are used to understand the genomic similarity and diversity among three tribal (Paite, Thadou, and Kom) and one nontribal communities of Manipur (Northeast India). Two of the markers (CD4 and HB9) are monomorphic in Paite and one (the CD4 marker) in Kom. Data suggest the Meitei (nontribal groups) stand apart from the three tribal groups with respect to higher heterozygosity (0.366) and presence of the highest ancestor haplotypes of DRD2 markers (0.228); this is also supported by principal co-ordinate analysis. These populations are found to be genomically closer to the Chinese population than to other Indian populations.

Co-Expression of Neighboring Genes in the Zebrafish (Danio rerio Genome

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Daryi Wang

2009-08-01

Full Text Available Neighboring genes in the eukaryotic genome have a tendency to express concurrently, and the proximity of two adjacent genes is often considered a possible explanation for their co-expression behavior. However, the actual contribution of the physical distance between two genes to their co-expression behavior has yet to be defined. To further investigate this issue, we studied the co-expression of neighboring genes in zebrafish, which has a compact genome and has experienced a whole genome duplication event. Our analysis shows that the proportion of highly co-expressed neighboring pairs (Pearson’s correlation coefficient R>0.7 is low (0.24% ~ 0.67%; however, it is still significantly higher than that of random pairs. In particular, the statistical result implies that the co-expression tendency of neighboring pairs is negatively correlated with their physical distance. Our findings therefore suggest that physical distance may play an important role in the co-expression of neighboring genes. Possible mechanisms related to the neighboring genes’ co-expression are also discussed.

Molecular abundances and C/O ratios in chemically evolving planet-forming disk midplanes

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Eistrup, Christian; Walsh, Catherine; van Dishoeck, Ewine F.

2018-05-01

Context. Exoplanet atmospheres are thought be built up from accretion of gas as well as pebbles and planetesimals in the midplanes of planet-forming disks. The chemical composition of this material is usually assumed to be unchanged during the disk lifetime. However, chemistry can alter the relative abundances of molecules in this planet-building material. Aims: We aim to assess the impact of disk chemistry during the era of planet formation. This is done by investigating the chemical changes to volatile gases and ices in a protoplanetary disk midplane out to 30 AU for up to 7 Myr, considering a variety of different conditions, including a physical midplane structure that is evolving in time, and also considering two disks with different masses. Methods: An extensive kinetic chemistry gas-grain reaction network was utilised to evolve the abundances of chemical species over time. Two disk midplane ionisation levels (low and high) were explored, as well as two different makeups of the initial abundances ("inheritance" or "reset"). Results: Given a high level of ionisation, chemical evolution in protoplanetary disk midplanes becomes significant after a few times 105 yr, and is still ongoing by 7 Myr between the H2O and the O2 icelines. Inside the H2O iceline, and in the outer, colder regions of the disk midplane outside the O2 iceline, the relative abundances of the species reach (close to) steady state by 7 Myr. Importantly, the changes in the abundances of the major elemental carbon and oxygen-bearing molecules imply that the traditional "stepfunction" for the C/O ratios in gas and ice in the disk midplane (as defined by sharp changes at icelines of H2O, CO2 and CO) evolves over time, and cannot be assumed fixed, with the C/O ratio in the gas even becoming smaller than the C/O ratio in the ice. In addition, at lower temperatures (C/O ratios of exoplanets to where and how the atmospheres have formed in a disk midplane, chemical evolution needs to be considered and

Group normalization for genomic data.

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Mahmoud Ghandi

Full Text Available Data normalization is a crucial preliminary step in analyzing genomic datasets. The goal of normalization is to remove global variation to make readings across different experiments comparable. In addition, most genomic loci have non-uniform sensitivity to any given assay because of variation in local sequence properties. In microarray experiments, this non-uniform sensitivity is due to different DNA hybridization and cross-hybridization efficiencies, known as the probe effect. In this paper we introduce a new scheme, called Group Normalization (GN, to remove both global and local biases in one integrated step, whereby we determine the normalized probe signal by finding a set of reference probes with similar responses. Compared to conventional normalization methods such as Quantile normalization and physically motivated probe effect models, our proposed method is general in the sense that it does not require the assumption that the underlying signal distribution be identical for the treatment and control, and is flexible enough to correct for nonlinear and higher order probe effects. The Group Normalization algorithm is computationally efficient and easy to implement. We also describe a variant of the Group Normalization algorithm, called Cross Normalization, which efficiently amplifies biologically relevant differences between any two genomic datasets.

Social networks and online environments: when science and practice co-evolve

OpenAIRE

Rosen, Devan; Barnett, George A.; Kim, Jang Hyun

2011-01-01

The science of social network analysis has co-evolved with the development of online environments and computer-mediated communication. Unique and precise data available from computer and information systems have allowed network scientists to explore novel social phenomena and develop new methods. Additionally, advances in the structural analysis and visualization of computer-mediated social networks have informed developers and shaped the design of social media tools. This article reviews som...

MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes.

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Vallenet, David; Calteau, Alexandra; Cruveiller, Stéphane; Gachet, Mathieu; Lajus, Aurélie; Josso, Adrien; Mercier, Jonathan; Renaux, Alexandre; Rollin, Johan; Rouy, Zoe; Roche, David; Scarpelli, Claude; Médigue, Claudine

2017-01-04

The annotation of genomes from NGS platforms needs to be automated and fully integrated. However, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. This shortcoming limits the knowledge that can be extracted from genomes and metabolic models. Launched in 2005, the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Effective comparative analysis requires a consistent and complete view of biological data, and therefore, support for reviewing the quality of functional annotation is critical. MicroScope allows users to analyze microbial (meta)genomes together with post-genomic experiment results if any (i.e. transcriptomics, re-sequencing of evolved strains, mutant collections, phenotype data). It combines tools and graphical interfaces to analyze genomes and to perform the expert curation of gene functions in a comparative context. Starting with a short overview of the MicroScope system, this paper focuses on some major improvements of the Web interface, mainly for the submission of genomic data and on original tools and pipelines that have been developed and integrated in the platform: computation of pan-genomes and prediction of biosynthetic gene clusters. Today the resource contains data for more than 6000 microbial genomes, and among the 2700 personal accounts (65% of which are now from foreign countries), 14% of the users are performing expert annotations, on at least a weekly basis, contributing to improve the quality of microbial genome annotations. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

How Life and Rocks Have Co-Evolved

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Hazen, R.

2014-04-01

The near-surface environment of terrestrial planets and moons evolves as a consequence of selective physical, chemical, and biological processes - an evolution that is preserved in the mineralogical record. Mineral evolution begins with approximately 12 different refractory minerals that form in the cooling envelopes of exploding stars. Subsequent aqueous and thermal alteration of planetessimals results in the approximately 250 minerals now found in unweathered lunar and meteorite samples. Following Earth's accretion and differentiation, mineral evolution resulted from a sequence of geochemical and petrologic processes, which led to perhaps 1500 mineral species. According to some origin-of-life scenarios, a planet must progress through at least some of these stages of chemical processing as a prerequisite for life. Once life emerged, mineralogy and biology co-evolved and dramatically increased Earth's mineral diversity to >4000 species. Sequential stages of a planet's near-surface evolution arise from three primary mechanisms: (1) the progressive separation and concentration of the elements from their original relatively uniform distribution in the presolar nebula; (2) the increase in range of intensive variables such as pressure, temperature, and volatile activities; and (3) the generation of far-from-equilibrium conditions by living systems. Remote observations of the mineralogy of other terrestrial bodies may thus provide evidence for biological influences beyond Earth. Recent studies of mineral diversification through time reveal striking correlations with major geochemical, tectonic, and biological events, including large-changes in ocean chemistry, the supercontinent cycle, the increase of atmospheric oxygen, and the rise of the terrestrial biosphere.

Co-evolving prisoner's dilemma: Performance indicators and analytic approaches

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Zhang, W.; Choi, C. W.; Li, Y. S.; Xu, C.; Hui, P. M.

2017-02-01

Understanding the intrinsic relation between the dynamical processes in a co-evolving network and the necessary ingredients in formulating a reliable theory is an important question and a challenging task. Using two slightly different definitions of performance indicator in the context of a co-evolving prisoner's dilemma game, it is shown that very different cooperative levels result and theories of different complexity are required to understand the key features. When the payoff per opponent is used as the indicator (Case A), non-cooperative strategy has an edge and dominates in a large part of the parameter space formed by the cutting-and-rewiring probability and the strategy imitation probability. When the payoff from all opponents is used (Case B), cooperative strategy has an edge and dominates the parameter space. Two distinct phases, one homogeneous and dynamical and another inhomogeneous and static, emerge and the phase boundary in the parameter space is studied in detail. A simple theory assuming an average competing environment for cooperative agents and another for non-cooperative agents is shown to perform well in Case A. The same theory, however, fails badly for Case B. It is necessary to include more spatial correlation into a theory for Case B. We show that the local configuration approximation, which takes into account of the different competing environments for agents with different strategies and degrees, is needed to give reliable results for Case B. The results illustrate that formulating a proper theory requires both a conceptual understanding of the effects of the adaptive processes in the problem and a delicate balance between simplicity and accuracy.

Nonsynonymous substitution rate (Ka is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genes

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Wang Lei

2011-02-01

Full Text Available Abstract Background Mammalian genome sequence data are being acquired in large quantities and at enormous speeds. We now have a tremendous opportunity to better understand which genes are the most variable or conserved, and what their particular functions and evolutionary dynamics are, through comparative genomics. Results We chose human and eleven other high-coverage mammalian genome data–as well as an avian genome as an outgroup–to analyze orthologous protein-coding genes using nonsynonymous (Ka and synonymous (Ks substitution rates. After evaluating eight commonly-used methods of Ka and Ks calculation, we observed that these methods yielded a nearly uniform result when estimating Ka, but not Ks (or Ka/Ks. When sorting genes based on Ka, we noticed that fast-evolving and slow-evolving genes often belonged to different functional classes, with respect to species-specificity and lineage-specificity. In particular, we identified two functional classes of genes in the acquired immune system. Fast-evolving genes coded for signal-transducing proteins, such as receptors, ligands, cytokines, and CDs (cluster of differentiation, mostly surface proteins, whereas the slow-evolving genes were for function-modulating proteins, such as kinases and adaptor proteins. In addition, among slow-evolving genes that had functions related to the central nervous system, neurodegenerative disease-related pathways were enriched significantly in most mammalian species. We also confirmed that gene expression was negatively correlated with evolution rate, i.e. slow-evolving genes were expressed at higher levels than fast-evolving genes. Our results indicated that the functional specializations of the three major mammalian clades were: sensory perception and oncogenesis in primates, reproduction and hormone regulation in large mammals, and immunity and angiotensin in rodents. Conclusion Our study suggests that Ka calculation, which is less biased compared to Ks and Ka

Genomic instability--an evolving hallmark of cancer.

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Negrini, Simona; Gorgoulis, Vassilis G; Halazonetis, Thanos D

2010-03-01

Genomic instability is a characteristic of most cancers. In hereditary cancers, genomic instability results from mutations in DNA repair genes and drives cancer development, as predicted by the mutator hypothesis. In sporadic (non-hereditary) cancers the molecular basis of genomic instability remains unclear, but recent high-throughput sequencing studies suggest that mutations in DNA repair genes are infrequent before therapy, arguing against the mutator hypothesis for these cancers. Instead, the mutation patterns of the tumour suppressor TP53 (which encodes p53), ataxia telangiectasia mutated (ATM) and cyclin-dependent kinase inhibitor 2A (CDKN2A; which encodes p16INK4A and p14ARF) support the oncogene-induced DNA replication stress model, which attributes genomic instability and TP53 and ATM mutations to oncogene-induced DNA damage.

Adaptive cyclically dominating game on co-evolving networks: numerical and analytic results

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Choi, Chi Wun; Xu, Chen; Hui, Pak Ming

2017-10-01

A co-evolving and adaptive Rock (R)-Paper (P)-Scissors (S) game (ARPS) in which an agent uses one of three cyclically dominating strategies is proposed and studied numerically and analytically. An agent takes adaptive actions to achieve a neighborhood to his advantage by rewiring a dissatisfying link with a probability p or switching strategy with a probability 1 - p. Numerical results revealed two phases in the steady state. An active phase for p pc has three separate clusters of agents using only R, P, and S, respectively with terminated adaptive actions. A mean-field theory based on the link densities in co-evolving network is formulated and the trinomial closure scheme is applied to obtain analytical solutions. The analytic results agree with simulation results on ARPS well. In addition, the different probabilities of winning, losing, and drawing a game among the agents are identified as the origin of the small discrepancy between analytic and simulation results. As a result of the adaptive actions, agents of higher degrees are often those being taken advantage of. Agents with a smaller (larger) degree than the mean degree have a higher (smaller) probability of winning than losing. The results are informative for future attempts on formulating more accurate theories.

Directed evolution to re-adapt a co-evolved network within an enzyme.

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Strafford, John; Payongsri, Panwajee; Hibbert, Edward G; Morris, Phattaraporn; Batth, Sukhjeet S; Steadman, David; Smith, Mark E B; Ward, John M; Hailes, Helen C; Dalby, Paul A

2012-01-01

We have previously used targeted active-site saturation mutagenesis to identify a number of transketolase single mutants that improved activity towards either glycolaldehyde (GA), or the non-natural substrate propionaldehyde (PA). Here, all attempts to recombine the singles into double mutants led to unexpected losses of specific activity towards both substrates. A typical trade-off occurred between soluble expression levels and specific activity for all single mutants, but many double mutants decreased both properties more severely suggesting a critical loss of protein stability or native folding. Statistical coupling analysis (SCA) of a large multiple sequence alignment revealed a network of nine co-evolved residues that affected all but one double mutant. Such networks maintain important functional properties such as activity, specificity, folding, stability, and solubility and may be rapidly disrupted by introducing one or more non-naturally occurring mutations. To identify variants of this network that would accept and improve upon our best D469 mutants for activity towards PA, we created a library of random single, double and triple mutants across seven of the co-evolved residues, combining our D469 variants with only naturally occurring mutations at the remaining sites. A triple mutant cluster at D469, E498 and R520 was found to behave synergistically for the specific activity towards PA. Protein expression was severely reduced by E498D and improved by R520Q, yet variants containing both mutations led to improved specific activity and enzyme expression, but with loss of solubility and the formation of inclusion bodies. D469S and R520Q combined synergistically to improve k(cat) 20-fold for PA, more than for any previous transketolase mutant. R520Q also doubled the specific activity of the previously identified D469T to create our most active transketolase mutant to date. Our results show that recombining active-site mutants obtained by saturation mutagenesis

The impacts of drift and selection on genomic evolution in insects

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K. Jun Tong

2017-04-01

Full Text Available Genomes evolve through a combination of mutation, drift, and selection, all of which act heterogeneously across genes and lineages. This leads to differences in branch-length patterns among gene trees. Genes that yield trees with the same branch-length patterns can be grouped together into clusters. Here, we propose a novel phylogenetic approach to explain the factors that influence the number and distribution of these gene-tree clusters. We apply our method to a genomic dataset from insects, an ancient and diverse group of organisms. We find some evidence that when drift is the dominant evolutionary process, each cluster tends to contain a large number of fast-evolving genes. In contrast, strong negative selection leads to many distinct clusters, each of which contains only a few slow-evolving genes. Our work, although preliminary in nature, illustrates the use of phylogenetic methods to shed light on the factors driving rate variation in genomic evolution.

Analysis of IAV Replication and Co-infection Dynamics by a Versatile RNA Viral Genome Labeling Method

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Dan Dou

2017-07-01

Full Text Available Genome delivery to the proper cellular compartment for transcription and replication is a primary goal of viruses. However, methods for analyzing viral genome localization and differentiating genomes with high identity are lacking, making it difficult to investigate entry-related processes and co-examine heterogeneous RNA viral populations. Here, we present an RNA labeling approach for single-cell analysis of RNA viral replication and co-infection dynamics in situ, which uses the versatility of padlock probes. We applied this method to identify influenza A virus (IAV infections in cells and lung tissue with single-nucleotide specificity and to classify entry and replication stages by gene segment localization. Extending the classification strategy to co-infections of IAVs with single-nucleotide variations, we found that the dependence on intracellular trafficking places a time restriction on secondary co-infections necessary for genome reassortment. Altogether, these data demonstrate how RNA viral genome labeling can help dissect entry and co-infections.

Partially satisfied to fully satisfied transitions in co-evolving inverse voter model and possible scaling behavior

International Nuclear Information System (INIS)

Choi, C.W.; Xu, C.; Hui, P.M.

2015-01-01

Understanding co-evolving networks characterized by the mutual influence of agents' actions and network structure remains a challenge. We study a co-evolving inverse voter model in which agents adapt to achieve a preferred environment with more opposite-opinion neighbors by rewiring their connections and switching opinion. Numerical studies reveal a transition from a dynamic partially satisfied phase to a frozen fully satisfied phase as the rewiring probability is varied. A simple mean field theory is shown to capture the behavior only qualitatively. An improved mean field theory carrying a longer spatial correlation gives better results. Motivated by numerical results in networks of different degrees and mean field results, we propose a scaling variable that combines the rewiring probability and mean degree in a special form. The scaling variable is shown to work well in analyzing data corresponding to different networks and different rewiring probabilities. An application is to predict the results for networks of different degrees based solely on results obtained from networks of one degree. Studying scaling behavior provides an alternative path for understanding co-evolving agent-based dynamical systems, especially in light of the trade-off between complexity of a theory and its accuracy. - Highlights: • Identified key features and phase transitions in coevolving inverse voter model. • Constructed a better theory incorporating longer spatial correlation. • Proposed scaling variable and illustrated possible scaling behavior. • Used scaling behavior to predict results of IVM in a different network.

Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics

DEFF Research Database (Denmark)

Quaiser, Achim; Ochsenreiter, Torsten; Lanz, Christa

2003-01-01

fragments differed between 2.3% and 19.9% and were placed into two different subgroups of Acidobacteria (groups III and V). Although partial co-linearity was found between genomic fragments, the gene content around the rRNA operons was generally not conserved. Phylogenetic reconstructions with orthologues......Acidobacteria have been established as a novel phylum of Bacteria that is consistently detected in many different habitats around the globe by 16S rDNA-based molecular surveys. The phylogenetic diversity, ubiquity and abundance of this group, particularly in soil habitats, suggest an important...... palustris and Bradyrhizobium japonicum, including a conserved two-component system. Phylogenetic analysis of the putative response regulator confirmed that this similarity between Rhizobiales and Acidobacteria might be due to a horizontal gene transfer. In total, our data give first insight into the genome...

Unraveling the mystery of music: music as an evolved group process.

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Loersch, Chris; Arbuckle, Nathan L

2013-11-01

As prominently highlighted by Charles Darwin, music is one of the most mysterious aspects of human nature. Despite its ubiquitous presence across cultures and throughout recorded history, the reason humans respond emotionally to music remains unknown. Although many scientists and philosophers have offered hypotheses, there is little direct empirical evidence for any perspective. Here we address this issue, providing data which support the idea that music evolved in service of group living. Using 7 studies, we demonstrate that people's emotional responses to music are intricately tied to the other core social phenomena that bind us together into groups. In sum, this work establishes human musicality as a special form of social cognition and provides the first direct support for the hypothesis that music evolved as a tool of social living. In addition, the findings provide a reason for the intense psychological pull of music in modern life, suggesting that the pleasure we derive from listening to music results from its innate connection to the basic social drives that create our interconnected world. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Group sparse canonical correlation analysis for genomic data integration.

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Lin, Dongdong; Zhang, Jigang; Li, Jingyao; Calhoun, Vince D; Deng, Hong-Wen; Wang, Yu-Ping

2013-08-12

The emergence of high-throughput genomic datasets from different sources and platforms (e.g., gene expression, single nucleotide polymorphisms (SNP), and copy number variation (CNV)) has greatly enhanced our understandings of the interplay of these genomic factors as well as their influences on the complex diseases. It is challenging to explore the relationship between these different types of genomic data sets. In this paper, we focus on a multivariate statistical method, canonical correlation analysis (CCA) method for this problem. Conventional CCA method does not work effectively if the number of data samples is significantly less than that of biomarkers, which is a typical case for genomic data (e.g., SNPs). Sparse CCA (sCCA) methods were introduced to overcome such difficulty, mostly using penalizations with l-1 norm (CCA-l1) or the combination of l-1and l-2 norm (CCA-elastic net). However, they overlook the structural or group effect within genomic data in the analysis, which often exist and are important (e.g., SNPs spanning a gene interact and work together as a group). We propose a new group sparse CCA method (CCA-sparse group) along with an effective numerical algorithm to study the mutual relationship between two different types of genomic data (i.e., SNP and gene expression). We then extend the model to a more general formulation that can include the existing sCCA models. We apply the model to feature/variable selection from two data sets and compare our group sparse CCA method with existing sCCA methods on both simulation and two real datasets (human gliomas data and NCI60 data). We use a graphical representation of the samples with a pair of canonical variates to demonstrate the discriminating characteristic of the selected features. Pathway analysis is further performed for biological interpretation of those features. The CCA-sparse group method incorporates group effects of features into the correlation analysis while performs individual feature

Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes.

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Puigbò, Pere; Lobkovsky, Alexander E; Kristensen, David M; Wolf, Yuri I; Koonin, Eugene V

2014-08-21

Genomes of bacteria and archaea (collectively, prokaryotes) appear to exist in incessant flux, expanding via horizontal gene transfer and gene duplication, and contracting via gene loss. However, the actual rates of genome dynamics and relative contributions of different types of event across the diversity of prokaryotes are largely unknown, as are the sizes of microbial supergenomes, i.e. pools of genes that are accessible to the given microbial species. We performed a comprehensive analysis of the genome dynamics in 35 groups (34 bacterial and one archaeal) of closely related microbial genomes using a phylogenetic birth-and-death maximum likelihood model to quantify the rates of gene family gain and loss, as well as expansion and reduction. The results show that loss of gene families dominates the evolution of prokaryotes, occurring at approximately three times the rate of gain. The rates of gene family expansion and reduction are typically seven and twenty times less than the gain and loss rates, respectively. Thus, the prevailing mode of evolution in bacteria and archaea is genome contraction, which is partially compensated by the gain of new gene families via horizontal gene transfer. However, the rates of gene family gain, loss, expansion and reduction vary within wide ranges, with the most stable genomes showing rates about 25 times lower than the most dynamic genomes. For many groups, the supergenome estimated from the fraction of repetitive gene family gains includes about tenfold more gene families than the typical genome in the group although some groups appear to have vast, 'open' supergenomes. Reconstruction of evolution for groups of closely related bacteria and archaea reveals an extremely rapid and highly variable flux of genes in evolving microbial genomes, demonstrates that extensive gene loss and horizontal gene transfer leading to innovation are the two dominant evolutionary processes, and yields robust estimates of the supergenome size.

Genomics of Volvocine Algae

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Umen, James G.; Olson, Bradley J.S.C.

2015-01-01

Volvocine algae are a group of chlorophytes that together comprise a unique model for evolutionary and developmental biology. The species Chlamydomonas reinhardtii and Volvox carteri represent extremes in morphological diversity within the Volvocine clade. Chlamydomonas is unicellular and reflects the ancestral state of the group, while Volvox is multicellular and has evolved numerous innovations including germ-soma differentiation, sexual dimorphism, and complex morphogenetic patterning. The Chlamydomonas genome sequence has shed light on several areas of eukaryotic cell biology, metabolism and evolution, while the Volvox genome sequence has enabled a comparison with Chlamydomonas that reveals some of the underlying changes that enabled its transition to multicellularity, but also underscores the subtlety of this transition. Many of the tools and resources are in place to further develop Volvocine algae as a model for evolutionary genomics. PMID:25883411

Mitochondrial genome evolution in the Saccharomyces sensu stricto complex.

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Ruan, Jiangxing; Cheng, Jian; Zhang, Tongcun; Jiang, Huifeng

2017-01-01

Exploring the evolutionary patterns of mitochondrial genomes is important for our understanding of the Saccharomyces sensu stricto (SSS) group, which is a model system for genomic evolution and ecological analysis. In this study, we first obtained the complete mitochondrial sequences of two important species, Saccharomyces mikatae and Saccharomyces kudriavzevii. We then compared the mitochondrial genomes in the SSS group with those of close relatives, and found that the non-coding regions evolved rapidly, including dramatic expansion of intergenic regions, fast evolution of introns and almost 20-fold higher rearrangement rates than those of the nuclear genomes. However, the coding regions, and especially the protein-coding genes, are more conserved than those in the nuclear genomes of the SSS group. The different evolutionary patterns of coding and non-coding regions in the mitochondrial and nuclear genomes may be related to the origin of the aerobic fermentation lifestyle in this group. Our analysis thus provides novel insights into the evolution of mitochondrial genomes.

Detection and full genome characterization of two beta CoV viruses related to Middle East respiratory syndrome from bats in Italy.

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Moreno, Ana; Lelli, Davide; de Sabato, Luca; Zaccaria, Guendalina; Boni, Arianna; Sozzi, Enrica; Prosperi, Alice; Lavazza, Antonio; Cella, Eleonora; Castrucci, Maria Rita; Ciccozzi, Massimo; Vaccari, Gabriele

2017-12-19

Middle East respiratory syndrome coronavirus (MERS-CoV), which belongs to beta group of coronavirus, can infect multiple host species and causes severe diseases in humans. Multiple surveillance and phylogenetic studies suggest a bat origin. In this study, we describe the detection and full genome characterization of two CoVs closely related to MERS-CoV from two Italian bats, Pipistrellus kuhlii and Hypsugo savii. Pool of viscera were tested by a pan-coronavirus RT-PCR. Virus isolation was attempted by inoculation in different cell lines. Full genome sequencing was performed using the Ion Torrent platform and phylogenetic trees were performed using IQtree software. Similarity plots of CoV clade c genomes were generated by using SSE v1.2. The three dimensional macromolecular structure (3DMMS) of the receptor binding domain (RBD) in the S protein was predicted by sequence-homology method using the protein data bank (PDB). Both samples resulted positive to the pan-coronavirus RT-PCR (IT-batCoVs) and their genome organization showed identical pattern of MERS CoV. Phylogenetic analysis showed a monophyletic group placed in the Beta2c clade formed by MERS-CoV sequences originating from humans and camels and bat-related sequences from Africa, Italy and China. The comparison of the secondary and 3DMMS of the RBD of IT-batCoVs with MERS, HKU4 and HKU5 bat sequences showed two aa deletions located in a region corresponding to the external subdomain of MERS-RBD in IT-batCoV and HKU5 RBDs. This study reported two beta CoVs closely related to MERS that were obtained from two bats belonging to two commonly recorded species in Italy (P. kuhlii and H. savii). The analysis of the RBD showed similar structure in IT-batCoVs and HKU5 respect to HKU4 sequences. Since the RBD domain of HKU4 but not HKU5 can bind to the human DPP4 receptor for MERS-CoV, it is possible to suggest also for IT-batCoVs the absence of DPP4-binding potential. More surveillance studies are needed to better

Comparative genomics of a plant-parasitic nematode endosymbiont suggest a role in nutritional symbiosis

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Bacterial mutualists can increase the biochemical capacity of animals. Highly co-evolved nutritional mutualists do this by synthesizing nutrients missing from the host's diet. Genomics tools have recently advanced the study of these partnerships. Here we examined the endosymbiont Xiphinematobacter (...

Alignment-free genome tree inference by learning group-specific distance metrics.

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Patil, Kaustubh R; McHardy, Alice C

2013-01-01

Understanding the evolutionary relationships between organisms is vital for their in-depth study. Gene-based methods are often used to infer such relationships, which are not without drawbacks. One can now attempt to use genome-scale information, because of the ever increasing number of genomes available. This opportunity also presents a challenge in terms of computational efficiency. Two fundamentally different methods are often employed for sequence comparisons, namely alignment-based and alignment-free methods. Alignment-free methods rely on the genome signature concept and provide a computationally efficient way that is also applicable to nonhomologous sequences. The genome signature contains evolutionary signal as it is more similar for closely related organisms than for distantly related ones. We used genome-scale sequence information to infer taxonomic distances between organisms without additional information such as gene annotations. We propose a method to improve genome tree inference by learning specific distance metrics over the genome signature for groups of organisms with similar phylogenetic, genomic, or ecological properties. Specifically, our method learns a Mahalanobis metric for a set of genomes and a reference taxonomy to guide the learning process. By applying this method to more than a thousand prokaryotic genomes, we showed that, indeed, better distance metrics could be learned for most of the 18 groups of organisms tested here. Once a group-specific metric is available, it can be used to estimate the taxonomic distances for other sequenced organisms from the group. This study also presents a large scale comparison between 10 methods--9 alignment-free and 1 alignment-based.

Genomics and the making of yeast biodiversity.

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Hittinger, Chris Todd; Rokas, Antonis; Bai, Feng-Yan; Boekhout, Teun; Gonçalves, Paula; Jeffries, Thomas W; Kominek, Jacek; Lachance, Marc-André; Libkind, Diego; Rosa, Carlos A; Sampaio, José Paulo; Kurtzman, Cletus P

2015-12-01

Yeasts are unicellular fungi that do not form fruiting bodies. Although the yeast lifestyle has evolved multiple times, most known species belong to the subphylum Saccharomycotina (syn. Hemiascomycota, hereafter yeasts). This diverse group includes the premier eukaryotic model system, Saccharomyces cerevisiae; the common human commensal and opportunistic pathogen, Candida albicans; and over 1000 other known species (with more continuing to be discovered). Yeasts are found in every biome and continent and are more genetically diverse than angiosperms or chordates. Ease of culture, simple life cycles, and small genomes (∼10-20Mbp) have made yeasts exceptional models for molecular genetics, biotechnology, and evolutionary genomics. Here we discuss recent developments in understanding the genomic underpinnings of the making of yeast biodiversity, comparing and contrasting natural and human-associated evolutionary processes. Only a tiny fraction of yeast biodiversity and metabolic capabilities has been tapped by industry and science. Expanding the taxonomic breadth of deep genomic investigations will further illuminate how genome function evolves to encode their diverse metabolisms and ecologies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Values in the Smart Grid: The co-evolving political economy of smart distribution

International Nuclear Information System (INIS)

Hall, Stephen; Foxon, Timothy J.

2014-01-01

Investing in smart grid infrastructure is a key enabler for the transition to low carbon energy systems. Recent work has characterised the costs and benefits of individual “smart” investments. The political economy of the UK electricity system, however, has co-evolved such that there is a mismatch between where benefits accrue and where costs are incurred, leading to a problem of value capture and redeployment. Further, some benefits of smart grids are less easy to price directly and can be classified as public goods, such as energy security and decarbonisation. This paper builds on systemic treatments of energy system transitions to characterise the co-evolution of value capture and structural incentives in the electricity distribution system, drawing on semi-structured interviews and focus groups undertaken with smart grid stakeholders in the UK. This leads to an identification of municipal scale values that may be important for business models for the delivery of smart infrastructure. Municipalities may thus pursue specific economic opportunities through smart grid investment. This supports recent practical interest in an expanded role for municipalities as partners and investors in smart grid infrastructures. - Highlights: • Smart grid investments can benefit municipal economic development. • Drawing on urban political economy we describe these values. • New values alter the smart grid investment problem. • New integration of urban policy and DNOs are proposed by this research. • Socio-technical approaches are enhanced by urban political economy and vice versa

Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps

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Zhang, Xian; Liu, Xueduan; Liang, Yili; Xiao, Yunhua; Ma, Liyuan; Guo, Xue; Miao, Bo; Liu, Hongwei; Peng, Deliang; Huang, Wenkun; Yin, Huaqun

2017-01-01

The spatial-temporal distribution of populations in various econiches is thought to be potentially related to individual differences in the utilization of nutrients or other resources, but their functional roles in the microbial communities remain elusive. We compared differentiation in gene repertoire and metabolic profiles, with a focus on the potential functional traits of three commonly recognized members (Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans) in bioleaching heaps. Comparative genomics revealed that intra-species divergence might be driven by horizontal gene transfer. These co-occurring bacteria shared a few homologous genes, which significantly suggested the genomic differences between these organisms. Notably, relatively more genes assigned to the Clusters of Orthologous Groups category [G] (carbohydrate transport and metabolism) were identified in Sulfobacillus thermosulfidooxidans compared to the two other species, which probably indicated their mixotrophic capabilities that assimilate both organic and inorganic forms of carbon. Further inspection revealed distinctive metabolic capabilities involving carbon assimilation, nitrogen uptake, and iron-sulfur cycling, providing robust evidence for functional differences with respect to nutrient utilization. Therefore, we proposed that the mutual compensation of functionalities among these co-occurring organisms might provide a selective advantage for efficiently utilizing the limited resources in their habitats. Furthermore, it might be favorable to chemoautotrophs' lifestyles to form mutualistic interactions with these heterotrophic and/or mixotrophic acidophiles, whereby the latter could degrade organic compounds to effectively detoxify the environments. Collectively, the findings shed light on the genetic traits and potential metabolic activities of these organisms, and enable us to make some inferences about genomic and functional differences that might

Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps

Directory of Open Access Journals (Sweden)

Xian Zhang

2017-05-01

Full Text Available The spatial-temporal distribution of populations in various econiches is thought to be potentially related to individual differences in the utilization of nutrients or other resources, but their functional roles in the microbial communities remain elusive. We compared differentiation in gene repertoire and metabolic profiles, with a focus on the potential functional traits of three commonly recognized members (Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans in bioleaching heaps. Comparative genomics revealed that intra-species divergence might be driven by horizontal gene transfer. These co-occurring bacteria shared a few homologous genes, which significantly suggested the genomic differences between these organisms. Notably, relatively more genes assigned to the Clusters of Orthologous Groups category [G] (carbohydrate transport and metabolism were identified in Sulfobacillus thermosulfidooxidans compared to the two other species, which probably indicated their mixotrophic capabilities that assimilate both organic and inorganic forms of carbon. Further inspection revealed distinctive metabolic capabilities involving carbon assimilation, nitrogen uptake, and iron-sulfur cycling, providing robust evidence for functional differences with respect to nutrient utilization. Therefore, we proposed that the mutual compensation of functionalities among these co-occurring organisms might provide a selective advantage for efficiently utilizing the limited resources in their habitats. Furthermore, it might be favorable to chemoautotrophs' lifestyles to form mutualistic interactions with these heterotrophic and/or mixotrophic acidophiles, whereby the latter could degrade organic compounds to effectively detoxify the environments. Collectively, the findings shed light on the genetic traits and potential metabolic activities of these organisms, and enable us to make some inferences about genomic and functional

Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs).

Science.gov (United States)

Natale, D A; Shankavaram, U T; Galperin, M Y; Wolf, Y I; Aravind, L; Koonin, E V

2000-01-01

Standard archival sequence databases have not been designed as tools for genome annotation and are far from being optimal for this purpose. We used the database of Clusters of Orthologous Groups of proteins (COGs) to reannotate the genomes of two archaea, Aeropyrum pernix, the first member of the Crenarchaea to be sequenced, and Pyrococcus abyssi. A. pernix and P. abyssi proteins were assigned to COGs using the COGNITOR program; the results were verified on a case-by-case basis and augmented by additional database searches using the PSI-BLAST and TBLASTN programs. Functions were predicted for over 300 proteins from A. pernix, which could not be assigned a function using conventional methods with a conservative sequence similarity threshold, an approximately 50% increase compared to the original annotation. A. pernix shares most of the conserved core of proteins that were previously identified in the Euryarchaeota. Cluster analysis or distance matrix tree construction based on the co-occurrence of genomes in COGs showed that A. pernix forms a distinct group within the archaea, although grouping with the two species of Pyrococci, indicative of similar repertoires of conserved genes, was observed. No indication of a specific relationship between Crenarchaeota and eukaryotes was obtained in these analyses. Several proteins that are conserved in Euryarchaeota and most bacteria are unexpectedly missing in A. pernix, including the entire set of de novo purine biosynthesis enzymes, the GTPase FtsZ (a key component of the bacterial and euryarchaeal cell-division machinery), and the tRNA-specific pseudouridine synthase, previously considered universal. A. pernix is represented in 48 COGs that do not contain any euryarchaeal members. Many of these proteins are TCA cycle and electron transport chain enzymes, reflecting the aerobic lifestyle of A. pernix. Special-purpose databases organized on the basis of phylogenetic analysis and carefully curated with respect to known and

CO J = 2-1 EMISSION FROM EVOLVED STARS IN THE GALACTIC BULGE

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Sargent, Benjamin A.; Meixner, M. [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Patel, N. A. [Harvard-Smithsonian Center for Astrophysics, Cambridge, MA 02138 (United States); Otsuka, M.; Srinivasan, S. [Institute of Astronomy and Astrophysics, Academia Sinica, P.O. Box 23-141, Taipei 10617, Taiwan (China); Riebel, D., E-mail: baspci@rit.edu [Department of Physics and Astronomy, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 (United States)

2013-03-01

We observe a sample of eight evolved stars in the Galactic bulge in the CO J = 2-1 line using the Submillimeter Array with angular resolution of 1''-4''. These stars have been detected previously at infrared wavelengths, and several of them have OH maser emission. We detect CO J = 2-1 emission from three of the sources in the sample: OH 359.943 +0.260, [SLO2003] A12, and [SLO2003] A51. We do not detect the remaining five stars in the sample because of heavy contamination from the galactic CO emission. Combining CO data with observations at infrared wavelengths constraining dust mass loss from these stars, we determine the gas-to-dust ratios of the Galactic bulge stars for which CO emission is detected. For OH 359.943 +0.260, we determine a gas mass-loss rate of 7.9 ({+-}2.2) Multiplication-Sign 10{sup -5} M {sub Sun} yr{sup -1} and a gas-to-dust ratio of 310 ({+-}89). For [SLO2003] A12, we find a gas mass-loss rate of 5.4 ({+-}2.8) Multiplication-Sign 10{sup -5} M {sub Sun} yr{sup -1} and a gas-to-dust ratio of 220 ({+-}110). For [SLO2003] A51, we find a gas mass-loss rate of 3.4 ({+-}3.0) Multiplication-Sign 10{sup -5} M {sub Sun} yr{sup -1} and a gas-to-dust ratio of 160 ({+-}140), reflecting the low quality of our tentative detection of the CO J = 2-1 emission from A51. We find that the CO J = 2-1 detections of OH/IR stars in the Galactic bulge require lower average CO J = 2-1 backgrounds.

Conserved genomic organisation of Group B Sox genes in insects.

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Woerfel Gertrud

2005-05-01

Full Text Available Abstract Background Sox domain containing genes are important metazoan transcriptional regulators implicated in a wide rage of developmental processes. The vertebrate B subgroup contains the Sox1, Sox2 and Sox3 genes that have early functions in neural development. Previous studies show that Drosophila Group B genes have been functionally conserved since they play essential roles in early neural specification and mutations in the Drosophila Dichaete and SoxN genes can be rescued with mammalian Sox genes. Despite their importance, the extent and organisation of the Group B family in Drosophila has not been fully characterised, an important step in using Drosophila to examine conserved aspects of Group B Sox gene function. Results We have used the directed cDNA sequencing along with the output from the publicly-available genome sequencing projects to examine the structure of Group B Sox domain genes in Drosophila melanogaster, Drosophila pseudoobscura, Anopheles gambiae and Apis mellifora. All of the insect genomes contain four genes encoding Group B proteins, two of which are intronless, as is the case with vertebrate group B genes. As has been previously reported and unusually for Group B genes, two of the insect group B genes, Sox21a and Sox21b, contain introns within their DNA-binding domains. We find that the highly unusual multi-exon structure of the Sox21b gene is common to the insects. In addition, we find that three of the group B Sox genes are organised in a linked cluster in the insect genomes. By in situ hybridisation we show that the pattern of expression of each of the four group B genes during embryogenesis is conserved between D. melanogaster and D. pseudoobscura. Conclusion The DNA-binding domain sequences and genomic organisation of the group B genes have been conserved over 300 My of evolution since the last common ancestor of the Hymenoptera and the Diptera. Our analysis suggests insects have two Group B1 genes, SoxN and

Global co-existence of two evolutionary lineages of parvovirus B19 1a, different in genome-wide synonymous positions.

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Marijke W A Molenaar-de Backer

Full Text Available Parvovirus B19 (B19V can cause infection in humans. To date, three genotypes of B19V, with subtypes, are known, of which genotype 1a is the most prevalent genotype in the Western world. We sequenced the genome of B19V strains of 65 asymptomatic, recently infected Dutch blood donors, to investigate the spatio-temporal distribution of B19V strains, in the years 2003-2009. The sequences were compared to B19V sequences from Dutch patients with fifth disease, and to global B19V sequences as available from GenBank. All Dutch B19V strains belonged to genotype 1a. Phylogenetic analysis of the strains from Dutch blood donors showed that two groups of genotype 1a co-exist. A clear-cut division into the two groups was also found among the B19V strains from Dutch patients, and among the B19V sequences in GenBank. The two groups of genotype 1a co-exist around the world and do not appear to differ in their ability to cause disease. Strikingly, the two groups of B19V predominantly differ in synonymous mutations, distributed throughout the entire genome of B19V. We propose to call the two groups of B19V genotype 1a respectively subtype 1a1 and 1a2.

Xylella fastidiosa CoDiRO strain associated with the olive quick decline syndrome in southern Italy belongs to a clonal complex of the subspecies pauca that evolved in Central America.

Science.gov (United States)

Marcelletti, Simone; Scortichini, Marco

2016-12-01

Xylella fastidiosa, a xylem-limited bacterium transmitted by xylem-fluid-feeding Hemiptera insects, causes economic losses of both woody and herbaceous plant species. A Xyl. fastidiosa subsp. pauca strain, namely CoDiRO, was recently found to be associated with the 'olive quick decline syndrome' in southern Italy (i.e. Apulia region). Recently, some Xyl. fastidiosa strains intercepted in France from Coffea spp. plant cuttings imported from Central and South America were characterized. The introduction of infected plant material from Central America in Apulia was also postulated even though an ad hoc study to confirm this hypothesis is lacking. In the present study, we assessed the complete and draft genome of 27 Xyl. fastidiosa strains. Through a genome-wide approach, we confirmed the occurrence of three subspecies within Xyl. fastidiosa, namely fastidiosa, multiplex and pauca, and demonstrated the occurrence of a genetic clonal complex of four Xyl. fastidiosa strains belonging to subspecies pauca which evolved in Central America. The CoDiRO strain displayed 13 SNPs when compared with a strain isolated in Costa Rica from Coffea sp. and 32 SNPs when compared with two strains obtained from Nerium oleander in Costa Rica. These results support the close relationships of the two strains. The four strains in the clonal complex contain prophage-like genes in their genomes. This study strongly supports the possibility of the introduction of Xyl. fastidiosa in southern Italy via coffee plants grown in Central America. The data also stress how the current global circulation of agricultural commodities potentially threatens the agrosystems worldwide.

Host-symbiont co-speciation and reductive genome evolution in gut symbiotic bacteria of acanthosomatid stinkbugs

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Kamagata Yoichi

2009-01-01

Full Text Available Abstract Background Host-symbiont co-speciation and reductive genome evolution have been commonly observed among obligate endocellular insect symbionts, while such examples have rarely been identified among extracellular ones, the only case reported being from gut symbiotic bacteria of stinkbugs of the family Plataspidae. Considering that gut symbiotic communities are vulnerable to invasion of foreign microbes, gut symbiotic associations have been thought to be evolutionarily not stable. Stinkbugs of the family Acanthosomatidae harbor a bacterial symbiont in the midgut crypts, the lumen of which is completely sealed off from the midgut main tract, thereby retaining the symbiont in the isolated cryptic cavities. We investigated histological, ecological, phylogenetic, and genomic aspects of the unique gut symbiosis of the acanthosomatid stinkbugs. Results Phylogenetic analyses showed that the acanthosomatid symbionts constitute a distinct clade in the γ-Proteobacteria, whose sister groups are the obligate endocellular symbionts of aphids Buchnera and the obligate gut symbionts of plataspid stinkbugs Ishikawaella. In addition to the midgut crypts, the symbionts were located in a pair of peculiar lubricating organs associated with the female ovipositor, by which the symbionts are vertically transmitted via egg surface contamination. The symbionts were detected not from ovaries but from deposited eggs, and surface sterilization of eggs resulted in symbiont-free hatchlings. The symbiont-free insects suffered retarded growth, high mortality, and abnormal morphology, suggesting important biological roles of the symbiont for the host insects. The symbiont phylogeny was generally concordant with the host phylogeny, indicating host-symbiont co-speciation over evolutionary time despite the extracellular association. Meanwhile, some local host-symbiont phylogenetic discrepancies were found, suggesting occasional horizontal symbiont transfers across the host

Co-regulation of a large and rapidly evolving repertoire of odorant receptor genes

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Lane Robert P

2007-09-01

Full Text Available Abstract The olfactory system meets niche- and species-specific demands by an accelerated evolution of its odorant receptor repertoires. In this review, we describe evolutionary processes that have shaped olfactory and vomeronasal receptor gene families in vertebrate genomes. We emphasize three important periods in the evolution of the olfactory system evident by comparative genomics: the adaptation to land in amphibian ancestors, the decline of olfaction in primates, and the delineation of putative pheromone receptors concurrent with rodent speciation. The rapid evolution of odorant receptor genes, the sheer size of the repertoire, as well as their wide distribution in the genome, presents a developmental challenge: how are these ever-changing odorant receptor repertoires coordinated within the olfactory system? A central organizing principle in olfaction is the specialization of sensory neurons resulting from each sensory neuron expressing only ~one odorant receptor allele. In this review, we also discuss this mutually exclusive expression of odorant receptor genes. We have considered several models to account for co-regulation of odorant receptor repertoires, as well as discussed a new hypothesis that invokes important epigenetic properties of the system.

Comparative Genomics of the Bacterial Genus Streptococcus Illuminates Evolutionary Implications of Species Groups

Science.gov (United States)

Gao, Xiao-Yang; Zhi, Xiao-Yang; Li, Hong-Wei; Klenk, Hans-Peter; Li, Wen-Jun

2014-01-01

Members of the genus Streptococcus within the phylum Firmicutes are among the most diverse and significant zoonotic pathogens. This genus has gone through considerable taxonomic revision due to increasing improvements of chemotaxonomic approaches, DNA hybridization and 16S rRNA gene sequencing. It is proposed to place the majority of streptococci into “species groups”. However, the evolutionary implications of species groups are not clear presently. We use comparative genomic approaches to yield a better understanding of the evolution of Streptococcus through genome dynamics, population structure, phylogenies and virulence factor distribution of species groups. Genome dynamics analyses indicate that the pan-genome size increases with the addition of newly sequenced strains, while the core genome size decreases with sequential addition at the genus level and species group level. Population structure analysis reveals two distinct lineages, one including Pyogenic, Bovis, Mutans and Salivarius groups, and the other including Mitis, Anginosus and Unknown groups. Phylogenetic dendrograms show that species within the same species group cluster together, and infer two main clades in accordance with population structure analysis. Distribution of streptococcal virulence factors has no obvious patterns among the species groups; however, the evolution of some common virulence factors is congruous with the evolution of species groups, according to phylogenetic inference. We suggest that the proposed streptococcal species groups are reasonable from the viewpoints of comparative genomics; evolution of the genus is congruent with the individual evolutionary trajectories of different species groups. PMID:24977706

The visualCMAT: A web-server to select and interpret correlated mutations/co-evolving residues in protein families.

Science.gov (United States)

Suplatov, Dmitry; Sharapova, Yana; Timonina, Daria; Kopylov, Kirill; Švedas, Vytas

2018-04-01

The visualCMAT web-server was designed to assist experimental research in the fields of protein/enzyme biochemistry, protein engineering, and drug discovery by providing an intuitive and easy-to-use interface to the analysis of correlated mutations/co-evolving residues. Sequence and structural information describing homologous proteins are used to predict correlated substitutions by the Mutual information-based CMAT approach, classify them into spatially close co-evolving pairs, which either form a direct physical contact or interact with the same ligand (e.g. a substrate or a crystallographic water molecule), and long-range correlations, annotate and rank binding sites on the protein surface by the presence of statistically significant co-evolving positions. The results of the visualCMAT are organized for a convenient visual analysis and can be downloaded to a local computer as a content-rich all-in-one PyMol session file with multiple layers of annotation corresponding to bioinformatic, statistical and structural analyses of the predicted co-evolution, or further studied online using the built-in interactive analysis tools. The online interactivity is implemented in HTML5 and therefore neither plugins nor Java are required. The visualCMAT web-server is integrated with the Mustguseal web-server capable of constructing large structure-guided sequence alignments of protein families and superfamilies using all available information about their structures and sequences in public databases. The visualCMAT web-server can be used to understand the relationship between structure and function in proteins, implemented at selecting hotspots and compensatory mutations for rational design and directed evolution experiments to produce novel enzymes with improved properties, and employed at studying the mechanism of selective ligand's binding and allosteric communication between topologically independent sites in protein structures. The web-server is freely available at https

Differentiation of strains from the Bacillus cereus group by RFLP-PFGE genomic fingerprinting.

Science.gov (United States)

Otlewska, Anna; Oltuszak-Walczak, Elzbieta; Walczak, Piotr

2013-11-01

Bacillus mycoides, Bacillus pseudomycoides, Bacillus weihenstephanensis, Bacillus anthracis, Bacillus thuringiensis, and Bacillus cereus belong to the B. cereus group. The last three species are characterized by different phenotype features and pathogenicity spectrum, but it has been shown that these species are genetically closely related. The macrorestriction analysis of the genomic DNA with the NotI enzyme was used to generate polymorphism of restriction profiles for 39 food-borne isolates (B. cereus, B. mycoides) and seven reference strains (B. mycoides, B. thuringiensis, B. weihenstephanensis, and B. cereus). The PFGE method was applied to differentiate the examined strains of the B. cereus group. On the basis of the unweighted pair group method with the arithmetic mean method and Dice coefficient, the strains were divided into five clusters (types A-E), and the most numerous group was group A (25 strains). A total of 21 distinct pulsotypes were observed. The RFLP-PFGE analysis was successfully used for the differentiation and characterization of B. cereus and B. mycoides strains isolated from different food products. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evolution of small prokaryotic genomes

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David José Martínez-Cano

2015-01-01

Full Text Available As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ~800 genes as well as endosymbiotic bacteria with as few as ~140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent role. However, new experimental data suggest that selective processes may be at operation as well for endosymbiotic prokaryotes at least during the first stages of genome reduction. Endosymbiotic prokaryotes have evolved diverse strategies for living with reduced gene sets inside a host-defined medium. These include utilization of host-encoded functions (some of them coded by genes acquired by gene transfer from the endosymbiont and/or other bacteria; metabolic complementation between co-symbionts; and forming consortiums with other bacteria within the host. Recent genome sequencing projects of intracellular mutualistic bacteria showed that previously believed universal evolutionary trends like reduced G+C content and conservation of genome synteny are not always present in highly reduced genomes. Finally, the simplified molecular machinery of some of these organisms with small genomes may be used to aid in the design of artificial minimal cells. Here we review recent genomic discoveries of the biology of prokaryotes endowed with small gene sets and discuss the evolutionary mechanisms that have been proposed to explain their peculiar nature.

Modeling growth and dissemination of lymphoma in a co-evolving lymph node: a diffuse-domain approach

Science.gov (United States)

Chuang, Yao-Li; Cristini, Vittorio; Chen, Ying; Li, Xiangrong; Frieboes, Hermann; Lowengrub, John

2013-03-01

While partial differential equation models of tumor growth have successfully described various spatiotemporal phenomena observed for in-vitro tumor spheroid experiments, one challenge towards taking these models to further study in-vivo tumors is that instead of relatively static tissue culture with regular boundary conditions, in-vivo tumors are often confined in organ tissues that co-evolve with the tumor growth. Here we adopt a recently developed diffuse-domain method to account for the co-evolving domain boundaries, adapting our previous in-vitro tumor model for the development of lymphoma encapsulated in a lymph node, which may swell or shrink due to proliferation and dissemination of lymphoma cells and treatment by chemotherapy. We use the model to study the induced spatial heterogeneity, which may arise as an emerging phenomenon in experimental observations and model analysis. Spatial heterogeneity is believed to lead to tumor infiltration patterns and reduce the efficacy of chemotherapy, leaving residuals that cause cancer relapse after the treatment. Understanding the spatiotemporal evolution of in-vivo tumors can be an essential step towards more effective strategies of curing cancer. Supported by NIH-PSOC grant 1U54CA143907-01.

Molecular cytogenetic and genomic analyses reveal new insights into the origin of the wheat B genome.

Science.gov (United States)

Zhang, Wei; Zhang, Mingyi; Zhu, Xianwen; Cao, Yaping; Sun, Qing; Ma, Guojia; Chao, Shiaoman; Yan, Changhui; Xu, Steven S; Cai, Xiwen

2018-02-01

This work pinpointed the goatgrass chromosomal segment in the wheat B genome using modern cytogenetic and genomic technologies, and provided novel insights into the origin of the wheat B genome. Wheat is a typical allopolyploid with three homoeologous subgenomes (A, B, and D). The donors of the subgenomes A and D had been identified, but not for the subgenome B. The goatgrass Aegilops speltoides (genome SS) has been controversially considered a possible candidate for the donor of the wheat B genome. However, the relationship of the Ae. speltoides S genome with the wheat B genome remains largely obscure. The present study assessed the homology of the B and S genomes using an integrative cytogenetic and genomic approach, and revealed the contribution of Ae. speltoides to the origin of the wheat B genome. We discovered noticeable homology between wheat chromosome 1B and Ae. speltoides chromosome 1S, but not between other chromosomes in the B and S genomes. An Ae. speltoides-originated segment spanning a genomic region of approximately 10.46 Mb was detected on the long arm of wheat chromosome 1B (1BL). The Ae. speltoides-originated segment on 1BL was found to co-evolve with the rest of the B genome. Evidently, Ae. speltoides had been involved in the origin of the wheat B genome, but should not be considered an exclusive donor of this genome. The wheat B genome might have a polyphyletic origin with multiple ancestors involved, including Ae. speltoides. These novel findings will facilitate genome studies in wheat and other polyploids.

A synergism between adaptive effects and evolvability drives whole genome duplication to fixation.

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Cuypers, Thomas D; Hogeweg, Paulien

2014-04-01

Whole genome duplication has shaped eukaryotic evolutionary history and has been associated with drastic environmental change and species radiation. While the most common fate of WGD duplicates is a return to single copy, retained duplicates have been found enriched for highly interacting genes. This pattern has been explained by a neutral process of subfunctionalization and more recently, dosage balance selection. However, much about the relationship between environmental change, WGD and adaptation remains unknown. Here, we study the duplicate retention pattern postWGD, by letting virtual cells adapt to environmental changes. The virtual cells have structured genomes that encode a regulatory network and simple metabolism. Populations are under selection for homeostasis and evolve by point mutations, small indels and WGD. After populations had initially adapted fully to fluctuating resource conditions re-adaptation to a broad range of novel environments was studied by tracking mutations in the line of descent. WGD was established in a minority (≈30%) of lineages, yet, these were significantly more successful at re-adaptation. Unexpectedly, WGD lineages conserved more seemingly redundant genes, yet had higher per gene mutation rates. While WGD duplicates of all functional classes were significantly over-retained compared to a model of neutral losses, duplicate retention was clearly biased towards highly connected TFs. Importantly, no subfunctionalization occurred in conserved pairs, strongly suggesting that dosage balance shaped retention. Meanwhile, singles diverged significantly. WGD, therefore, is a powerful mechanism to cope with environmental change, allowing conservation of a core machinery, while adapting the peripheral network to accommodate change.

A synergism between adaptive effects and evolvability drives whole genome duplication to fixation.

Directory of Open Access Journals (Sweden)

Thomas D Cuypers

2014-04-01

Full Text Available Whole genome duplication has shaped eukaryotic evolutionary history and has been associated with drastic environmental change and species radiation. While the most common fate of WGD duplicates is a return to single copy, retained duplicates have been found enriched for highly interacting genes. This pattern has been explained by a neutral process of subfunctionalization and more recently, dosage balance selection. However, much about the relationship between environmental change, WGD and adaptation remains unknown. Here, we study the duplicate retention pattern postWGD, by letting virtual cells adapt to environmental changes. The virtual cells have structured genomes that encode a regulatory network and simple metabolism. Populations are under selection for homeostasis and evolve by point mutations, small indels and WGD. After populations had initially adapted fully to fluctuating resource conditions re-adaptation to a broad range of novel environments was studied by tracking mutations in the line of descent. WGD was established in a minority (≈30% of lineages, yet, these were significantly more successful at re-adaptation. Unexpectedly, WGD lineages conserved more seemingly redundant genes, yet had higher per gene mutation rates. While WGD duplicates of all functional classes were significantly over-retained compared to a model of neutral losses, duplicate retention was clearly biased towards highly connected TFs. Importantly, no subfunctionalization occurred in conserved pairs, strongly suggesting that dosage balance shaped retention. Meanwhile, singles diverged significantly. WGD, therefore, is a powerful mechanism to cope with environmental change, allowing conservation of a core machinery, while adapting the peripheral network to accommodate change.

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

DEFF Research Database (Denmark)

Nielsen, Henrik Bjørn; Almeida, Mathieu; Juncker, Agnieszka

2014-01-01

of microbial genomes without the need for reference sequences. We demonstrate the method on data from 396 human gut microbiome samples and identify 7,381 co-abundance gene groups (CAGs), including 741 metagenomic species (MGS). We use these to assemble 238 high-quality microbial genomes and identify...

Adaptation of the short intergenic spacers between co-directional genes to the Shine-Dalgarno motif among prokaryote genomes

DEFF Research Database (Denmark)

Caro, Albert Pallejà; García-Vallvé, Santiago; Romeu, Antoni

2009-01-01

ABSTRACT: BACKGROUND: In prokaryote genomes most of the co-directional genes are in close proximity. Even the coding sequence or the stop codon of a gene can overlap with the Shine-Dalgarno (SD) sequence of the downstream co-directional gene. In this paper we analyze how the presence of SD may...... influence the stop codon usage or the spacing lengths between co-directional genes. RESULTS: The SD sequences for 530 prokaryote genomes have been predicted using computer calculations of the base-pairing free energy between translation initiation regions and the 16S rRNA 3' tail. Genomes with a large...... to the discussion of which factors affect the intergenic lengths, which cannot be totally explained by the pressure to compact the prokaryote genomes....

The Capsaspora genome reveals a complex unicellular prehistory of animals.

Science.gov (United States)

Suga, Hiroshi; Chen, Zehua; de Mendoza, Alex; Sebé-Pedrós, Arnau; Brown, Matthew W; Kramer, Eric; Carr, Martin; Kerner, Pierre; Vervoort, Michel; Sánchez-Pons, Núria; Torruella, Guifré; Derelle, Romain; Manning, Gerard; Lang, B Franz; Russ, Carsten; Haas, Brian J; Roger, Andrew J; Nusbaum, Chad; Ruiz-Trillo, Iñaki

2013-01-01

To reconstruct the evolutionary origin of multicellular animals from their unicellular ancestors, the genome sequences of diverse unicellular relatives are essential. However, only the genome of the choanoflagellate Monosiga brevicollis has been reported to date. Here we completely sequence the genome of the filasterean Capsaspora owczarzaki, the closest known unicellular relative of metazoans besides choanoflagellates. Analyses of this genome alter our understanding of the molecular complexity of metazoans' unicellular ancestors showing that they had a richer repertoire of proteins involved in cell adhesion and transcriptional regulation than previously inferred only with the choanoflagellate genome. Some of these proteins were secondarily lost in choanoflagellates. In contrast, most intercellular signalling systems controlling development evolved later concomitant with the emergence of the first metazoans. We propose that the acquisition of these metazoan-specific developmental systems and the co-option of pre-existing genes drove the evolutionary transition from unicellular protists to metazoans.

StreptoBase: An Oral Streptococcus mitis Group Genomic Resource and Analysis Platform.

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Wenning Zheng

Full Text Available The oral streptococci are spherical Gram-positive bacteria categorized under the phylum Firmicutes which are among the most common causative agents of bacterial infective endocarditis (IE and are also important agents in septicaemia in neutropenic patients. The Streptococcus mitis group is comprised of 13 species including some of the most common human oral colonizers such as S. mitis, S. oralis, S. sanguinis and S. gordonii as well as species such as S. tigurinus, S. oligofermentans and S. australis that have only recently been classified and are poorly understood at present. We present StreptoBase, which provides a specialized free resource focusing on the genomic analyses of oral species from the mitis group. It currently hosts 104 S. mitis group genomes including 27 novel mitis group strains that we sequenced using the high throughput Illumina HiSeq technology platform, and provides a comprehensive set of genome sequences for analyses, particularly comparative analyses and visualization of both cross-species and cross-strain characteristics of S. mitis group bacteria. StreptoBase incorporates sophisticated in-house designed bioinformatics web tools such as Pairwise Genome Comparison (PGC tool and Pathogenomic Profiling Tool (PathoProT, which facilitate comparative pathogenomics analysis of Streptococcus strains. Examples are provided to demonstrate how StreptoBase can be employed to compare genome structure of different S. mitis group bacteria and putative virulence genes profile across multiple streptococcal strains. In conclusion, StreptoBase offers access to a range of streptococci genomic resources as well as analysis tools and will be an invaluable platform to accelerate research in streptococci. Database URL: http://streptococcus.um.edu.my.

StreptoBase: An Oral Streptococcus mitis Group Genomic Resource and Analysis Platform.

Science.gov (United States)

Zheng, Wenning; Tan, Tze King; Paterson, Ian C; Mutha, Naresh V R; Siow, Cheuk Chuen; Tan, Shi Yang; Old, Lesley A; Jakubovics, Nicholas S; Choo, Siew Woh

2016-01-01

The oral streptococci are spherical Gram-positive bacteria categorized under the phylum Firmicutes which are among the most common causative agents of bacterial infective endocarditis (IE) and are also important agents in septicaemia in neutropenic patients. The Streptococcus mitis group is comprised of 13 species including some of the most common human oral colonizers such as S. mitis, S. oralis, S. sanguinis and S. gordonii as well as species such as S. tigurinus, S. oligofermentans and S. australis that have only recently been classified and are poorly understood at present. We present StreptoBase, which provides a specialized free resource focusing on the genomic analyses of oral species from the mitis group. It currently hosts 104 S. mitis group genomes including 27 novel mitis group strains that we sequenced using the high throughput Illumina HiSeq technology platform, and provides a comprehensive set of genome sequences for analyses, particularly comparative analyses and visualization of both cross-species and cross-strain characteristics of S. mitis group bacteria. StreptoBase incorporates sophisticated in-house designed bioinformatics web tools such as Pairwise Genome Comparison (PGC) tool and Pathogenomic Profiling Tool (PathoProT), which facilitate comparative pathogenomics analysis of Streptococcus strains. Examples are provided to demonstrate how StreptoBase can be employed to compare genome structure of different S. mitis group bacteria and putative virulence genes profile across multiple streptococcal strains. In conclusion, StreptoBase offers access to a range of streptococci genomic resources as well as analysis tools and will be an invaluable platform to accelerate research in streptococci. Database URL: http://streptococcus.um.edu.my.

Molecular Epidemiology and Genomics of Group A Streptococcus

Science.gov (United States)

Bessen, Debra E.; McShan, W. Michael; Nguyen, Scott V.; Shetty, Amol; Agrawal, Sonia; Tettelin, Hervé

2014-01-01

Streptococcus pyogenes (group A streptococcus; GAS) is a strict human pathogen with a very high prevalence worldwide. This review highlights the genetic organization of the species and the important ecological considerations that impact its evolution. Recent advances are presented on the topics of molecular epidemiology, population biology, molecular basis for genetic change, genome structure and genetic flux, phylogenomics and closely related streptococcal species, and the long- and short-term evolution of GAS. The application of whole genome sequence data to addressing key biological questions is discussed. PMID:25460818

HelmCoP: an online resource for helminth functional genomics and drug and vaccine targets prioritization.

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Sahar Abubucker

Full Text Available A vast majority of the burden from neglected tropical diseases result from helminth infections (nematodes and platyhelminthes. Parasitic helminthes infect over 2 billion, exerting a high collective burden that rivals high-mortality conditions such as AIDS or malaria, and cause devastation to crops and livestock. The challenges to improve control of parasitic helminth infections are multi-fold and no single category of approaches will meet them all. New information such as helminth genomics, functional genomics and proteomics coupled with innovative bioinformatic approaches provide fundamental molecular information about these parasites, accelerating both basic research as well as development of effective diagnostics, vaccines and new drugs. To facilitate such studies we have developed an online resource, HelmCoP (Helminth Control and Prevention, built by integrating functional, structural and comparative genomic data from plant, animal and human helminthes, to enable researchers to develop strategies for drug, vaccine and pesticide prioritization, while also providing a useful comparative genomics platform. HelmCoP encompasses genomic data from several hosts, including model organisms, along with a comprehensive suite of structural and functional annotations, to assist in comparative analyses and to study host-parasite interactions. The HelmCoP interface, with a sophisticated query engine as a backbone, allows users to search for multi-factorial combinations of properties and serves readily accessible information that will assist in the identification of various genes of interest. HelmCoP is publicly available at: http://www.nematode.net/helmcop.html.

Phage morphology recapitulates phylogeny: the comparative genomics of a new group of myoviruses.

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André M Comeau

Full Text Available Among dsDNA tailed bacteriophages (Caudovirales, members of the Myoviridae family have the most sophisticated virion design that includes a complex contractile tail structure. The Myoviridae generally have larger genomes than the other phage families. Relatively few "dwarf" myoviruses, those with a genome size of less than 50 kb such as those of the Mu group, have been analyzed in extenso. Here we report on the genome sequencing and morphological characterization of a new group of such phages that infect a diverse range of Proteobacteria, namely Aeromonas salmonicida phage 56, Vibrio cholerae phages 138 and CP-T1, Bdellovibrio phage φ1422, and Pectobacterium carotovorum phage ZF40. This group of dwarf myoviruses shares an identical virion morphology, characterized by usually short contractile tails, and have genome sizes of approximately 45 kb. Although their genome sequences are variable in their lysogeny, replication, and host adaption modules, presumably reflecting differing lifestyles and hosts, their structural and morphogenesis modules have been evolutionarily constrained by their virion morphology. Comparative genomic analysis reveals that these phages, along with related prophage genomes, form a new coherent group within the Myoviridae. The results presented in this communication support the hypothesis that the diversity of phages may be more structured than generally believed and that the innumerable phages in the biosphere all belong to discrete lineages or families.

NMR evidence for Co-Al-Co molecular groups trapped in cages of Co4Al13

International Nuclear Information System (INIS)

Jeglic, P.; Heggen, M.; Feuerbacher, M.; Bauer, B.; Gille, P.; Haarmann, F.

2009-01-01

We present the results of 27 Al nuclear magnetic resonance (NMR) experiments on the phase Co 4 Al 13 . These results are compared to a recent structure model [1], which demonstrates a unique bonding for Al atoms in the Co-Al-Co molecular groups. In our measurement, two 27 Al signals were identified. The first one originates from Al atoms forming cages. The second signal corresponds to Al sites with exceptionally large almost axially symmetric quadrupole coupling. This finding is in perfect agreement with isolated Co-Al-Co molecular groups in accordance to Ref. [1].

Effect of co-payment on behavioral response to consumer genomic testing.

Science.gov (United States)

Liu, Wendy; Outlaw, Jessica J; Wineinger, Nathan; Boeldt, Debra; Bloss, Cinnamon S

2018-01-29

Existing research in consumer behavior suggests that perceptions and usage of a product post-purchase depends, in part, on how the product was marketed, including price paid. In the current study, we examine the effect of providing an out-of-pocket co-payment for consumer genomic testing (CGT) on consumer post-purchase behavior using both correlational field evidence and a hypothetical online experiment. Participants were enrolled in a longitudinal cohort study of the impact of CGT and completed behavioral assessments before and after receipt of CGT results. Most participants provided a co-payment for the test (N = 1668), while others (N = 369) received fully subsidized testing. The two groups were compared regarding changes in health behaviors and post-test use of health care resources. Participants who paid were more likely to share results with their physician (p = .012) and obtain follow-up health screenings (p = .005) relative to those who received fully subsidized testing. A follow-up online experiment in which participants (N = 303) were randomized to a "fully-subsidized" versus "co-payment" condition found that simulating provision of a co-payment significantly increased intentions to seek follow-up screening tests (p = .050) and perceptions of the test results as more trustworthy (p = .02). Provision of an out-of-pocket co-payment for CGT may influence consumer's post-purchase behavior consistent with a price placebo effect. Cognitive dissonance or sunk cost may help explain the increase in screening propensity among paying consumers. Such individuals may obtain follow-up screenings to validate their initial decision to expend personal resources to obtain CGT. © Society of Behavioral Medicine 2018.

In situ characterization of cofacial Co(IV) centers in Co4O4 cubane: Modeling the high-valent active site in oxygen-evolving catalysts.

Science.gov (United States)

Brodsky, Casey N; Hadt, Ryan G; Hayes, Dugan; Reinhart, Benjamin J; Li, Nancy; Chen, Lin X; Nocera, Daniel G

2017-04-11

The Co 4 O 4 cubane is a representative structural model of oxidic cobalt oxygen-evolving catalysts (Co-OECs). The Co-OECs are active when residing at two oxidation levels above an all-Co(III) resting state. This doubly oxidized Co(IV) 2 state may be captured in a Co(III) 2 (IV) 2 cubane. We demonstrate that the Co(III) 2 (IV) 2 cubane may be electrochemically generated and the electronic properties of this unique high-valent state may be probed by in situ spectroscopy. Intervalence charge-transfer (IVCT) bands in the near-IR are observed for the Co(III) 2 (IV) 2 cubane, and spectroscopic analysis together with electrochemical kinetics measurements reveal a larger reorganization energy and a smaller electron transfer rate constant for the doubly versus singly oxidized cubane. Spectroelectrochemical X-ray absorption data further reveal systematic spectral changes with successive oxidations from the cubane resting state. Electronic structure calculations correlated to experimental data suggest that this state is best represented as a localized, antiferromagnetically coupled Co(IV) 2 dimer. The exchange coupling in the cofacial Co(IV) 2 site allows for parallels to be drawn between the electronic structure of the Co 4 O 4 cubane model system and the high-valent active site of the Co-OEC, with specific emphasis on the manifestation of a doubly oxidized Co(IV) 2 center on O-O bond formation.

A common genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria.

Directory of Open Access Journals (Sweden)

Lisa C Crossman

2008-07-01

Full Text Available This work centres on the genomic comparisons of two closely-related nitrogen-fixing symbiotic bacteria, Rhizobium leguminosarum biovar viciae 3841 and Rhizobium etli CFN42. These strains maintain a stable genomic core that is also common to other rhizobia species plus a very variable and significant accessory component. The chromosomes are highly syntenic, whereas plasmids are related by fewer syntenic blocks and have mosaic structures. The pairs of plasmids p42f-pRL12, p42e-pRL11 and p42b-pRL9 as well large parts of p42c with pRL10 are shown to be similar, whereas the symbiotic plasmids (p42d and pRL10 are structurally unrelated and seem to follow distinct evolutionary paths. Even though purifying selection is acting on the whole genome, the accessory component is evolving more rapidly. This component is constituted largely for proteins for transport of diverse metabolites and elements of external origin. The present analysis allows us to conclude that a heterogeneous and quickly diversifying group of plasmids co-exists in a common genomic framework.

Large clusters of co-expressed genes in the Drosophila genome.

Science.gov (United States)

Boutanaev, Alexander M; Kalmykova, Alla I; Shevelyov, Yuri Y; Nurminsky, Dmitry I

2002-12-12

Clustering of co-expressed, non-homologous genes on chromosomes implies their co-regulation. In lower eukaryotes, co-expressed genes are often found in pairs. Clustering of genes that share aspects of transcriptional regulation has also been reported in higher eukaryotes. To advance our understanding of the mode of coordinated gene regulation in multicellular organisms, we performed a genome-wide analysis of the chromosomal distribution of co-expressed genes in Drosophila. We identified a total of 1,661 testes-specific genes, one-third of which are clustered on chromosomes. The number of clusters of three or more genes is much higher than expected by chance. We observed a similar trend for genes upregulated in the embryo and in the adult head, although the expression pattern of individual genes cannot be predicted on the basis of chromosomal position alone. Our data suggest that the prevalent mechanism of transcriptional co-regulation in higher eukaryotes operates with extensive chromatin domains that comprise multiple genes.

Phylogenomics and the Dynamic Genome Evolution of the Genus Streptococcus

Science.gov (United States)

Richards, Vincent P.; Palmer, Sara R.; Pavinski Bitar, Paulina D.; Qin, Xiang; Weinstock, George M.; Highlander, Sarah K.; Town, Christopher D.; Burne, Robert A.; Stanhope, Michael J.

2014-01-01

The genus Streptococcus comprises important pathogens that have a severe impact on human health and are responsible for substantial economic losses to agriculture. Here, we utilize 46 Streptococcus genome sequences (44 species), including eight species sequenced here, to provide the first genomic level insight into the evolutionary history and genetic basis underlying the functional diversity of all major groups of this genus. Gene gain/loss analysis revealed a dynamic pattern of genome evolution characterized by an initial period of gene gain followed by a period of loss, as the major groups within the genus diversified. This was followed by a period of genome expansion associated with the origins of the present extant species. The pattern is concordant with an emerging view that genomes evolve through a dynamic process of expansion and streamlining. A large proportion of the pan-genome has experienced lateral gene transfer (LGT) with causative factors, such as relatedness and shared environment, operating over different evolutionary scales. Multiple gene ontology terms were significantly enriched for each group, and mapping terms onto the phylogeny showed that those corresponding to genes born on branches leading to the major groups represented approximately one-fifth of those enriched. Furthermore, despite the extensive LGT, several biochemical characteristics have been retained since group formation, suggesting genomic cohesiveness through time, and that these characteristics may be fundamental to each group. For example, proteolysis: mitis group; urea metabolism: salivarius group; carbohydrate metabolism: pyogenic group; and transcription regulation: bovis group. PMID:24625962

Uncovering genomic causes of co-morbidity in epilepsy: gene-driven phenotypic characterization of rare microdeletions.

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Dalia Kasperavičiūtė

Full Text Available Patients with epilepsy often suffer from other important conditions. The existence of such co-morbidities is frequently not recognized and their relationship with epilepsy usually remains unexplained.We describe three patients with common, sporadic, non-syndromic epilepsies in whom large genomic microdeletions were found during a study of genetic susceptibility to epilepsy. We performed detailed gene-driven clinical investigations in each patient. Disruption of the function of genes in the deleted regions can explain co-morbidities in these patients.Co-morbidities in patients with epilepsy can be part of a genomic abnormality even in the absence of (known congenital malformations or intellectual disabilities. Gene-driven phenotype examination can also reveal clinically significant unsuspected condition.

Genome plasticity of Vibrio parahaemolyticus: microevolution of the 'pandemic group'

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Liu Xiumei

2008-11-01

Full Text Available Abstract Background Outbreak of V. parahaemolyticus infections occurred since 1996 was linked to a proposed clonal complex, the pandemic group. The whole genome sequence provides an unprecedented opportunity for dissecting genome plasticity and phylogeny of the populations of V. parahaemolyticus. In the present work, a whole-genome cDNA microarray was constructed to compare the genomic contents of a collection of 174 strains of V. parahaemolyticus. Results Genes that present variably in the genome accounted for about 22% of the whole gene pool on the genome. The phylogenetic analysis of microarray data generated a minimum spanning tree that depicted the phylogenetic structure of the 174 strains. Strains were assigned into five complexes (C1 to C5, and those in each complex were related genetically and phylogenetically. C3 and C4 represented highly virulent clinical clones. C2 and C3 constituted two different clonal complexes 'old-O3:K6 clone' and 'pandemic clone', respectively. C3 included all the 39 pandemic strains tested (trh-, tdh+ and GS-PCR+, while C2 contained 12 pre-1996 'old' O3:K6 strains (trh+, tdh- and GS-PCR- tested herein. The pandemic clone (post-1996 'new' O3:K6 and its derivates O4:K68, O1:K25, O1:KUT and O6:K18 might be emerged from the old-O3:K6 clone, which was promoted by acquisition of toxRS/new sequence and genomic islands. A phylogenetic intermediate O3:K6 clade (trh-, tdh- and GS-PCR+ was identified between the pandemic and old-O3:K6 clones. Conclusion A comprehensive overview of genomic contents in a large collection of global isolates from the microarray-based comparative genomic hybridization data enabled us to construct a phylogenetic structure of V. parahaemolyticus and an evolutionary history of the pandemic group (clone of this pathogen.

Signatures of co-evolutionary host-pathogen interactions in the genome of the entomopathogenic nematode Steinernema carpocapsae.

Science.gov (United States)

Flores-Ponce, Mitzi; Vallebueno-Estrada, Miguel; González-Orozco, Eduardo; Ramos-Aboites, Hilda E; García-Chávez, J Noé; Simões, Nelson; Montiel, Rafael

2017-04-26

The entomopathogenic nematode Steinernema carpocapsae has been used worldwide as a biocontrol agent for insect pests, making it an interesting model for understanding parasite-host interactions. Two models propose that these interactions are co-evolutionary processes in such a way that equilibrium is never reached. In one model, known as "arms race", new alleles in relevant genes are fixed in both host and pathogens by directional positive selection, producing recurrent and alternating selective sweeps. In the other model, known as"trench warfare", persistent dynamic fluctuations in allele frequencies are sustained by balancing selection. There are some examples of genes evolving according to both models, however, it is not clear to what extent these interactions might alter genome-level evolutionary patterns and intraspecific diversity. Here we investigate some of these aspects by studying genomic variation in S. carpocapsae and other pathogenic and free-living nematodes from phylogenetic clades IV and V. To look for signatures of an arms-race dynamic, we conducted massive scans to detect directional positive selection in interspecific data. In free-living nematodes, we detected a significantly higher proportion of genes with sites under positive selection than in parasitic nematodes. However, in these genes, we found more enriched Gene Ontology terms in parasites. To detect possible effects of dynamic polymorphisms interactions we looked for signatures of balancing selection in intraspecific genomic data. The observed distribution of Tajima's D values in S. carpocapsae was more skewed to positive values and significantly different from the observed distribution in the free-living Caenorhabditis briggsae. Also, the proportion of significant positive values of Tajima's D was elevated in genes that were differentially expressed after induction with insect tissues as compared to both non-differentially expressed genes and the global scan. Our study provides a first

Genome Analysis of a Transmissible Lineage of Pseudomonas aeruginosa Reveals Pathoadaptive Mutations and Distinct Evolutionary Paths of Hypermutators

DEFF Research Database (Denmark)

Marvig, Rasmus Lykke; Johansen, Helle Krogh; Molin, Søren

2013-01-01

Genome sequencing of bacterial pathogens has advanced our understanding of their evolution, epidemiology, and response to antibiotic therapy. However, we still have only a limited knowledge of the molecular changes in in vivo evolving bacterial populations in relation to long-term, chronic...... targeted by mutations to optimize pathogen fitness (pathoadaptive mutations). These genes were related to antibiotic resistance, the cell envelope, or regulatory functions, and we find that the prevalence of pathoadaptive mutations correlates with evolutionary success of co-evolving sub-lineages. The long...... likelihood to acquire mutations and identify two homopolymer-containing genes preferentially mutated in hypermutators. This homopolymer facilitated differential mutagenesis provides a novel genome-wide perspective on the different evolutionary trajectories of hypermutators, which may help explain...

Highly evolvable malaria vectors : The genomes of 16 Anopheles mosquitoes

NARCIS (Netherlands)

Neafsey, D. E.; Waterhouse, R. M.; Abai, M. R.; Aganezov, S. S.; Alekseyev, M. A.; Allen, J. E.; Amon, J.; Arca, B.; Arensburger, P.; Artemov, G.; Assour, L. A.; Basseri, H.; Berlin, A.; Birren, B. W.; Blandin, S. A.; Brockman, A. I.; Burkot, T. R.; Burt, A.; Chan, C. S.; Chauve, C.; Chiu, J. C.; Christensen, M.; Costantini, C.; Davidson, V. L. M.; Deligianni, E.; Dottorini, T.; Dritsou, V.; Gabriel, S. B.; Guelbeogo, W. M.; Hall, A. B.; Han, M. V.; Hlaing, T.; Hughes, D. S. T.; Jenkins, A. M.; Jiang, X.; Jungreis, I.; Kakani, E. G.; Kamali, M.; Kemppainen, P.; Kennedy, R. C.; Kirmitzoglou, I. K.; Koekemoer, L. L.; Laban, N.; Langridge, N.; Lawniczak, M. K. N.; Lirakis, M.; Lobo, N. F.; Lowy, E.; Maccallum, R. M.; Mao, C.; Maslen, G.; Mbogo, C.; Mccarthy, J.; Michel, K.; Mitchell, S. N.; Moore, W.; Murphy, K. A.; Naumenko, A. N.; Nolan, T.; Novoa, E. M.; O'loughlin, S.; Oringanje, C.; Oshaghi, M. A.; Pakpour, N.; Papathanos, P. A.; Peery, A. N.; Povelones, M.; Prakash, A.; Price, D. P.; Rajaraman, A.; Reimer, L. J.; Rinker, D. C.; Rokas, A.; Russell, T. L.; Sagnon, N.; Sharakhova, M. V.; Shea, T.; Simao, F. A.; Simard, F.; Slotman, M. A.; Somboon, P.; Stegniy, V.; Struchiner, C. J.; Thomas, G. W. C.; Tojo, M.; Topalis, P.; Tubio, J. M. C.; Unger, M. F.; Vontas, J.; Walton, C.; Wilding, C. S.; Willis, J. H.; Wu, Y.-c.; Yan, G.; Zdobnov, E. M.; Zhou, X.; Catteruccia, F.; Christophides, G. K.; Collins, F. H.; Cornman, R. S.; Crisanti, A.; Donnelly, M. J.; Emrich, S. J.; Fontaine, M. C.; Gelbart, W.; Hahn, M. W.; Hansen, I. A.; Howell, P. I.; Kafatos, F. C.; Kellis, M.; Lawson, D.; Louis, C.; Luckhart, S.; Muskavitch, M. A. T.; Ribeiro, J. M.; Riehle, M. A.; Sharakhov, I. V.; Tu, Z.; Zwiebel, L. J.; Besansky, N. J.

2015-01-01

Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16

Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes.

Directory of Open Access Journals (Sweden)

John F Heidelberg

Full Text Available CRISPR arrays and associated cas genes are widespread in bacteria and archaea and confer acquired resistance to viruses. To examine viral immunity in the context of naturally evolving microbial populations we analyzed genomic data from two thermophilic Synechococcus isolates (Syn OS-A and Syn OS-B' as well as a prokaryotic metagenome and viral metagenome derived from microbial mats in hotsprings at Yellowstone National Park. Two distinct CRISPR types, distinguished by the repeat sequence, are found in both the Syn OS-A and Syn OS-B' genomes. The genome of Syn OS-A contains a third CRISPR type with a distinct repeat sequence, which is not found in Syn OS-B', but appears to be shared with other microorganisms that inhabit the mat. The CRISPR repeats identified in the microbial metagenome are highly conserved, while the spacer sequences (hereafter referred to as "viritopes" to emphasize their critical role in viral immunity were mostly unique and had no high identity matches when searched against GenBank. Searching the viritopes against the viral metagenome, however, yielded several matches with high similarity some of which were within a gene identified as a likely viral lysozyme/lysin protein. Analysis of viral metagenome sequences corresponding to this lysozyme/lysin protein revealed several mutations all of which translate into silent or conservative mutations which are unlikely to affect protein function, but may help the virus evade the host CRISPR resistance mechanism. These results demonstrate the varied challenges presented by a natural virus population, and support the notion that the CRISPR/viritope system must be able to adapt quickly to provide host immunity. The ability of metagenomics to track population-level variation in viritope sequences allows for a culture-independent method for evaluating the fast co-evolution of host and viral genomes and its consequence on the structuring of complex microbial communities.

Complete Genome Sequence of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) from the First Imported MERS-CoV Case in China.

Science.gov (United States)

Lu, Roujian; Wang, Yanqun; Wang, Wenling; Nie, Kai; Zhao, Yanjie; Su, Juan; Deng, Yao; Zhou, Weimin; Li, Yang; Wang, Huijuan; Wang, Wen; Ke, Changwen; Ma, Xuejun; Wu, Guizhen; Tan, Wenjie

2015-08-13

On 26 May 2015, an imported Middle East respiratory syndrome coronavirus (MERS-CoV) was identified in Guangdong Province, China, and found to be closely related to the MERS-CoV strain prevalent in South Korea. The full genome of the ChinaGD01 strain was sequenced and analyzed to investigate the epidemiology and evolution of MERS-CoV circulating in South Korea and China. Copyright © 2015 Lu et al.

Complete mitochondrial genome of four pheretimoid earthworms (Clitellata: Oligochaeta) and their phylogenetic reconstruction.

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Zhang, Liangliang; Jiang, Jibao; Dong, Yan; Qiu, Jiangping

2015-12-15

Among oligochaetes, the Pheretima complex within the Megascolecidae is a major earthworm group. Recently, however, the systematics of the Pheretima complex based on morphology are challenged by molecular studies. Since little comparative analysis of earthworm complete mitochondrial genomes has been reported yet, we sequenced mitogenomes of four pheretimoid earthworm species to explore their phylogenetic relationships. The general earthworm genomic features are also found in four earthworms: all genes transcribed from the same strand, the same initiation codon ATG for each PCGs, and conserved structures of RNA genes. Interestingly we find an extra potential tRNA-leucine (CUN) in Amynthas longisiphonus. The earthworm mitochondrial ATP8 exhibits the highest evolutionary rate, while the gene CO1 evolves slowest. Phylogenetic analysis based on protein-coding genes (PCGs) strongly supports the monophyly of the Clitellata, Hirudinea, Oligochaeta, Megascolecidae and Pheretima complex. Our analysis, however, reveals non-monophyly within the genara Amynthas and Metaphire. Thus the generic divisions based on morphology in the Pheretima complex should be reconsidered. Copyright © 2015 Elsevier B.V. All rights reserved.

Compositional and mutational rate heterogeneity in mitochondrial genomes and its effect on the phylogenetic inferences of Cimicomorpha (Hemiptera: Heteroptera).

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Yang, Huanhuan; Li, Teng; Dang, Kai; Bu, Wenjun

2018-04-18

Mitochondrial genome (mt-genome) data can potentially return artefactual relationships in the higher-level phylogenetic inference of insects due to the biases of accelerated substitution rates and compositional heterogeneity. Previous studies based on mt-genome data alone showed a paraphyly of Cimicomorpha (Insecta, Hemiptera) due to the positions of the families Tingidae and Reduviidae rather than the monophyly that was supported based on morphological characters, morphological and molecular combined data and large scale molecular datasets. Various strategies have been proposed to ameliorate the effects of potential mt-genome biases, including dense taxon sampling, removal of third codon positions or purine-pyrimidine coding and the use of site-heterogeneous models. In this study, we sequenced the mt-genomes of five additional Tingidae species and discussed the compositional and mutational rate heterogeneity in mt-genomes and its effect on the phylogenetic inferences of Cimicomorpha by implementing the bias-reduction strategies mentioned above. Heterogeneity in nucleotide composition and mutational biases were found in mt protein-coding genes, and the third codon exhibited high levels of saturation. Dense taxon sampling of Tingidae and Reduviidae and the other common strategies mentioned above were insufficient to recover the monophyly of the well-established group Cimicomorpha. When the sites with weak phylogenetic signals in the dataset were removed, the remaining dataset of mt-genomes can support the monophyly of Cimicomorpha; this support demonstrates that mt-genomes possess strong phylogenetic signals for the inference of higher-level phylogeny of this group. Comparison of the ratio of the removal of amino acids for each PCG showed that ATP8 has the highest ratio while CO1 has the lowest. This pattern is largely congruent with the evolutionary rate of 13 PCGs that ATP8 represents the highest evolutionary rate, whereas CO1 appears to be the lowest. Notably

Genome-nutrition divergence: evolving understanding of the malnutrition spectrum.

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Eaton, Jacob C; Iannotti, Lora L

2017-11-01

Humans adapted over a period of 2.3 million years to a diet high in quality and diversity. Genome-nutrition divergence describes the misalignment between modern global diets and the genome formed through evolution. A survey of hominin diets over time shows that humans have thrived on a broad range of foods. Earlier diets were highly diverse and nutrient dense, in contrast to modern food systems in which monotonous diets of staple cereals and ultraprocessed foods play a more prominent role. Applying the lens of genome-nutrition divergence to malnutrition reveals shared risk factors for undernutrition and overnutrition at nutrient, food, and environmental levels. Mechanisms for food system shifts, such as crop-neutral agricultural policy, agroecology, and social policy, are explored as a means to realign modern diets with the nutritional patterns to which humans may be better adapted to thrive. © The Author(s) 2017. Published by Oxford University Press on behalf of the International Life Sciences Institute. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Autonomous Agent-Based Systems and Their Applications in Fluid Dynamics, Particle Separation, and Co-evolving Networks

Science.gov (United States)

Graeser, Oliver

This thesis comprises three parts, reporting research results in Fluid Dynamics (Part I), Particle Separation (Part II) and Co-evolving Networks (Part III). Part I deals with the simulation of fluid dynamics using the lattice-Boltzmann method. Microfluidic devices often feature two-dimensional, repetitive arrays. Flows through such devices are pressure-driven and confined by solid walls. We have defined new adaptive generalised periodic boundary conditions to represent the effects of outer solid walls, and are thus able to exploit the periodicity of the array by simulating the flow through one unit cell in lieu of the entire device. The so-calculated fully developed flow describes the flow through the entire array accurately, but with computational requirements that are reduced according to the dimensions of the array. Part II discusses the problem of separating macromolecules like proteins or DNA coils. The reliable separation of such molecules is a crucial task in molecular biology. The use of Brownian ratchets as mechanisms for the separation of such particles has been proposed and discussed during the last decade. Pressure-driven flows have so far been dismissed as possible driving forces for Brownian ratchets, as they do not generate ratchet asymmetry. We propose a microfluidic design that uses pressure-driven flows to create asymmetry and hence allows particle separation. The dependence of the asymmetry on various factors of the microfluidic geometry is discussed. We further exemplify the feasibility of our approach using Brownian dynamics simulations of particles of different sizes in such a device. The results show that ratchet-based particle separation using flows as the driving force is possible. Simulation results and ratchet theory predictions are in excellent agreement. Part III deals with the co-evolution of networks and dynamic models. A group of agents occupies the nodes of a network, which defines the relationship between these agents. The

Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida.

Science.gov (United States)

Eoche-Bosy, D; Gautier, M; Esquibet, M; Legeai, F; Bretaudeau, A; Bouchez, O; Fournet, S; Grenier, E; Montarry, J

2017-09-01

Improving resistance durability involves to be able to predict the adaptation speed of pathogen populations. Identifying the genetic bases of pathogen adaptation to plant resistances is a useful step to better understand and anticipate this phenomenon. Globodera pallida is a major pest of potato crop for which a resistance QTL, GpaV vrn , has been identified in Solanum vernei. However, its durability is threatened as G. pallida populations are able to adapt to the resistance in few generations. The aim of this study was to investigate the genomic regions involved in the resistance breakdown by coupling experimental evolution and high-density genome scan. We performed a whole-genome resequencing of pools of individuals (Pool-Seq) belonging to G. pallida lineages derived from two independent populations having experimentally evolved on susceptible and resistant potato cultivars. About 1.6 million SNPs were used to perform the genome scan using a recent model testing for adaptive differentiation and association to population-specific covariables. We identified 275 outliers and 31 of them, which also showed a significant reduction in diversity in adapted lineages, were investigated for their genic environment. Some candidate genomic regions contained genes putatively encoding effectors and were enriched in SPRYSECs, known in cyst nematodes to be involved in pathogenicity and in (a)virulence. Validated candidate SNPs will provide a useful molecular tool to follow frequencies of virulence alleles in natural G. pallida populations and define efficient strategies of use of potato resistances maximizing their durability. © 2017 John Wiley & Sons Ltd.

Indel Group in Genomes (IGG) Molecular Genetic Markers1[OPEN

Science.gov (United States)

Burkart-Waco, Diana; Kuppu, Sundaram; Britt, Anne; Chetelat, Roger

2016-01-01

Genetic markers are essential when developing or working with genetically variable populations. Indel Group in Genomes (IGG) markers are primer pairs that amplify single-locus sequences that differ in size for two or more alleles. They are attractive for their ease of use for rapid genotyping and their codominant nature. Here, we describe a heuristic algorithm that uses a k-mer-based approach to search two or more genome sequences to locate polymorphic regions suitable for designing candidate IGG marker primers. As input to the IGG pipeline software, the user provides genome sequences and the desired amplicon sizes and size differences. Primer sequences flanking polymorphic insertions/deletions are produced as output. IGG marker files for three sets of genomes, Solanum lycopersicum/Solanum pennellii, Arabidopsis (Arabidopsis thaliana) Columbia-0/Landsberg erecta-0 accessions, and S. lycopersicum/S. pennellii/Solanum tuberosum (three-way polymorphic) are included. PMID:27436831

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.

Science.gov (United States)

Nielsen, H Bjørn; Almeida, Mathieu; Juncker, Agnieszka Sierakowska; Rasmussen, Simon; Li, Junhua; Sunagawa, Shinichi; Plichta, Damian R; Gautier, Laurent; Pedersen, Anders G; Le Chatelier, Emmanuelle; Pelletier, Eric; Bonde, Ida; Nielsen, Trine; Manichanh, Chaysavanh; Arumugam, Manimozhiyan; Batto, Jean-Michel; Quintanilha Dos Santos, Marcelo B; Blom, Nikolaj; Borruel, Natalia; Burgdorf, Kristoffer S; Boumezbeur, Fouad; Casellas, Francesc; Doré, Joël; Dworzynski, Piotr; Guarner, Francisco; Hansen, Torben; Hildebrand, Falk; Kaas, Rolf S; Kennedy, Sean; Kristiansen, Karsten; Kultima, Jens Roat; Léonard, Pierre; Levenez, Florence; Lund, Ole; Moumen, Bouziane; Le Paslier, Denis; Pons, Nicolas; Pedersen, Oluf; Prifti, Edi; Qin, Junjie; Raes, Jeroen; Sørensen, Søren; Tap, Julien; Tims, Sebastian; Ussery, David W; Yamada, Takuji; Renault, Pierre; Sicheritz-Ponten, Thomas; Bork, Peer; Wang, Jun; Brunak, Søren; Ehrlich, S Dusko

2014-08-01

Most current approaches for analyzing metagenomic data rely on comparisons to reference genomes, but the microbial diversity of many environments extends far beyond what is covered by reference databases. De novo segregation of complex metagenomic data into specific biological entities, such as particular bacterial strains or viruses, remains a largely unsolved problem. Here we present a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences. We demonstrate the method on data from 396 human gut microbiome samples and identify 7,381 co-abundance gene groups (CAGs), including 741 metagenomic species (MGS). We use these to assemble 238 high-quality microbial genomes and identify affiliations between MGS and hundreds of viruses or genetic entities. Our method provides the means for comprehensive profiling of the diversity within complex metagenomic samples.

History of genome editing in yeast.

Science.gov (United States)

Fraczek, Marcin G; Naseeb, Samina; Delneri, Daniela

2018-05-01

For thousands of years humans have used the budding yeast Saccharomyces cerevisiae for the production of bread and alcohol; however, in the last 30-40 years our understanding of the yeast biology has dramatically increased, enabling us to modify its genome. Although S. cerevisiae has been the main focus of many research groups, other non-conventional yeasts have also been studied and exploited for biotechnological purposes. Our experiments and knowledge have evolved from recombination to high-throughput PCR-based transformations to highly accurate CRISPR methods in order to alter yeast traits for either research or industrial purposes. Since the release of the genome sequence of S. cerevisiae in 1996, the precise and targeted genome editing has increased significantly. In this 'Budding topic' we discuss the significant developments of genome editing in yeast, mainly focusing on Cre-loxP mediated recombination, delitto perfetto and CRISPR/Cas. © 2018 The Authors. Yeast published by John Wiley & Sons, Ltd.

The 5S rDNA family evolves through concerted and birth-and-death evolution in fish genomes: an example from freshwater stingrays

Science.gov (United States)

2011-01-01

Background Ribosomal 5S genes are well known for the critical role they play in ribosome folding and functionality. These genes are thought to evolve in a concerted fashion, with high rates of homogenization of gene copies. However, the majority of previous analyses regarding the evolutionary process of rDNA repeats were conducted in invertebrates and plants. Studies have also been conducted on vertebrates, but these analyses were usually restricted to the 18S, 5.8S and 28S rRNA genes. The recent identification of divergent 5S rRNA gene paralogs in the genomes of elasmobranches and teleost fishes indicate that the eukaryotic 5S rRNA gene family has a more complex genomic organization than previously thought. The availability of new sequence data from lower vertebrates such as teleosts and elasmobranches enables an enhanced evolutionary characterization of 5S rDNA among vertebrates. Results We identified two variant classes of 5S rDNA sequences in the genomes of Potamotrygonidae stingrays, similar to the genomes of other vertebrates. One class of 5S rRNA genes was shared only by elasmobranches. A broad comparative survey among 100 vertebrate species suggests that the 5S rRNA gene variants in fishes originated from rounds of genome duplication. These variants were then maintained or eliminated by birth-and-death mechanisms, under intense purifying selection. Clustered multiple copies of 5S rDNA variants could have arisen due to unequal crossing over mechanisms. Simultaneously, the distinct genome clusters were independently homogenized, resulting in the maintenance of clusters of highly similar repeats through concerted evolution. Conclusions We believe that 5S rDNA molecular evolution in fish genomes is driven by a mixed mechanism that integrates birth-and-death and concerted evolution. PMID:21627815

Different selective pressures lead to different genomic outcomes as newly-formed hybrid yeasts evolve

Directory of Open Access Journals (Sweden)

Piotrowski Jeff S

2012-04-01

Full Text Available Abstract Background Interspecific hybridization occurs in every eukaryotic kingdom. While hybrid progeny are frequently at a selective disadvantage, in some instances their increased genome size and complexity may result in greater stress resistance than their ancestors, which can be adaptively advantageous at the edges of their ancestors' ranges. While this phenomenon has been repeatedly documented in the field, the response of hybrid populations to long-term selection has not often been explored in the lab. To fill this knowledge gap we crossed the two most distantly related members of the Saccharomyces sensu stricto group, S. cerevisiae and S. uvarum, and established a mixed population of homoploid and aneuploid hybrids to study how different types of selection impact hybrid genome structure. Results As temperature was raised incrementally from 31°C to 46.5°C over 500 generations of continuous culture, selection favored loss of the S. uvarum genome, although the kinetics of genome loss differed among independent replicates. Temperature-selected isolates exhibited greater inherent and induced thermal tolerance than parental species and founding hybrids, and also exhibited ethanol resistance. In contrast, as exogenous ethanol was increased from 0% to 14% over 500 generations of continuous culture, selection favored euploid S. cerevisiae x S. uvarum hybrids. Ethanol-selected isolates were more ethanol tolerant than S. uvarum and one of the founding hybrids, but did not exhibit resistance to temperature stress. Relative to parental and founding hybrids, temperature-selected strains showed heritable differences in cell wall structure in the forms of increased resistance to zymolyase digestion and Micafungin, which targets cell wall biosynthesis. Conclusions This is the first study to show experimentally that the genomic fate of newly-formed interspecific hybrids depends on the type of selection they encounter during the course of evolution

CyanoClust: comparative genome resources of cyanobacteria and plastids.

Science.gov (United States)

Sasaki, Naobumi V; Sato, Naoki

2010-01-01

Cyanobacteria, which perform oxygen-evolving photosynthesis as do chloroplasts of plants and algae, are one of the best-studied prokaryotic phyla and one from which many representative genomes have been sequenced. Lack of a suitable comparative genomic database has been a problem in cyanobacterial genomics because many proteins involved in physiological functions such as photosynthesis and nitrogen fixation are not catalogued in commonly used databases, such as Clusters of Orthologous Proteins (COG). CyanoClust is a database of homolog groups in cyanobacteria and plastids that are produced by the program Gclust. We have developed a web-server system for the protein homology database featuring cyanobacteria and plastids. Database URL: http://cyanoclust.c.u-tokyo.ac.jp/.

Origin of the Y genome in Elymus and its relationship to other genomes in Triticeae based on evidence from elongation factor G (EF-G) gene sequences.

Science.gov (United States)

Sun, Genlou; Komatsuda, Takao

2010-08-01

It is well known that Elymus arose through hybridization between representatives of different genera. Cytogenetic analyses show that all its members include the St genome in combination with one or more of four other genomes, the H, Y, P, and W genomes. The origins of the H, P, and W genomes are known, but not for the Y genome. We analyzed the single copy nuclear gene coding for elongation factor G (EF-G) from 28 accessions of polyploid Elymus species and 45 accessions of diploid Triticeae species in order to investigate origin of the Y genome and its relationship to other genomes in the tribe Triticeae. Sequence comparisons among the St, H, Y, P, W, and E genomes detected genome-specific polymorphisms at 66 nucleotide positions. The St and Y genomes are relatively dissimilar. The phylogeny of the Y genome sequences was investigated for the first time. They were most similar to the W genome sequences. The Y genome sequences were placed in two different groups. These two groups were included in an unresolved clade that included the W and E sequences as well as sequences from many annual species. The H genomes sequences were in a clade with the F, P, and Ns genome sequences as sister groups. These two clades were more closely related to each other and to the L and Xp genomes than they were to the St genome sequences. These data support the hypothesis that the Y genome evolved in a diploid species and has a different origin from the St genome. Copyright 2010 Elsevier Inc. All rights reserved.

Genomics, evolution and development of amphioxus and tunicates: The Goldilocks principle.

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Holland, Linda Z

2015-06-01

Morphological comparisons among extant animals have long been used to infer their long-extinct ancestors for which the fossil record is poor or non-existent. For evolution of the vertebrates, the comparison has typically involved amphioxus and vertebrates. Both groups are evolving relatively slowly, and their genomes share a high level of synteny. Both vertebrates and amphioxus have regulative development in which cell fates become fixed only gradually during embryogenesis. Thus, their development fits a modified hourglass model in which constraints are greatest at the phylotypic stage (i.e., the late neurula/early larva), but are somewhat greater on earlier development than on later development. In contrast, the third group of chordates, the tunicates, which are sister group to vertebrates, are evolving rapidly. Constraints on evolution of tunicate genomes are relaxed, and they have discarded key developmental genes and organized much of their coding sequences into operons, which are transcribed as a single mRNA that undergoes trans-splicing. This contrasts with vertebrates and amphioxus, whose genomes are not organized into operons. Concomitantly, tunicates have switched to determinant development with very early fixation of cell fates. Thus, tunicate development more closely fits a progressive divergence model (shaped more like a wine glass than an hourglass) in which the constraints on the zygote and very early development are greatest. This model can help explain why tunicate body plans are so very diverse. The relaxed constraints on development after early cleavage stages are correlated with relaxed constraints on genome evolution. The question remains: which came first? © 2014 Wiley Periodicals, Inc.

Genome Evolution of Plant-Parasitic Nematodes.

Science.gov (United States)

Kikuchi, Taisei; Eves-van den Akker, Sebastian; Jones, John T

2017-08-04

Plant parasitism has evolved independently on at least four separate occasions in the phylum Nematoda. The application of next-generation sequencing (NGS) to plant-parasitic nematodes has allowed a wide range of genome- or transcriptome-level comparisons, and these have identified genome adaptations that enable parasitism of plants. Current genome data suggest that horizontal gene transfer, gene family expansions, evolution of new genes that mediate interactions with the host, and parasitism-specific gene regulation are important adaptations that allow nematodes to parasitize plants. Sequencing of a larger number of nematode genomes, including plant parasites that show different modes of parasitism or that have evolved in currently unsampled clades, and using free-living taxa as comparators would allow more detailed analysis and a better understanding of the organization of key genes within the genomes. This would facilitate a more complete understanding of the way in which parasitism has shaped the genomes of plant-parasitic nematodes.

Selection-driven extinction dynamics for group II introns in Enterobacteriales.

Directory of Open Access Journals (Sweden)

Sébastien Leclercq

Full Text Available Transposable elements (TEs are one of the major driving forces of genome evolution, raising the question of the long-term dynamics underlying their evolutionary success. Some TEs were proposed to evolve under a pattern of periodic extinctions-recolonizations, in which elements recurrently invade and quickly proliferate within their host genomes, then start to disappear until total extinction. Depending on the model, TE extinction is assumed to be driven by purifying selection against colonized host genomes (Sel-DE model or by saturation of host genomes (Sat-DE model. Bacterial group II introns are suspected to follow an extinction-recolonization model of evolution, but whether they follow Sel-DE or Sat-DE dynamics is not known. Our analysis of almost 200 group II intron copies from 90 sequenced Enterobacteriales genomes confirms their extinction-recolonization dynamics: patchy element distributions among genera and even among strains within genera, acquisition of new group II introns through plasmids or other mobile genetic elements, and evidence for recent proliferations in some genomes. Distributions of recent and past proliferations and of their respective homing sites further provide strong support for the Sel-DE model, suggesting that group II introns are deleterious to their hosts. Overall, our observations emphasize the critical impact of host properties on TE dynamics.

Evolving molecular era of childhood medulloblastoma: time to revisit therapy.

Science.gov (United States)

Khatua, Soumen

2016-01-01

Currently medulloblastoma is treated with a uniform therapeutic approach based on histopathology and clinico-radiological risk stratification, resulting in unpredictable treatment failure and relapses. Improved understanding of the biological, molecular and genetic make-up of these tumors now clearly identifies it as a compendium of four distinct subtypes (WNT, SHH, group 3 and 4). Advances in utilization of the genomic and epigenomic machinery have now delineated genetic aberrations and epigenetic perturbations in each subgroup as potential druggable targets. This has resulted in endeavors to profile targeted therapy. The challenge and future of medulloblastoma therapeutics will be to keep pace with the evolving novel biological insights and translating them into optimal targeted treatment regimens.

Genome organization, instabilities, stem cells, and cancer

Directory of Open Access Journals (Sweden)

Senthil Kumar Pazhanisamy

2009-01-01

Full Text Available It is now widely recognized that advances in exploring genome organization provide remarkable insights on the induction and progression of chromosome abnormalities. Much of what we know about how mutations evolve and consequently transform into genome instabilities has been characterized in the spatial organization context of chromatin. Nevertheless, many underlying concepts of impact of the chromatin organization on perpetuation of multiple mutations and on propagation of chromosomal aberrations remain to be investigated in detail. Genesis of genome instabilities from accumulation of multiple mutations that drive tumorigenesis is increasingly becoming a focal theme in cancer studies. This review focuses on structural alterations evolve to raise a variety of genome instabilities that are manifested at the nucleotide, gene or sub-chromosomal, and whole chromosome level of genome. Here we explore an underlying connection between genome instability and cancer in the light of genome architecture. This review is limited to studies directed towards spatial organizational aspects of origin and propagation of aberrations into genetically unstable tumors.

Evidence that viral RNAs have evolved for efficient, two-stage packaging.

Science.gov (United States)

Borodavka, Alexander; Tuma, Roman; Stockley, Peter G

2012-09-25

Genome packaging is an essential step in virus replication and a potential drug target. Single-stranded RNA viruses have been thought to encapsidate their genomes by gradual co-assembly with capsid subunits. In contrast, using a single molecule fluorescence assay to monitor RNA conformation and virus assembly in real time, with two viruses from differing structural families, we have discovered that packaging is a two-stage process. Initially, the genomic RNAs undergo rapid and dramatic (approximately 20-30%) collapse of their solution conformations upon addition of cognate coat proteins. The collapse occurs with a substoichiometric ratio of coat protein subunits and is followed by a gradual increase in particle size, consistent with the recruitment of additional subunits to complete a growing capsid. Equivalently sized nonviral RNAs, including high copy potential in vivo competitor mRNAs, do not collapse. They do support particle assembly, however, but yield many aberrant structures in contrast to viral RNAs that make only capsids of the correct size. The collapse is specific to viral RNA fragments, implying that it depends on a series of specific RNA-protein interactions. For bacteriophage MS2, we have shown that collapse is driven by subsequent protein-protein interactions, consistent with the RNA-protein contacts occurring in defined spatial locations. Conformational collapse appears to be a distinct feature of viral RNA that has evolved to facilitate assembly. Aspects of this process mimic those seen in ribosome assembly.

Identification and genome organization of saponin pathway genes from a wild crucifer, and their use for transient production of saponins in Nicotiana benthamiana.

Science.gov (United States)

Khakimov, Bekzod; Kuzina, Vera; Erthmann, Pernille Ø; Fukushima, Ery Odette; Augustin, Jörg M; Olsen, Carl Erik; Scholtalbers, Jelle; Volpin, Hanne; Andersen, Sven Bode; Hauser, Thure P; Muranaka, Toshiya; Bak, Søren

2015-11-01

The ability to evolve novel metabolites has been instrumental for the defence of plants against antagonists. A few species in the Barbarea genus are the only crucifers known to produce saponins, some of which make plants resistant to specialist herbivores, like Plutella xylostella, the diamondback moth. Genetic mapping in Barbarea vulgaris revealed that genes for saponin biosynthesis are not clustered but are located in different linkage groups. Using co-location with quantitative trait loci (QTLs) for resistance, transcriptome and genome sequences, we identified two 2,3-oxidosqualene cyclases that form the major triterpenoid backbones. LUP2 mainly produces lupeol, and is preferentially expressed in insect-susceptible B. vulgaris plants, whereas LUP5 produces β-amyrin and α-amyrin, and is preferentially expressed in resistant plants; β-amyrin is the backbone for the resistance-conferring saponins in Barbarea. Two loci for cytochromes P450, predicted to add functional groups to the saponin backbone, were identified: CYP72As co-localized with insect resistance, whereas CYP716As did not. When B. vulgaris sapogenin biosynthesis genes were transiently expressed by CPMV-HT technology in Nicotiana benthamiana, high levels of hydroxylated and carboxylated triterpenoid structures accumulated, including oleanolic acid, which is a precursor of the major resistance-conferring saponins. When the B. vulgaris gene for sapogenin 3-O-glucosylation was co-expressed, the insect deterrent 3-O-oleanolic acid monoglucoside accumulated, as well as triterpene structures with up to six hexoses, demonstrating that N. benthamiana further decorates the monoglucosides. We argue that saponin biosynthesis in the Barbarea genus evolved by a neofunctionalized glucosyl transferase, whereas the difference between resistant and susceptible B. vulgaris chemotypes evolved by different expression of oxidosqualene cyclases (OSCs). © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons

Bioinformatics analysis of SARS coronavirus genome polymorphism

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Pavlović-Lažetić Gordana M

2004-05-01

Full Text Available Abstract Background We have compared 38 isolates of the SARS-CoV complete genome. The main goal was twofold: first, to analyze and compare nucleotide sequences and to identify positions of single nucleotide polymorphism (SNP, insertions and deletions, and second, to group them according to sequence similarity, eventually pointing to phylogeny of SARS-CoV isolates. The comparison is based on genome polymorphism such as insertions or deletions and the number and positions of SNPs. Results The nucleotide structure of all 38 isolates is presented. Based on insertions and deletions and dissimilarity due to SNPs, the dataset of all the isolates has been qualitatively classified into three groups each having their own subgroups. These are the A-group with "regular" isolates (no insertions / deletions except for 5' and 3' ends, the B-group of isolates with "long insertions", and the C-group of isolates with "many individual" insertions and deletions. The isolate with the smallest average number of SNPs, compared to other isolates, has been identified (TWH. The density distribution of SNPs, insertions and deletions for each group or subgroup, as well as cumulatively for all the isolates is also presented, along with the gene map for TWH. Since individual SNPs may have occurred at random, positions corresponding to multiple SNPs (occurring in two or more isolates are identified and presented. This result revises some previous results of a similar type. Amino acid changes caused by multiple SNPs are also identified (for the annotated sequences, as well as presupposed amino acid changes for non-annotated ones. Exact SNP positions for the isolates in each group or subgroup are presented. Finally, a phylogenetic tree for the SARS-CoV isolates has been produced using the CLUSTALW program, showing high compatibility with former qualitative classification. Conclusions The comparative study of SARS-CoV isolates provides essential information for genome

Genomic Signatures of Reinforcement

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Austin G. Garner

2018-04-01

Full Text Available Reinforcement is the process by which selection against hybridization increases reproductive isolation between taxa. Much research has focused on demonstrating the existence of reinforcement, yet relatively little is known about the genetic basis of reinforcement or the evolutionary conditions under which reinforcement can occur. Inspired by reinforcement’s characteristic phenotypic pattern of reproductive trait divergence in sympatry but not in allopatry, we discuss whether reinforcement also leaves a distinct genomic pattern. First, we describe three patterns of genetic variation we expect as a consequence of reinforcement. Then, we discuss a set of alternative processes and complicating factors that may make the identification of reinforcement at the genomic level difficult. Finally, we consider how genomic analyses can be leveraged to inform if and to what extent reinforcement evolved in the face of gene flow between sympatric lineages and between allopatric and sympatric populations of the same lineage. Our major goals are to understand if genome scans for particular patterns of genetic variation could identify reinforcement, isolate the genetic basis of reinforcement, or infer the conditions under which reinforcement evolved.

Genomic Signatures of Reinforcement

Science.gov (United States)

Goulet, Benjamin E.

2018-01-01

Reinforcement is the process by which selection against hybridization increases reproductive isolation between taxa. Much research has focused on demonstrating the existence of reinforcement, yet relatively little is known about the genetic basis of reinforcement or the evolutionary conditions under which reinforcement can occur. Inspired by reinforcement’s characteristic phenotypic pattern of reproductive trait divergence in sympatry but not in allopatry, we discuss whether reinforcement also leaves a distinct genomic pattern. First, we describe three patterns of genetic variation we expect as a consequence of reinforcement. Then, we discuss a set of alternative processes and complicating factors that may make the identification of reinforcement at the genomic level difficult. Finally, we consider how genomic analyses can be leveraged to inform if and to what extent reinforcement evolved in the face of gene flow between sympatric lineages and between allopatric and sympatric populations of the same lineage. Our major goals are to understand if genome scans for particular patterns of genetic variation could identify reinforcement, isolate the genetic basis of reinforcement, or infer the conditions under which reinforcement evolved. PMID:29614048

Iron-Rich Carbonates as the Potential Source of Evolved CO2 Detected by the Sample Analysis at Mars (SAM) Instrument in Gale Crater

Science.gov (United States)

Sutter, B.; Heil, E.; Rampe, E. B.; Morris, R. V.; Ming, D. W.; Archer, P. D.; Eigenbrode, J. L.; Franz, H. B.; Glavin, D. P.; McAdam, A. C.;

"Is It Worth Knowing?" Focus Group Participants' Perceived Utility of Genomic Preconception Carrier Screening.

Science.gov (United States)

Schneider, Jennifer L; Goddard, Katrina A B; Davis, James; Wilfond, Benjamin; Kauffman, Tia L; Reiss, Jacob A; Gilmore, Marian; Himes, Patricia; Lynch, Frances L; Leo, Michael C; McMullen, Carmit

2016-02-01

As genome sequencing technology advances, research is needed to guide decision-making about what results can or should be offered to patients in different clinical settings. We conducted three focus groups with individuals who had prior preconception genetic testing experience to explore perceived advantages and disadvantages of genome sequencing for preconception carrier screening, compared to usual care. Using a discussion guide, a trained qualitative moderator facilitated the audio-recorded focus groups. Sixteen individuals participated. Thematic analysis of transcripts started with a grounded approach and subsequently focused on participants' perceptions of the value of genetic information. Analysis uncovered two orientations toward genomic preconception carrier screening: "certain" individuals desiring all possible screening information; and "hesitant" individuals who were more cautious about its value. Participants revealed valuable information about barriers to screening: fear/anxiety about results; concerns about the method of returning results; concerns about screening necessity; and concerns about partner participation. All participants recommended offering choice to patients to enhance the value of screening and reduce barriers. Overall, two groups of likely users of genome sequencing for preconception carrier screening demonstrated different perceptions of the advantages or disadvantages of screening, suggesting tailored approaches to education, consent, and counseling may be warranted with each group.

Infidelity of SARS-CoV Nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing.

Directory of Open Access Journals (Sweden)

Lance D Eckerle

2010-05-01

Full Text Available Most RNA viruses lack the mechanisms to recognize and correct mutations that arise during genome replication, resulting in quasispecies diversity that is required for pathogenesis and adaptation. However, it is not known how viruses encoding large viral RNA genomes such as the Coronaviridae (26 to 32 kb balance the requirements for genome stability and quasispecies diversity. Further, the limits of replication infidelity during replication of large RNA genomes and how decreased fidelity impacts virus fitness over time are not known. Our previous work demonstrated that genetic inactivation of the coronavirus exoribonuclease (ExoN in nonstructural protein 14 (nsp14 of murine hepatitis virus results in a 15-fold decrease in replication fidelity. However, it is not known whether nsp14-ExoN is required for replication fidelity of all coronaviruses, nor the impact of decreased fidelity on genome diversity and fitness during replication and passage. We report here the engineering and recovery of nsp14-ExoN mutant viruses of severe acute respiratory syndrome coronavirus (SARS-CoV that have stable growth defects and demonstrate a 21-fold increase in mutation frequency during replication in culture. Analysis of complete genome sequences from SARS-ExoN mutant viral clones revealed unique mutation sets in every genome examined from the same round of replication and a total of 100 unique mutations across the genome. Using novel bioinformatic tools and deep sequencing across the full-length genome following 10 population passages in vitro, we demonstrate retention of ExoN mutations and continued increased diversity and mutational load compared to wild-type SARS-CoV. The results define a novel genetic and bioinformatics model for introduction and identification of multi-allelic mutations in replication competent viruses that will be powerful tools for testing the effects of decreased fidelity and increased quasispecies diversity on viral replication

Extending the cereus group genomics to putative food-bornepathogens of different toxicity

Energy Technology Data Exchange (ETDEWEB)

Lapidus, Alla; Goltsman, Eugene; Auger, Sandrine; Galleron,Nathalie; Segurens, Beatrice; Dossat, Carole; Land, Miriam L.; Broussole,Veronique; Brillard, Julien; Guinebretiere, Marie-Helene; Sanchis,Vincent; Nguen-the, Christophe; Lereclus, Didier; Richardson, Paul; Winker, Patrick; Weissenbach, Jean; Ehrlich, S.Dusko; Sorokin, Alexei

2006-08-24

The cereus group represents sporulating soil bacteriacontaining pathogenic strains which may cause diarrheic or emetic foodpoisoning outbreaks. Multiple locus sequence typing revealed a presencein natural samples of these bacteria of about thirty clonal complexes.Application of genomic methods to this group was however biased due tothe major interest for representatives closely related to B. anthracis.Albeit the most important food-borne pathogens were not yet defined,existing dataindicate that they are scattered all over the phylogenetictree. The preliminary analysis of the sequences of three genomesdiscussed in this paper narrows down the gaps in our knowledge of thecereus group. The strain NVH391-98 is a rare but particularly severefood-borne pathogen. Sequencing revealed that the strain must be arepresentative of a novel bacterial species, for which the name Bacilluscytotoxis is proposed. This strain has a reduced genome size compared toother cereus group strains. Genome analysis revealed absence of sigma Bfactor and the presence of genes encoding diarrheic Nhe toxin, notdetected earlier. The strain B. cereus F837/76 represents a clonalcomplex close to that of B. anthracis. Including F837/76, three such B.cereus strains had been sequenced. Alignment of genomes suggests that B.anthracis is their common ancestor. Since such strains often emerge fromclinical cases, they merit a special attention. The third strain, KBAB4,is a typical psychrotrophe characteristic to unbiased soil communities.Phylogenic studies show that in nature it is the most active group interms of gene exchange. Genomic sequence revealed high presence ofextra-chromosomal genetic material (about 530 kb) that may account forthis phenomenon. Genes coding Nhe-like toxin were found on a big plasmidin this strain. This may indicate a potential mechanism of toxicityspread from the psychrotrophic strain community. The results of thisgenomic work and ecological compartments of different strains incite

Complete genome sequence of Bacillus amyloliquefaciens strain Co1-6, a plant growth-promoting rhizobacterium of Calendula officinalis

Energy Technology Data Exchange (ETDEWEB)

Koeberl, Martina; White, Richard A.; Erschen, Sabine; Spanberger, Nora; El-Arabi, Tarek F.; Jansson, Janet K.; Berg, Gabriele

2015-08-13

The genome sequence of Bacillus amyloliquefaciens strain Co1-6, a plant growth-promoting rhizobacterium (PGPR) with broad-spectrum antagonistic activities against plant pathogenic fungi, bacteria and nematodes, consists of a single 3.9 Mb circular chromosome. The genome reveals genes putatively responsible for its promising biocontrol and PGP properties.

Assignment of simian rotavirus SA11 temperature-sensitive mutant groups B and E to genome segments

International Nuclear Information System (INIS)

Gombold, J.L.; Estes, M.K.; Ramig, R.F.

1985-01-01

Recombinant (reassortant) viruses were selected from crosses between temperature-sensitive (ts) mutants of simian rotavirus SA11 and wild-type human rotavirus Wa. The double-stranded genome RNAs of the reassortants were examined by electrophoresis in Tris-glycine-buffered polyacrylamide gels and by dot hybridization with a cloned DNA probe for genome segment 2. Analysis of replacements of genome segments in the reassortants allowed construction of a map correlating genome segments providing functions interchangeable between SA11 and Wa. The reassortants revealed a functional correspondence in order of increasing electrophoretic mobility of genome segments. Analysis of the parental origin of genome segments in ts+ SA11/Wa reassortants derived from the crosses SA11 tsB(339) X Wa and SA11 tsE(1400) X Wa revealed that the group B lesion of tsB(339) was located on genome segment 3 and the group E lesion of tsE(1400) was on segment 8

Assignment of simian rotavirus SA11 temperature-sensitive mutant groups B and E to genome segments

Energy Technology Data Exchange (ETDEWEB)

Gombold, J.L.; Estes, M.K.; Ramig, R.F.

1985-05-01

Recombinant (reassortant) viruses were selected from crosses between temperature-sensitive (ts) mutants of simian rotavirus SA11 and wild-type human rotavirus Wa. The double-stranded genome RNAs of the reassortants were examined by electrophoresis in Tris-glycine-buffered polyacrylamide gels and by dot hybridization with a cloned DNA probe for genome segment 2. Analysis of replacements of genome segments in the reassortants allowed construction of a map correlating genome segments providing functions interchangeable between SA11 and Wa. The reassortants revealed a functional correspondence in order of increasing electrophoretic mobility of genome segments. Analysis of the parental origin of genome segments in ts+ SA11/Wa reassortants derived from the crosses SA11 tsB(339) X Wa and SA11 tsE(1400) X Wa revealed that the group B lesion of tsB(339) was located on genome segment 3 and the group E lesion of tsE(1400) was on segment 8.

Applied Genomics of Foodborne Pathogens

DEFF Research Database (Denmark)

and customized source of information designed for and accessible to microbiologists interested in applying cutting-edge genomics in food safety and public health research. This book fills this void with a well-selected collection of topics, case studies, and bioinformatics tools contributed by experts......This book provides a timely and thorough snapshot into the emerging and fast evolving area of applied genomics of foodborne pathogens. Driven by the drastic advance of whole genome shot gun sequencing (WGS) technologies, genomics applications are becoming increasingly valuable and even essential...... at the forefront of foodborne pathogen genomics research....

Australians' views on personal genomic testing: focus group findings from the Genioz study.

Science.gov (United States)

Metcalfe, Sylvia A; Hickerton, Chriselle; Savard, Jacqueline; Terrill, Bronwyn; Turbitt, Erin; Gaff, Clara; Gray, Kathleen; Middleton, Anna; Wilson, Brenda; Newson, Ainsley J

2018-04-30

Personal genomic testing provides healthy individuals with access to information about their genetic makeup for purposes including ancestry, paternity, sporting ability and health. Such tests are available commercially and globally, with accessibility expected to continue to grow, including in Australia; yet little is known of the views/expectations of Australians. Focus groups were conducted within a multi-stage, cross-disciplinary project (Genioz) to explore this. In mid-2015, 56 members of the public participated in seven focus groups, allocated into three age groups: 18-24, 25-49, and ≥50 years. Three researchers coded transcripts independently and generated themes. Awareness of personal genomic testing was low, but most could deduce what "personal genomics" might entail. Very few had heard of the term "direct-to-consumer" testing, which has implications for organisations developing information to support individuals in their decision-making. Participants' understanding of genetics was varied and drawn from several sources. There were diverse perceptions of the relative influence of genetics and environment on health, mental health, behavior, talent, or personality. Views about having a personal genomic test were mixed, with greater interest in health-related tests if they believed there was a reason for doing so. However, many expressed scepticisms about the types of tests available, and how the information might be used; concerns were also raised about privacy and the potential for discrimination. These exploratory findings inform subsequent stages of the Genioz study, thereby contributing to strategies of supporting Australians to understand and make meaningful and well-considered decisions about the benefits, harms, and implications of personal genomic tests.

Spider genomes provide insight into composition and evolution of venom and silk

Science.gov (United States)

Sanggaard, Kristian W.; Bechsgaard, Jesper S.; Fang, Xiaodong; Duan, Jinjie; Dyrlund, Thomas F.; Gupta, Vikas; Jiang, Xuanting; Cheng, Ling; Fan, Dingding; Feng, Yue; Han, Lijuan; Huang, Zhiyong; Wu, Zongze; Liao, Li; Settepani, Virginia; Thøgersen, Ida B.; Vanthournout, Bram; Wang, Tobias; Zhu, Yabing; Funch, Peter; Enghild, Jan J.; Schauser, Leif; Andersen, Stig U.; Villesen, Palle; Schierup, Mikkel H; Bilde, Trine; Wang, Jun

2014-01-01

Spiders are ecologically important predators with complex venom and extraordinarily tough silk that enables capture of large prey. Here we present the assembled genome of the social velvet spider and a draft assembly of the tarantula genome that represent two major taxonomic groups of spiders. The spider genomes are large with short exons and long introns, reminiscent of mammalian genomes. Phylogenetic analyses place spiders and ticks as sister groups supporting polyphyly of the Acari. Complex sets of venom and silk genes/proteins are identified. We find that venom genes evolved by sequential duplication, and that the toxic effect of venom is most likely activated by proteases present in the venom. The set of silk genes reveals a highly dynamic gene evolution, new types of silk genes and proteins, and a novel use of aciniform silk. These insights create new opportunities for pharmacological applications of venom and biomaterial applications of silk. PMID:24801114

Co-invading symbiotic mutualists of Medicago polymorpha retain high ancestral diversity and contain diverse accessory genomes.

Science.gov (United States)

Porter, Stephanie S; Faber-Hammond, Joshua J; Friesen, Maren L

2018-01-01

Exotic, invasive plants and animals can wreak havoc on ecosystems by displacing natives and altering environmental conditions. However, much less is known about the identities or evolutionary dynamics of the symbiotic microbes that accompany invasive species. Most leguminous plants rely upon symbiotic rhizobium bacteria to fix nitrogen and are incapable of colonizing areas devoid of compatible rhizobia. We compare the genomes of symbiotic rhizobia in a portion of the legume's invaded range with those of the rhizobium symbionts from across the legume's native range. We show that in an area of California the legume Medicago polymorpha has invaded, its Ensifer medicae symbionts: (i) exhibit genome-wide patterns of relatedness that together with historical evidence support host-symbiont co-invasion from Europe into California, (ii) exhibit population genomic patterns consistent with the introduction of the majority of deep diversity from the native range, rather than a genetic bottleneck during colonization of California and (iii) harbor a large set of accessory genes uniquely enriched in binding functions, which could play a role in habitat invasion. Examining microbial symbiont genome dynamics during biological invasions is critical for assessing host-symbiont co-invasions whereby microbial symbiont range expansion underlies plant and animal invasions. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Conditional Selection of Genomic Alterations Dictates Cancer Evolution and Oncogenic Dependencies.

Science.gov (United States)

Mina, Marco; Raynaud, Franck; Tavernari, Daniele; Battistello, Elena; Sungalee, Stephanie; Saghafinia, Sadegh; Laessle, Titouan; Sanchez-Vega, Francisco; Schultz, Nikolaus; Oricchio, Elisa; Ciriello, Giovanni

2017-08-14

Cancer evolves through the emergence and selection of molecular alterations. Cancer genome profiling has revealed that specific events are more or less likely to be co-selected, suggesting that the selection of one event depends on the others. However, the nature of these evolutionary dependencies and their impact remain unclear. Here, we designed SELECT, an algorithmic approach to systematically identify evolutionary dependencies from alteration patterns. By analyzing 6,456 genomes from multiple tumor types, we constructed a map of oncogenic dependencies associated with cellular pathways, transcriptional readouts, and therapeutic response. Finally, modeling of cancer evolution shows that alteration dependencies emerge only under conditional selection. These results provide a framework for the design of strategies to predict cancer progression and therapeutic response. Copyright © 2017 Elsevier Inc. All rights reserved.

Genomes Behave as Social Entities: Alien Chromatin Minorities Evolve Through Specificities Reduction

Science.gov (United States)

Hybridization and chromosome doubling entailed by allopolyploidization requires genetic and epigenetic modifications, resulting in the adjustment of different genomes to the same nuclear environment. Recently, the main role of retrotransposon/microsatellite-rich regions of the genome in DNA sequenc...

Network analysis of genomic alteration profiles reveals co-altered functional modules and driver genes for glioblastoma.

Science.gov (United States)

Gu, Yunyan; Wang, Hongwei; Qin, Yao; Zhang, Yujing; Zhao, Wenyuan; Qi, Lishuang; Zhang, Yuannv; Wang, Chenguang; Guo, Zheng

2013-03-01

The heterogeneity of genetic alterations in human cancer genomes presents a major challenge to advancing our understanding of cancer mechanisms and identifying cancer driver genes. To tackle this heterogeneity problem, many approaches have been proposed to investigate genetic alterations and predict driver genes at the individual pathway level. However, most of these approaches ignore the correlation of alteration events between pathways and miss many genes with rare alterations collectively contributing to carcinogenesis. Here, we devise a network-based approach to capture the cooperative functional modules hidden in genome-wide somatic mutation and copy number alteration profiles of glioblastoma (GBM) from The Cancer Genome Atlas (TCGA), where a module is a set of altered genes with dense interactions in the protein interaction network. We identify 7 pairs of significantly co-altered modules that involve the main pathways known to be altered in GBM (TP53, RB and RTK signaling pathways) and highlight the striking co-occurring alterations among these GBM pathways. By taking into account the non-random correlation of gene alterations, the property of co-alteration could distinguish oncogenic modules that contain driver genes involved in the progression of GBM. The collaboration among cancer pathways suggests that the redundant models and aggravating models could shed new light on the potential mechanisms during carcinogenesis and provide new indications for the design of cancer therapeutic strategies.

Uncovering genomic causes of co-morbidity in epilepsy: gene-driven phenotypic characterization of rare microdeletions

NARCIS (Netherlands)

Kasperavičiūtė, Dalia; Catarino, Claudia B.; Chinthapalli, Krishna; Clayton, Lisa M. S.; Thom, Maria; Martinian, Lillian; Cohen, Hannah; Adalat, Shazia; Bockenhauer, Detlef; Pope, Simon A.; Lench, Nicholas; Koltzenburg, Martin; Duncan, John S.; Hammond, Peter; Hennekam, Raoul C. M.; Land, John M.; Sisodiya, Sanjay M.

2011-01-01

Patients with epilepsy often suffer from other important conditions. The existence of such co-morbidities is frequently not recognized and their relationship with epilepsy usually remains unexplained. We describe three patients with common, sporadic, non-syndromic epilepsies in whom large genomic

Insights into pyrolysis and co-pyrolysis of biomass and polystyrene: Thermochemical behaviors, kinetics and evolved gas analysis

International Nuclear Information System (INIS)

Özsin, Gamzenur; Pütün, Ayşe Eren

2017-01-01

Highlights: • TGA/MS/FT-IR was used to explore effect of polystyrene on pyrolytic decomposition of biomass. • The model-free iso-conversional methods were used for kinetic analysis. • Interactions occurred depending on the characteristics of the biomass. • TGA/MS and TGA/FT-IR coupling were used for gas analysis of co-pyrolysis for the first time. - Abstract: The purpose of this study was to investigate the effect on polystyrene (PS) during co-pyrolysis with biomass through thermal decomposition. The model-free iso-conversional methods (Kissinger, Friedman, Flynn-Wall-Ozawa, Kissinger-Akahira-Sunose, Starink and Vyazovkin) were adopted to calculate activation energy of the pyrolysis and co-pyrolysis process of two biomass samples (walnut shell: WS and peach stones: PST) with PS. It is found that biomass blending to PS decreased activation energy values and resulted in multi-step reaction mechanisms. Furthermore, changes in the evolution profiles of methyl, water, methoxy, carbon dioxide, benzene and styrene was monitored through evolved gas analysis via TGA/FT-IR and TGA/MS. Detection of temperature dependent release of volatiles indicated the differences occur as a result of compositional differences of biomass.

Zinc and group V element co-implantation in indium phosphide

International Nuclear Information System (INIS)

Yu, Kin Man; Ridgway, M.C.

2000-01-01

Group V elements with mass ranging from 35 to 122 amu have been co-implanted with Zn in InP substrates. Co-implantation with all group V elements drastically reduced Zn out-diffusion and to a certain extent also inhibited Zn in-diffusion. The reduction in out-diffusion was insensitive to the group V element mass and thus, to implantation-induced damage. We believe the group V element excess created an In-vacancy excess that enhanced Zn substitution into the In sublattice. A maximum hole concentration of 7x10 18 cm -3 was achieved with P co-implantation. Electrochemical capacitance-voltage profiling clearly showed a decrease in hole concentration as a function of increasing group V element mass. This was attributed to differences in compensating residual implantation-induced damage

Resolution effects in reconstructing ancestral genomes.

Science.gov (United States)

Zheng, Chunfang; Jeong, Yuji; Turcotte, Madisyn Gabrielle; Sankoff, David

2018-05-09

The reconstruction of ancestral genomes must deal with the problem of resolution, necessarily involving a trade-off between trying to identify genomic details and being overwhelmed by noise at higher resolutions. We use the median reconstruction at the synteny block level, of the ancestral genome of the order Gentianales, based on coffee, Rhazya stricta and grape, to exemplify the effects of resolution (granularity) on comparative genomic analyses. We show how decreased resolution blurs the differences between evolving genomes, with respect to rate, mutational process and other characteristics.

Crisis Communication Competence in Co-Producing Safety with Citizen Groups

Directory of Open Access Journals (Sweden)

Anne Laajalahti

2016-03-01

Full Text Available The aim of this article is to explore interpersonal communication competence needed by crisis communication and management experts when co-operating with citizen groups in response to emergencies. Moreover, the purpose is to understand how response organizations can further develop this crisis communication competence and so contribute to the functioning of response networks. The research task is approached qualitatively by eliciting crisis communication and management experts’ (n = 33 perceptions of the interpersonal communication competence response organizations needs when co-operating with citizen groups. The data were gathered via an international online questionnaire using a method referred to as “thematic writing” and consist of written responses to open-ended questions on what constitutes the core of crisis communication competence and what aspects of it need more attention. The research findings indicate that co-producing safety with citizen groups demands crisis communication competence related to message production, message reception, and interaction between experts and citizen groups. In addition, the findings clarify what areas of crisis communication competence need to be further developed to facilitate co-operation between experts and citizen groups. However, the authors suggest that crisis communication competence should not be seen solely as a characteristic of individual crisis communicators but approached as a networked and co-created area of competence.

Personalized medicine: new genomics, old lessons

OpenAIRE

Offit, Kenneth

2011-01-01

Personalized medicine uses traditional, as well as emerging concepts of the genetic and environmental basis of disease to individualize prevention, diagnosis and treatment. Personalized genomics plays a vital, but not exclusive role in this evolving model of personalized medicine. The distinctions between genetic and genomic medicine are more quantitative than qualitative. Personalized genomics builds on principles established by the integration of genetics into medical practice. Principles s...

Detection of genomic rearrangements in cucumber using genomecmp software

Science.gov (United States)

Kulawik, Maciej; Pawełkowicz, Magdalena Ewa; Wojcieszek, Michał; PlÄ der, Wojciech; Nowak, Robert M.

2017-08-01

Comparative genomic by increasing information about the genomes sequences available in the databases is a rapidly evolving science. A simple comparison of the general features of genomes such as genome size, number of genes, and chromosome number presents an entry point into comparative genomic analysis. Here we present the utility of the new tool genomecmp for finding rearrangements across the compared sequences and applications in plant comparative genomics.

Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans

DEFF Research Database (Denmark)

Song, Yajun; Tong, Zongzhong; Wang, Jin

2004-01-01

pseudo-genes. Due to the rearrangements mediated by insertion elements, the structure of the 91001 chromosome shows dramatic differences compared with CO92 and KIM. Based on the analysis of plasmids and chromosome architectures, pseudogene distribution, nitrate reduction negative mechanism and gene...... comparison, we conclude that strain 91001 and other strains isolated from M. brandti might have evolved from ancestral Y. pestis in a different lineage. The large genome fragment deletions in the 91001 chromosome and some pseudogenes may contribute to its unique nonpathogenicity to humans and host...

Role of transposon-derived small RNAs in the interplay between genomes and parasitic DNA in rice.

Directory of Open Access Journals (Sweden)

Misuzu Nosaka

2012-09-01

Full Text Available RNA silencing is a defense system against "genomic parasites" such as transposable elements (TE, which are potentially harmful to host genomes. In plants, transcripts from TEs induce production of double-stranded RNAs (dsRNAs and are processed into small RNAs (small interfering RNAs, siRNAs that suppress TEs by RNA-directed DNA methylation. Thus, the majority of TEs are epigenetically silenced. On the other hand, most of the eukaryotic genome is composed of TEs and their remnants, suggesting that TEs have evolved countermeasures against host-mediated silencing. Under some circumstances, TEs can become active and increase in copy number. Knowledge is accumulating on the mechanisms of TE silencing by the host; however, the mechanisms by which TEs counteract silencing are poorly understood. Here, we show that a class of TEs in rice produces a microRNA (miRNA to suppress host silencing. Members of the microRNA820 (miR820 gene family are located within CACTA DNA transposons in rice and target a de novo DNA methyltransferase gene, OsDRM2, one of the components of epigenetic silencing. We confirmed that miR820 negatively regulates the expression of OsDRM2. In addition, we found that expression levels of various TEs are increased quite sensitively in response to decreased OsDRM2 expression and DNA methylation at TE loci. Furthermore, we found that the nucleotide sequence of miR820 and its recognition site within the target gene in some Oryza species have co-evolved to maintain their base-pairing ability. The co-evolution of these sequences provides evidence for the functionality of this regulation. Our results demonstrate how parasitic elements in the genome escape the host's defense machinery. Furthermore, our analysis of the regulation of OsDRM2 by miR820 sheds light on the action of transposon-derived small RNAs, not only as a defense mechanism for host genomes but also as a regulator of interactions between hosts and their parasitic elements.

Genetic variability, local selection and demographic history: genomic evidence of evolving towards allopatric speciation in Asian seabass.

Science.gov (United States)

Wang, Le; Wan, Zi Yi; Lim, Huan Sein; Yue, Gen Hua

2016-08-01

Genomewide analysis of genetic divergence is critically important in understanding the genetic processes of allopatric speciation. We sequenced RAD tags of 131 Asian seabass individuals of six populations from South-East Asia and Australia/Papua New Guinea. Using 32 433 SNPs, we examined the genetic diversity and patterns of population differentiation across all the populations. We found significant evidence of genetic heterogeneity between South-East Asian and Australian/Papua New Guinean populations. The Australian/Papua New Guinean populations showed a rather lower level of genetic diversity. FST and principal components analysis revealed striking divergence between South-East Asian and Australian/Papua New Guinean populations. Interestingly, no evidence of contemporary gene flow was observed. The demographic history was further tested based on the folded joint site frequency spectrum. The scenario of ancient migration with historical population size changes was suggested to be the best fit model to explain the genetic divergence of Asian seabass between South-East Asia and Australia/Papua New Guinea. This scenario also revealed that Australian/Papua New Guinean populations were founded by ancestors from South-East Asia during mid-Pleistocene and were completely isolated from the ancestral population after the last glacial retreat. We also detected footprints of local selection, which might be related to differential ecological adaptation. The ancient gene flow was examined and deemed likely insufficient to counteract the genetic differentiation caused by genetic drift. The observed genomic pattern of divergence conflicted with the 'genomic islands' scenario. Altogether, Asian seabass have likely been evolving towards allopatric speciation since the split from the ancestral population during mid-Pleistocene. © 2016 John Wiley & Sons Ltd.

Genome-wide analysis of the SBP-box gene family in Chinese cabbage (Brassica rapa subsp. pekinensis).

Science.gov (United States)

Tan, Hua-Wei; Song, Xiao-Ming; Duan, Wei-Ke; Wang, Yan; Hou, Xi-Lin

2015-11-01

The SQUAMOSA PROMOTER BINDING PROTEIN (SBP)-box gene family contains highly conserved plant-specific transcription factors that play an important role in plant development, especially in flowering. Chinese cabbage (Brassica rapa subsp. pekinensis) is a leafy vegetable grown worldwide and is used as a model crop for research in genome duplication. The present study aimed to characterize the SBP-box transcription factor genes in Chinese cabbage. Twenty-nine SBP-box genes were identified in the Chinese cabbage genome and classified into six groups. We identified 23 orthologous and 5 co-orthologous SBP-box gene pairs between Chinese cabbage and Arabidopsis. An interaction network among these genes was constructed. Sixteen SBP-box genes were expressed more abundantly in flowers than in other tissues, suggesting their involvement in flowering. We show that the MiR156/157 family members may regulate the coding regions or 3'-UTR regions of Chinese cabbage SBP-box genes. As SBP-box genes were found to potentially participate in some plant development pathways, quantitative real-time PCR analysis was performed and showed that Chinese cabbage SBP-box genes were also sensitive to the exogenous hormones methyl jasmonic acid and salicylic acid. The SBP-box genes have undergone gene duplication and loss, evolving a more refined regulation for diverse stimulation in plant tissues. Our comprehensive genome-wide analysis provides insights into the SBP-box gene family of Chinese cabbage.

The Genome Sequence of the psychrophilic archaeon, Methanococcoides burtonii: the Role of Genome Evolution in Cold-adaptation

Energy Technology Data Exchange (ETDEWEB)

Allen, Michelle A.; Lauro, Federico M.; Williams, Timothy J.; Burg, Dominic; Siddiqui, Khawar S.; De Francisci, David; Chong, Kevin W.Y.; Pilak, Oliver; Chew, Hwee H.; De Maere, Matthew Z.; Ting, Lily; Katrib, Marilyn; Ng, Charmaine; Sowers, Kevin R.; Galperin, Michael Y.; Anderson, Iain J.; Ivanova, Natalia; Dalin, Eileen; Martinez, Michelle; Lapidus, Alla; Hauser, Loren; Land, Miriam; Thomas, Torsten; Cavicchioli, Ricardo

2009-04-01

Psychrophilic archaea are abundant and perform critical roles throughout the Earth's expansive cold biosphere. Here we report the first complete genome sequence for a psychrophilic methanogenic archaeon, Methanococcoides burtonii. The genome sequence was manually annotated including the use of a five tiered Evidence Rating system that ranked annotations from Evidence Rating (ER) 1 (gene product experimentally characterized from the parent organism) to ER5 (hypothetical gene product) to provide a rapid means of assessing the certainty of gene function predictions. The genome is characterized by a higher level of aberrant sequence composition (51%) than any other archaeon. In comparison to hyper/thermophilic archaea which are subject to selection of synonymous codon usage, M. burtonii has evolved cold adaptation through a genomic capacity to accommodate highly skewed amino acid content, while retaining codon usage in common with its mesophilic Methanosarcina cousins. Polysaccharide biosynthesis genes comprise at least 3.3% of protein coding genes in the genome, and Cell wall/membrane/envelope biogenesis COG genes are over-represented. Likewise, signal transduction (COG category T) genes are over-represented and M. burtonii has a high 'IQ' (a measure of adaptive potential) compared to many methanogens. Numerous genes in these two over-represented COG categories appear to have been acquired from {var_epsilon}- and {delta}-proteobacteria, as do specific genes involved in central metabolism such as a novel B form of aconitase. Transposases also distinguish M. burtonii from other archaea, and their genomic characteristics indicate they play an important role in evolving the M. burtonii genome. Our study reveals a capacity for this model psychrophile to evolve through genome plasticity (including nucleotide skew, horizontal gene transfer and transposase activity) that enables adaptation to the cold, and to the biological and physical changes that have

ConGEMs: Condensed Gene Co-Expression Module Discovery Through Rule-Based Clustering and Its Application to Carcinogenesis

Directory of Open Access Journals (Sweden)

Saurav Mallik

2017-12-01

Full Text Available For transcriptomic analysis, there are numerous microarray-based genomic data, especially those generated for cancer research. The typical analysis measures the difference between a cancer sample-group and a matched control group for each transcript or gene. Association rule mining is used to discover interesting item sets through rule-based methodology. Thus, it has advantages to find causal effect relationships between the transcripts. In this work, we introduce two new rule-based similarity measures—weighted rank-based Jaccard and Cosine measures—and then propose a novel computational framework to detect condensed gene co-expression modules ( C o n G E M s through the association rule-based learning system and the weighted similarity scores. In practice, the list of evolved condensed markers that consists of both singular and complex markers in nature depends on the corresponding condensed gene sets in either antecedent or consequent of the rules of the resultant modules. In our evaluation, these markers could be supported by literature evidence, KEGG (Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology annotations. Specifically, we preliminarily identified differentially expressed genes using an empirical Bayes test. A recently developed algorithm—RANWAR—was then utilized to determine the association rules from these genes. Based on that, we computed the integrated similarity scores of these rule-based similarity measures between each rule-pair, and the resultant scores were used for clustering to identify the co-expressed rule-modules. We applied our method to a gene expression dataset for lung squamous cell carcinoma and a genome methylation dataset for uterine cervical carcinogenesis. Our proposed module discovery method produced better results than the traditional gene-module discovery measures. In summary, our proposed rule-based method is useful for exploring biomarker modules from transcriptomic data.

ConGEMs: Condensed Gene Co-Expression Module Discovery Through Rule-Based Clustering and Its Application to Carcinogenesis.

Science.gov (United States)

Mallik, Saurav; Zhao, Zhongming

2017-12-28

For transcriptomic analysis, there are numerous microarray-based genomic data, especially those generated for cancer research. The typical analysis measures the difference between a cancer sample-group and a matched control group for each transcript or gene. Association rule mining is used to discover interesting item sets through rule-based methodology. Thus, it has advantages to find causal effect relationships between the transcripts. In this work, we introduce two new rule-based similarity measures-weighted rank-based Jaccard and Cosine measures-and then propose a novel computational framework to detect condensed gene co-expression modules ( C o n G E M s) through the association rule-based learning system and the weighted similarity scores. In practice, the list of evolved condensed markers that consists of both singular and complex markers in nature depends on the corresponding condensed gene sets in either antecedent or consequent of the rules of the resultant modules. In our evaluation, these markers could be supported by literature evidence, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway and Gene Ontology annotations. Specifically, we preliminarily identified differentially expressed genes using an empirical Bayes test. A recently developed algorithm-RANWAR-was then utilized to determine the association rules from these genes. Based on that, we computed the integrated similarity scores of these rule-based similarity measures between each rule-pair, and the resultant scores were used for clustering to identify the co-expressed rule-modules. We applied our method to a gene expression dataset for lung squamous cell carcinoma and a genome methylation dataset for uterine cervical carcinogenesis. Our proposed module discovery method produced better results than the traditional gene-module discovery measures. In summary, our proposed rule-based method is useful for exploring biomarker modules from transcriptomic data.

Adaptation of Escherichia coli to glucose promotes evolvability in lactose.

Science.gov (United States)

Phillips, Kelly N; Castillo, Gerardo; Wünsche, Andrea; Cooper, Tim F

2016-02-01

The selective history of a population can influence its subsequent evolution, an effect known as historical contingency. We previously observed that five of six replicate populations that were evolved in a glucose-limited environment for 2000 generations, then switched to lactose for 1000 generations, had higher fitness increases in lactose than populations started directly from the ancestor. To test if selection in glucose systematically increased lactose evolvability, we started 12 replay populations--six from a population subsample and six from a single randomly selected clone--from each of the six glucose-evolved founder populations. These replay populations and 18 ancestral populations were evolved for 1000 generations in a lactose-limited environment. We found that replay populations were initially slightly less fit in lactose than the ancestor, but were more evolvable, in that they increased in fitness at a faster rate and to higher levels. This result indicates that evolution in the glucose environment resulted in genetic changes that increased the potential of genotypes to adapt to lactose. Genome sequencing identified four genes--iclR, nadR, spoT, and rbs--that were mutated in most glucose-evolved clones and are candidates for mediating increased evolvability. Our results demonstrate that short-term selective costs during selection in one environment can lead to changes in evolvability that confer longer term benefits. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Genome characterization, antigenicity and pathogenicity of a novel infectious bronchitis virus type isolated from south China.

Science.gov (United States)

Jiang, Lei; Zhao, Wenjun; Han, Zongxi; Chen, Yuqiu; Zhao, Yan; Sun, Junfeng; Li, Huixin; Shao, Yuhao; Liu, Liangliang; Liu, Shengwang

2017-10-01

In 2014, three infectious bronchitis virus (IBV) strains, designated as γCoV/ck/China/I0111/14, γCoV/ck/China/I0114/14 and γCoV/ck/China/I0118/14, were isolated and identified from chickens suspected to be infected with IBV in Guangxi province, China. Based upon data arising from S1 sequence and phylogenetic analyses, the three IBV isolates were genetically different from other known IBV types, which represented a novel genotype (GI-29). Virus cross-neutralization tests, using γCoV/ck/China/I0111/14 as a representative, showed that genotype GI-29 was antigenically different from all other known IBV types, thus representing a novel serotype. Complete genomic analysis showed that GI-29 type viruses were closely related to and might originate from a GX-YL5-like virus by accumulation of substitutions in multiple genes. These GI-29 viral genomes are still evolving and diverging, particularly in the 3' region, although we cannot rule out the possibility of recombination events occurring. For isolate γCoV/ck/China/I0114/14, we found that recombination events had occurred between nsps 2 and 3 in gene 1 which led to the introduction of a 4/91 gene fragment into the γCoV/ck/China/I0114/14 viral genome. In addition, we found that the GI-29 type γCoV/ck/China/I0111/14 isolate was a nephropathogenic strain and high pathogenic to 1-day-old specific pathogen-free (SPF) chickens although cystic oviducts were not observed in the surviving layer chickens challenged with γCoV/ck/China/I0111/14 isolate. Copyright © 2017 Elsevier B.V. All rights reserved.

Genomics for paediatricians: promises and pitfalls.

Science.gov (United States)

Hammond, Carrie Louise; Willoughby, Josh Matthew; Parker, Michael James

2018-03-24

In recent years, there have been significant advances in genetic technologies, evolving the field of genomics from genetics. This has huge diagnostic potential, as genomic testing increasingly becomes part of mainstream medicine. However, there are numerous potential pitfalls in the interpretation of genomic data. It is therefore essential that we educate clinicians more widely about the appropriate interpretation and utilisation of genomic testing. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

The Transcriptome of the Reference Potato Genome Solanum tuberosum Group Phureja Clone DM1-3 516R44

Science.gov (United States)

Massa, Alicia N.; Childs, Kevin L.; Lin, Haining; Bryan, Glenn J.; Giuliano, Giovanni; Buell, C. Robin

2011-01-01

Advances in molecular breeding in potato have been limited by its complex biological system, which includes vegetative propagation, autotetraploidy, and extreme heterozygosity. The availability of the potato genome and accompanying gene complement with corresponding gene structure, location, and functional annotation are powerful resources for understanding this complex plant and advancing molecular breeding efforts. Here, we report a reference for the potato transcriptome using 32 tissues and growth conditions from the doubled monoploid Solanum tuberosum Group Phureja clone DM1-3 516R44 for which a genome sequence is available. Analysis of greater than 550 million RNA-Seq reads permitted the detection and quantification of expression levels of over 22,000 genes. Hierarchical clustering and principal component analyses captured the biological variability that accounts for gene expression differences among tissues suggesting tissue-specific gene expression, and genes with tissue or condition restricted expression. Using gene co-expression network analysis, we identified 18 gene modules that represent tissue-specific transcriptional networks of major potato organs and developmental stages. This information provides a powerful resource for potato research as well as studies on other members of the Solanaceae family. PMID:22046362

Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum.

Directory of Open Access Journals (Sweden)

Dongying Wu

Full Text Available In order to enrich the phylogenetic diversity represented in the available sequenced bacterial genomes and as part of an "Assembling the Tree of Life" project, we determined the genome sequence of Thermomicrobium roseum DSM 5159. T. roseum DSM 5159 is a red-pigmented, rod-shaped, Gram-negative extreme thermophile isolated from a hot spring that possesses both an atypical cell wall composition and an unusual cell membrane that is composed entirely of long-chain 1,2-diols. Its genome is composed of two circular DNA elements, one of 2,006,217 bp (referred to as the chromosome and one of 919,596 bp (referred to as the megaplasmid. Strikingly, though few standard housekeeping genes are found on the megaplasmid, it does encode a complete system for chemotaxis including both chemosensory components and an entire flagellar apparatus. This is the first known example of a complete flagellar system being encoded on a plasmid and suggests a straightforward means for lateral transfer of flagellum-based motility. Phylogenomic analyses support the recent rRNA-based analyses that led to T. roseum being removed from the phylum Thermomicrobia and assigned to the phylum Chloroflexi. Because T. roseum is a deep-branching member of this phylum, analysis of its genome provides insights into the evolution of the Chloroflexi. In addition, even though this species is not photosynthetic, analysis of the genome provides some insight into the origins of photosynthesis in the Chloroflexi. Metabolic pathway reconstructions and experimental studies revealed new aspects of the biology of this species. For example, we present evidence that T. roseum oxidizes CO aerobically, making it the first thermophile known to do so. In addition, we propose that glycosylation of its carotenoids plays a crucial role in the adaptation of the cell membrane to this bacterium's thermophilic lifestyle. Analyses of published metagenomic sequences from two hot springs similar to the one from which

Functional Genomics Group. Program Description

National Research Council Canada - National Science Library

Burian, Dennis

2008-01-01

.... This article reviews mechanisms of gene regulation and discusses how genomics is changing the way medicine is practiced today as a means of demonstrating that molecular medicine is here to stay...

Genome sequence of Yersinia pestis, the causative agent of plague.

Science.gov (United States)

Parkhill, J; Wren, B W; Thomson, N R; Titball, R W; Holden, M T; Prentice, M B; Sebaihia, M; James, K D; Churcher, C; Mungall, K L; Baker, S; Basham, D; Bentley, S D; Brooks, K; Cerdeño-Tárraga, A M; Chillingworth, T; Cronin, A; Davies, R M; Davis, P; Dougan, G; Feltwell, T; Hamlin, N; Holroyd, S; Jagels, K; Karlyshev, A V; Leather, S; Moule, S; Oyston, P C; Quail, M; Rutherford, K; Simmonds, M; Skelton, J; Stevens, K; Whitehead, S; Barrell, B G

2001-10-04

The Gram-negative bacterium Yersinia pestis is the causative agent of the systemic invasive infectious disease classically referred to as plague, and has been responsible for three human pandemics: the Justinian plague (sixth to eighth centuries), the Black Death (fourteenth to nineteenth centuries) and modern plague (nineteenth century to the present day). The recent identification of strains resistant to multiple drugs and the potential use of Y. pestis as an agent of biological warfare mean that plague still poses a threat to human health. Here we report the complete genome sequence of Y. pestis strain CO92, consisting of a 4.65-megabase (Mb) chromosome and three plasmids of 96.2 kilobases (kb), 70.3 kb and 9.6 kb. The genome is unusually rich in insertion sequences and displays anomalies in GC base-composition bias, indicating frequent intragenomic recombination. Many genes seem to have been acquired from other bacteria and viruses (including adhesins, secretion systems and insecticidal toxins). The genome contains around 150 pseudogenes, many of which are remnants of a redundant enteropathogenic lifestyle. The evidence of ongoing genome fluidity, expansion and decay suggests Y. pestis is a pathogen that has undergone large-scale genetic flux and provides a unique insight into the ways in which new and highly virulent pathogens evolve.

Convergent evolution of the genomes of marine mammals

Science.gov (United States)

Foote, Andrew D.; Liu, Yue; Thomas, Gregg W.C.; Vinař, Tomáš; Alföldi, Jessica; Deng, Jixin; Dugan, Shannon; van Elk, Cornelis E.; Hunter, Margaret; Joshi, Vandita; Khan, Ziad; Kovar, Christie; Lee, Sandra L.; Lindblad-Toh, Kerstin; Mancia, Annalaura; Nielsen, Rasmus; Qin, Xiang; Qu, Jiaxin; Raney, Brian J.; Vijay, Nagarjun; Wolf, Jochen B. W.; Hahn, Matthew W.; Muzny, Donna M.; Worley, Kim C.; Gilbert, M. Thomas P.; Gibbs, Richard A.

2015-01-01

Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.

Discovering Complete Quasispecies In Bacterial Genomes

OpenAIRE

Bertels, Frederic; Gokhale, Chaitanya; Traulsen, Arne

2017-01-01

Mobile genetic elements can be found in almost all genomes. Possibly the most common nonautonomous mobile genetic elements in bacteria are repetitive extragenic palindromic doublets forming hairpins (REPINs) that can occur hundreds of times within a genome. The sum of all REPINs in a genome can be viewed as an evolving population because REPINs replicate and mutate. In contrast to most other biological populations, we know the exact composition of the REPIN population and the sequence of each...

Functional genomics highlights differential induction of antiviral pathways in the lungs of SARS-CoV-infected macaques.

Directory of Open Access Journals (Sweden)

Anna de Lang

2007-08-01

Full Text Available The pathogenesis of severe acute respiratory syndrome coronavirus (SARS-CoV is likely mediated by disproportional immune responses and the ability of the virus to circumvent innate immunity. Using functional genomics, we analyzed early host responses to SARS-CoV infection in the lungs of adolescent cynomolgus macaques (Macaca fascicularis that show lung pathology similar to that observed in human adults with SARS. Analysis of gene signatures revealed induction of a strong innate immune response characterized by the stimulation of various cytokine and chemokine genes, including interleukin (IL-6, IL-8, and IP-10, which corresponds to the host response seen in acute respiratory distress syndrome. As opposed to many in vitro experiments, SARS-CoV induced a wide range of type I interferons (IFNs and nuclear translocation of phosphorylated signal transducer and activator of transcription 1 in the lungs of macaques. Using immunohistochemistry, we revealed that these antiviral signaling pathways were differentially regulated in distinctive subsets of cells. Our studies emphasize that the induction of early IFN signaling may be critical to confer protection against SARS-CoV infection and highlight the strength of combining functional genomics with immunohistochemistry to further unravel the pathogenesis of SARS.

Universal pacemaker of genome evolution.

Science.gov (United States)

Snir, Sagi; Wolf, Yuri I; Koonin, Eugene V

2012-01-01

A fundamental observation of comparative genomics is that the distribution of evolution rates across the complete sets of orthologous genes in pairs of related genomes remains virtually unchanged throughout the evolution of life, from bacteria to mammals. The most straightforward explanation for the conservation of this distribution appears to be that the relative evolution rates of all genes remain nearly constant, or in other words, that evolutionary rates of different genes are strongly correlated within each evolving genome. This correlation could be explained by a model that we denoted Universal PaceMaker (UPM) of genome evolution. The UPM model posits that the rate of evolution changes synchronously across genome-wide sets of genes in all evolving lineages. Alternatively, however, the correlation between the evolutionary rates of genes could be a simple consequence of molecular clock (MC). We sought to differentiate between the MC and UPM models by fitting thousands of phylogenetic trees for bacterial and archaeal genes to supertrees that reflect the dominant trend of vertical descent in the evolution of archaea and bacteria and that were constrained according to the two models. The goodness of fit for the UPM model was better than the fit for the MC model, with overwhelming statistical significance, although similarly to the MC, the UPM is strongly overdispersed. Thus, the results of this analysis reveal a universal, genome-wide pacemaker of evolution that could have been in operation throughout the history of life.

Whole-genome pyrosequencing of an epidemic multidrug-resistant Acinetobacter baumannii strain belonging to the European clone II group

DEFF Research Database (Denmark)

Iacono, M.; Villa, L.; Fortini, D.

2008-01-01

The whole-genome sequence of an epidemic, multidrug-resistant Acinetobacter baumannii strain (strain ACICU) belonging to the European clone II group and carrying the plasmid-mediated bla(OXA-58) carbapenem resistance gene was determined. The A. baumannii ACICU genome was compared with the genomes...

Structural genomics in endocrinology

NARCIS (Netherlands)

Smit, J. W.; Romijn, J. A.

2001-01-01

Traditionally, endocrine research evolved from the phenotypical characterisation of endocrine disorders to the identification of underlying molecular pathophysiology. This approach has been, and still is, extremely successful. The introduction of genomics and proteomics has resulted in a reversal of

Genomic comparison of closely related Giant Viruses supports an accordion-like model of evolution.

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Jonathan eFilée

2015-06-01

Full Text Available Genome gigantism occurs so far in Phycodnaviridae and Mimiviridae (order Megavirales. Origin and evolution of these Giant Viruses (GVs remain open questions. Interestingly, availability of a collection of closely related GV genomes enabling genomic comparisons offer the opportunity to better understand the different evolutionary forces acting on these genomes. Whole genome alignment for 5 groups of viruses belonging to the Mimiviridae and Phycodnaviridae families show that there is no trend of genome expansion or general tendency of genome contraction. Instead, GV genomes accumulated genomic mutations over the time with gene gains compensating the different losses. In addition, each lineage displays specific patterns of genome evolution. Mimiviridae (megaviruses and mimiviruses and Chlorella Phycodnaviruses evolved mainly by duplications and losses of genes belonging to large paralogous families (including movements of diverse mobiles genetic elements, whereas Micromonas and Ostreococcus Phycodnaviruses derive most of their genetic novelties thought lateral gene transfers. Taken together, these data support an accordion-like model of evolution in which GV genomes have undergone successive steps of gene gain and gene loss, accrediting the hypothesis that genome gigantism appears early, before the diversification of the different GV lineages.

Genomic comparison of closely related Giant Viruses supports an accordion-like model of evolution.

Science.gov (United States)

Filée, Jonathan

2015-01-01

Genome gigantism occurs so far in Phycodnaviridae and Mimiviridae (order Megavirales). Origin and evolution of these Giant Viruses (GVs) remain open questions. Interestingly, availability of a collection of closely related GV genomes enabling genomic comparisons offer the opportunity to better understand the different evolutionary forces acting on these genomes. Whole genome alignment for five groups of viruses belonging to the Mimiviridae and Phycodnaviridae families show that there is no trend of genome expansion or general tendency of genome contraction. Instead, GV genomes accumulated genomic mutations over the time with gene gains compensating the different losses. In addition, each lineage displays specific patterns of genome evolution. Mimiviridae (megaviruses and mimiviruses) and Chlorella Phycodnaviruses evolved mainly by duplications and losses of genes belonging to large paralogous families (including movements of diverse mobiles genetic elements), whereas Micromonas and Ostreococcus Phycodnaviruses derive most of their genetic novelties thought lateral gene transfers. Taken together, these data support an accordion-like model of evolution in which GV genomes have undergone successive steps of gene gain and gene loss, accrediting the hypothesis that genome gigantism appears early, before the diversification of the different GV lineages.

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

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.

Science.gov (United States)

Brewer, Michael S; Swafford, Lynn; Spruill, Chad L; Bond, Jason E

2013-01-01

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. 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. 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 signal renders the resulting tree topologies as suspect

DrawCompileEvolve: Sparking interactive evolutionary art with human creations

DEFF Research Database (Denmark)

Zhang, Jinhong; Taarnby, Rasmus; Liapis, Antonios

2015-01-01

This paper presents DrawCompileEvolve, a web-based drawing tool which allows users to draw simple primitive shapes, group them together or define patterns in their groupings (e.g. symmetry, repetition). The user’s vector drawing is then compiled into an indirectly encoded genetic representation......, which can be evolved interactively, allowing the user to change the image’s colors, patterns and ultimately transform it. The human artist has direct control while drawing the initial seed of an evolutionary run and indirect control while interactively evolving it, thus making DrawCompileEvolve a mixed...

Biodegradation of Poly(butylene succinate Powder in a Controlled Compost at 58 °C Evaluated by Naturally-Occurring Carbon 14 Amounts in Evolved CO2 Based on the ISO 14855-2 Method

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Masahiro Funabashi

2009-09-01

Full Text Available The biodegradabilities of poly(butylene succinate (PBS powders in a controlled compost at 58 °C have been studied using a Microbial Oxidative Degradation Analyzer (MODA based on the ISO 14855-2 method, entitled “Determination of the ultimate aerobic biodegradability of plastic materials under controlled composting conditions—Method by analysis of evolved carbon dioxide—Part 2: Gravimetric measurement of carbon dioxide evolved in a laboratory-scale test”. The evolved CO2 was trapped by an additional aqueous Ba(OH2 solution. The trapped BaCO3 was transformed into graphite via a serial vaporization and reduction reaction using a gas-tight tube and vacuum manifold system. This graphite was analyzed by accelerated mass spectrometry (AMS to determine the percent modern carbon [pMC (sample] based on the 14C radiocarbon concentration. By using the theory that pMC (sample was the sum of the pMC (compost (109.87% and pMC (PBS (0% as the respective ratio in the determined period, the CO2 (respiration was calculated from only one reaction vessel. It was found that the biodegradabilities determined by the CO2 amount from PBS in the sample vessel were about 30% lower than those based on the ISO method. These differences between the ISO and AMS methods are caused by the fact that part of the carbons from PBS are changed into metabolites by the microorganisms in the compost, and not changed into CO2.

Characterizing 3-D flow velocity in evolving pore networks driven by CaCO3 precipitation and dissolution

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Chojnicki, K. N.; Yoon, H.; Martinez, M. J.

2015-12-01

Understanding reactive flow in geomaterials is important for optimizing geologic carbon storage practices, such as using pore space efficiently. Flow paths can be complex in large degrees of geologic heterogeneities across scales. In addition, local heterogeneity can evolve as reactive transport processes alter the pore-scale morphology. For example, dissolved carbon dioxide may react with minerals in fractured rocks, confined aquifers, or faults, resulting in heterogeneous cementation (and/or dissolution) and evolving flow conditions. Both path and flow complexities are important and poorly characterized, making it difficult to determine their evolution with traditional 2-D transport models. Here we characterize the development of 3-D pore-scale flow with an evolving pore configuration due to calcium carbonate (CaCO3) precipitation and dissolution. A simple pattern of a microfluidic pore network is used initially and pore structures will become more complex due to precipitation and dissolution processes. At several stages of precipitation and dissolution, we directly visualize 3-D velocity vectors using micro particle image velocimetry and a laser scanning confocal microscope. Measured 3-D velocity vectors are then compared to 3-D simulated flow fields which will be used to simulate reactive transport. Our findings will highlight the importance of the 3-D flow dynamics and its impact on estimating reactive surface area over time. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. This material is based upon work supported as part of the Center for Frontiers of Subsurface Energy Security, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001114.

Co-production in practice: how people with assisted living needs can help design and evolve technologies and services.

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Wherton, Joseph; Sugarhood, Paul; Procter, Rob; Hinder, Sue; Greenhalgh, Trisha

2015-05-26

The low uptake of telecare and telehealth services by older people may be explained by the limited involvement of users in the design. If the ambition of 'care closer to home' is to be realised, then industry, health and social care providers must evolve ways to work with older people to co-produce useful and useable solutions. We conducted 10 co-design workshops with users of telehealth and telecare, their carers, service providers and technology suppliers. Using vignettes developed from in-depth ethnographic case studies, we explored participants' perspectives on the design features of technologies and services to enable and facilitate the co-production of new care solutions. Workshop discussions were audio recorded, transcribed and analysed thematically. Analysis revealed four main themes. First, there is a need to raise awareness and provide information to potential users of assisted living technologies (ALTs). Second, technologies must be highly customisable and adaptable to accommodate the multiple and changing needs of different users. Third, the service must align closely with the individual's wider social support network. Finally, the service must support a high degree of information sharing and coordination. The case vignettes within inclusive and democratic co-design workshops provided a powerful means for ALT users and their carers to contribute, along with other stakeholders, to technology and service design. The workshops identified a need to focus attention on supporting the social processes that facilitate the collective efforts of formal and informal care networks in ALT delivery and use.

Mixed-Gender Co-Facilitation in Therapeutic Groups for Men Who Have Perpetrated Intimate Partner Violence: Group Members' Perspectives

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Roy, Valerie; Lindsay, Jocelyn; Dallaire, Louis-Francois

2013-01-01

This article describes a study that explored the use of mixed-gender co-facilitation in intimate partner violence groups, especially regarding its potential for gender role socialization. Using an interpretive approach, interviews with men from different mixed-gender co-facilitated groups in Canada were analyzed, with a focus on the men's…

The mitochondrial genomes of the iguana (Iguana iguana) and the caiman (Caiman crocodylus): implications for amniote phylogeny.

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Janke, A; Erpenbeck, D; Nilsson, M; Arnason, U

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 2889 amino-acid sites from 35 mitochondrial genomes supported the bird-crocodile relationship, lending no support to the Haematotherma hypothesis (with birds and mammals representing sister groups). The analyses corroborated the view that turtles are at the base of the bird-crocodile branch. This position of the turtles makes Diapsida paraphyletic. The origin of the squamates was estimated at 294 million years (Myr) ago and that of the turtles at 278 Myr ago. Phylogenetic analysis of mammalian relationships using the additional outgroups corroborated the Marsupionta hypothesis, which joins the monotremes and the marsupials to the exclusion of the eutherians. PMID:11297180

Comparative Genomics of the Dual-Obligate Symbionts from the Treehopper, Entylia carinata (Hemiptera: Membracidae), Provide Insight into the Origins and Evolution of an Ancient Symbiosis.

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Mao, Meng; Yang, Xiushuai; Poff, Kirsten; Bennett, Gordon

2017-06-01

Insect species in the Auchenorrhyncha suborder (Hemiptera) maintain ancient obligate symbioses with bacteria that provide essential amino acids (EAAs) deficient in their plant-sap diets. Molecular studies have revealed that two complementary symbiont lineages, "Candidatus Sulcia muelleri" and a betaproteobacterium ("Ca. Zinderia insecticola" in spittlebugs [Cercopoidea] and "Ca. Nasuia deltocephalinicola" in leafhoppers [Cicadellidae]) may have persisted in the suborder since its origin ∼300 Ma. However, investigation of how this pair has co-evolved on a genomic level is limited to only a few host lineages. We sequenced the complete genomes of Sulcia and a betaproteobacterium from the treehopper, Entylia carinata (Membracidae: ENCA), as the first representative from this species-rich group. It also offers the opportunity to compare symbiont evolution across a major insect group, the Membracoidea (leafhoppers + treehoppers). Genomic analyses show that the betaproteobacteria in ENCA is a member of the Nasuia lineage. Both symbionts have larger genomes (Sulcia = 218 kb and Nasuia = 144 kb) than related lineages in Deltocephalinae leafhoppers, retaining genes involved in basic cellular functions and information processing. Nasuia-ENCA further exhibits few unique gene losses, suggesting that its parent lineage in the common ancestor to the Membracoidea was already highly reduced. Sulcia-ENCA has lost the abilities to synthesize menaquinone cofactor and to complete the synthesis of the branched-chain EAAs. Both capabilities are conserved in other Sulcia lineages sequenced from across the Auchenorrhyncha. Finally, metagenomic sequencing recovered the partial genome of an Arsenophonus symbiont, although it infects only 20% of individuals indicating a facultative role. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags.

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Paul A Hohenlohe

2010-02-01

Full Text Available Next-generation sequencing technology provides novel opportunities for gathering genome-scale sequence data in natural populations, laying the empirical foundation for the evolving field of population genomics. Here we conducted a genome scan of nucleotide diversity and differentiation in natural populations of threespine stickleback (Gasterosteus aculeatus. We used Illumina-sequenced RAD tags to identify and type over 45,000 single nucleotide polymorphisms (SNPs in each of 100 individuals from two oceanic and three freshwater populations. Overall estimates of genetic diversity and differentiation among populations confirm the biogeographic hypothesis that large panmictic oceanic populations have repeatedly given rise to phenotypically divergent freshwater populations. Genomic regions exhibiting signatures of both balancing and divergent selection were remarkably consistent across multiple, independently derived populations, indicating that replicate parallel phenotypic evolution in stickleback may be occurring through extensive, parallel genetic evolution at a genome-wide scale. Some of these genomic regions co-localize with previously identified QTL for stickleback phenotypic variation identified using laboratory mapping crosses. In addition, we have identified several novel regions showing parallel differentiation across independent populations. Annotation of these regions revealed numerous genes that are candidates for stickleback phenotypic evolution and will form the basis of future genetic analyses in this and other organisms. This study represents the first high-density SNP-based genome scan of genetic diversity and differentiation for populations of threespine stickleback in the wild. These data illustrate the complementary nature of laboratory crosses and population genomic scans by confirming the adaptive significance of previously identified genomic regions, elucidating the particular evolutionary and demographic history of such

The Emergence of Groups and Inequality through Co-Adaptation.

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Jon Atwell

Full Text Available The emergence of groups and of inequality is often traced to pre-existing differences, exclusionary practices, or resource accumulation processes, but can the emergence of groups and their differential success simply be a feature of the behaviors of a priori equally-capable actors who have mutually adapted? Using a simple model of behavioral co-adaptation among agents whose individual actions construct a common environment, we present evidence that the formation of unequal groups is endemic to co-adaptive processes that endogenously alter the environment; agents tend to separate into two groups, one whose members stop adapting earliest (the in-group, and another comprising agents who continue to adapt (the out-group. Over a wide range of model parameters, members of the in-group are rewarded more on average than members of the out-group. The primary reason is that the in-group is able to have a more profound influence on the environment and mold it to the benefit of its members. This molding capacity proves more beneficial than the persistence of adaptivity, yet, crucially, which agents are able to form a coalition to successfully exert this control is strongly contingent on random aspects of the set of agent behaviors. In this paper, we present the model, relevant definitions, and results. We then discuss its implications for the study of complex adaptive systems generally.

Yeast "make-accumulate-consume" life strategy evolved as a multi-step process that predates the whole genome duplication.

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Hagman, Arne; Säll, Torbjörn; Compagno, Concetta; Piskur, Jure

2013-01-01

When fruits ripen, microbial communities start a fierce competition for the freely available fruit sugars. Three yeast lineages, including baker's yeast Saccharomyces cerevisiae, have independently developed the metabolic activity to convert simple sugars into ethanol even under fully aerobic conditions. This fermentation capacity, named Crabtree effect, reduces the cell-biomass production but provides in nature a tool to out-compete other microorganisms. Here, we analyzed over forty Saccharomycetaceae yeasts, covering over 200 million years of the evolutionary history, for their carbon metabolism. The experiments were done under strictly controlled and uniform conditions, which has not been done before. We show that the origin of Crabtree effect in Saccharomycetaceae predates the whole genome duplication and became a settled metabolic trait after the split of the S. cerevisiae and Kluyveromyces lineages, and coincided with the origin of modern fruit bearing plants. Our results suggest that ethanol fermentation evolved progressively, involving several successive molecular events that have gradually remodeled the yeast carbon metabolism. While some of the final evolutionary events, like gene duplications of glucose transporters and glycolytic enzymes, have been deduced, the earliest molecular events initiating Crabtree effect are still to be determined.

The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima

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Chipman, Ariel D.; Ferrier, David E. K.; Brena, Carlo; Qu, Jiaxin; Hughes, Daniel S. T.; Schröder, Reinhard; Torres-Oliva, Montserrat; Znassi, Nadia; Jiang, Huaiyang; Almeida, Francisca C.; Alonso, Claudio R.; Apostolou, Zivkos; Aqrawi, Peshtewani; Arthur, Wallace; Barna, Jennifer C. J.; Blankenburg, Kerstin P.; Brites, Daniela; Capella-Gutiérrez, Salvador; Coyle, Marcus; Dearden, Peter K.; Du Pasquier, Louis; Duncan, Elizabeth J.; Ebert, Dieter; Eibner, Cornelius; Erikson, Galina; Evans, Peter D.; Extavour, Cassandra G.; Francisco, Liezl; Gabaldón, Toni; Gillis, William J.; Goodwin-Horn, Elizabeth A.; Green, Jack E.; Griffiths-Jones, Sam; Grimmelikhuijzen, Cornelis J. P.; Gubbala, Sai; Guigó, Roderic; Han, Yi; Hauser, Frank; Havlak, Paul; Hayden, Luke; Helbing, Sophie; Holder, Michael; Hui, Jerome H. L.; Hunn, Julia P.; Hunnekuhl, Vera S.; Jackson, LaRonda; Javaid, Mehwish; Jhangiani, Shalini N.; Jiggins, Francis M.; Jones, Tamsin E.; Kaiser, Tobias S.; Kalra, Divya; Kenny, Nathan J.; Korchina, Viktoriya; Kovar, Christie L.; Kraus, F. Bernhard; Lapraz, François; Lee, Sandra L.; Lv, Jie; Mandapat, Christigale; Manning, Gerard; Mariotti, Marco; Mata, Robert; Mathew, Tittu; Neumann, Tobias; Newsham, Irene; Ngo, Dinh N.; Ninova, Maria; Okwuonu, Geoffrey; Ongeri, Fiona; Palmer, William J.; Patil, Shobha; Patraquim, Pedro; Pham, Christopher; Pu, Ling-Ling; Putman, Nicholas H.; Rabouille, Catherine; Ramos, Olivia Mendivil; Rhodes, Adelaide C.; Robertson, Helen E.; Robertson, Hugh M.; Ronshaugen, Matthew; Rozas, Julio; Saada, Nehad; Sánchez-Gracia, Alejandro; Scherer, Steven E.; Schurko, Andrew M.; Siggens, Kenneth W.; Simmons, DeNard; Stief, Anna; Stolle, Eckart; Telford, Maximilian J.; Tessmar-Raible, Kristin; Thornton, Rebecca; van der Zee, Maurijn; von Haeseler, Arndt; Williams, James M.; Willis, Judith H.; Wu, Yuanqing; Zou, Xiaoyan; Lawson, Daniel; Muzny, Donna M.; Worley, Kim C.; Gibbs, Richard A.; Akam, Michael; Richards, Stephen

2014-01-01

Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific

WormBase: Annotating many nematode genomes.

Science.gov (United States)

Howe, Kevin; Davis, Paul; Paulini, Michael; Tuli, Mary Ann; Williams, Gary; Yook, Karen; Durbin, Richard; Kersey, Paul; Sternberg, Paul W

2012-01-01

WormBase (www.wormbase.org) has been serving the scientific community for over 11 years as the central repository for genomic and genetic information for the soil nematode Caenorhabditis elegans. The resource has evolved from its beginnings as a database housing the genomic sequence and genetic and physical maps of a single species, and now represents the breadth and diversity of nematode research, currently serving genome sequence and annotation for around 20 nematodes. In this article, we focus on WormBase's role of genome sequence annotation, describing how we annotate and integrate data from a growing collection of nematode species and strains. We also review our approaches to sequence curation, and discuss the impact on annotation quality of large functional genomics projects such as modENCODE.

Genomics of adaptation during experimental evolution of the opportunistic pathogen Pseudomonas aeruginosa.

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Alex Wong

2012-09-01

Full Text Available Adaptation is likely to be an important determinant of the success of many pathogens, for example when colonizing a new host species, when challenged by antibiotic treatment, or in governing the establishment and progress of long-term chronic infection. Yet, the genomic basis of adaptation is poorly understood in general, and for pathogens in particular. We investigated the genetics of adaptation to cystic fibrosis-like culture conditions in the presence and absence of fluoroquinolone antibiotics using the opportunistic pathogen Pseudomonas aeruginosa. Whole-genome sequencing of experimentally evolved isolates revealed parallel evolution at a handful of known antibiotic resistance genes. While the level of antibiotic resistance was largely determined by these known resistance genes, the costs of resistance were instead attributable to a number of mutations that were specific to individual experimental isolates. Notably, stereotypical quinolone resistance mutations in DNA gyrase often co-occurred with other mutations that, together, conferred high levels of resistance but no consistent cost of resistance. This result may explain why these mutations are so prevalent in clinical quinolone-resistant isolates. In addition, genes involved in cyclic-di-GMP signalling were repeatedly mutated in populations evolved in viscous culture media, suggesting a shared mechanism of adaptation to this CF-like growth environment. Experimental evolutionary approaches to understanding pathogen adaptation should provide an important complement to studies of the evolution of clinical isolates.

Complete genome sequence and comparative genomic analysis of Mycobacterium massiliense JCM 15300 in the Mycobacterium abscessus group reveal a conserved genomic island MmGI-1 related to putative lipid metabolism.

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Tsuyoshi Sekizuka

Full Text Available Mycobacterium abscessus group subsp., such as M. massiliense, M. abscessus sensu stricto and M. bolletii, are an environmental organism found in soil, water and other ecological niches, and have been isolated from respiratory tract infection, skin and soft tissue infection, postoperative infection of cosmetic surgery. To determine the unique genetic feature of M. massiliense, we sequenced the complete genome of M. massiliense type strain JCM 15300 (corresponding to CCUG 48898. Comparative genomic analysis was performed among Mycobacterium spp. and among M. abscessus group subspp., showing that additional ß-oxidation-related genes and, notably, the mammalian cell entry (mce operon were located on a genomic island, M. massiliense Genomic Island 1 (MmGI-1, in M. massiliense. In addition, putative anaerobic respiration system-related genes and additional mycolic acid cyclopropane synthetase-related genes were found uniquely in M. massiliense. Japanese isolates of M. massiliense also frequently possess the MmGI-1 (14/44, approximately 32% and three unique conserved regions (26/44; approximately 60%, 34/44; approximately 77% and 40/44; approximately 91%, as well as isolates of other countries (Malaysia, France, United Kingdom and United States. The well-conserved genomic island MmGI-1 may play an important role in high growth potential with additional lipid metabolism, extra factors for survival in the environment or synthesis of complex membrane-associated lipids. ORFs on MmGI-1 showed similarities to ORFs of phylogenetically distant M. avium complex (MAC, suggesting that horizontal gene transfer or genetic recombination events might have occurred within MmGI-1 among M. massiliense and MAC.

Whole-genome analyses resolve early branches in the tree of life of modern birds

DEFF Research Database (Denmark)

Sicheritz-Pontén, Thomas; Li, Cai; Li, Bo

2014-01-01

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister...... or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator...... and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high...

Exploration of plant genomes in the FLAGdb++ environment

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Leplé Jean-Charles

2011-03-01

Full Text Available Abstract Background In the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern. Databases provide crucial solutions: they store, organize and allow information to be queried, they enhance the visibility of newly produced data by comparing them with previously published results, and facilitate the exploration and development of both existing hypotheses and new ideas. Results The FLAGdb++ information system was developed with the aim of using whole plant genomes as physical references in order to gather and merge available genomic data from in silico or experimental approaches. Available through a JAVA application, original interfaces and tools assist the functional study of plant genes by considering them in their specific context: chromosome, gene family, orthology group, co-expression cluster and functional network. FLAGdb++ is mainly dedicated to the exploration of large gene groups in order to decipher functional connections, to highlight shared or specific structural or functional features, and to facilitate translational tasks between plant species (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera. Conclusion Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb++ presents a powerful complementary tool for exploring plant genomes and exploiting structural and functional resources, without the need for computer programming knowledge. First launched in 2002, a 15th version of FLAGdb++ is now available and comprises four model plant genomes and over eight million genomic features.

Large-scale genomic 2D visualization reveals extensive CG-AT skew correlation in bird genomes

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Deng Xuemei

2007-11-01

Full Text Available Abstract Background Bird genomes have very different compositional structure compared with other warm-blooded animals. The variation in the base skew rules in the vertebrate genomes remains puzzling, but it must relate somehow to large-scale genome evolution. Current research is inclined to relate base skew with mutations and their fixation. Here we wish to explore base skew correlations in bird genomes, to develop methods for displaying and quantifying such correlations at different scales, and to discuss possible explanations for the peculiarities of the bird genomes in skew correlation. Results We have developed a method called Base Skew Double Triangle (BSDT for exhibiting the genome-scale change of AT/CG skew as a two-dimensional square picture, showing base skews at many scales simultaneously in a single image. By this method we found that most chicken chromosomes have high AT/CG skew correlation (symmetry in 2D picture, except for some microchromosomes. No other organisms studied (18 species show such high skew correlations. This visualized high correlation was validated by three kinds of quantitative calculations with overlapping and non-overlapping windows, all indicating that chicken and birds in general have a special genome structure. Similar features were also found in some of the mammal genomes, but clearly much weaker than in chickens. We presume that the skew correlation feature evolved near the time that birds separated from other vertebrate lineages. When we eliminated the repeat sequences from the genomes, the AT and CG skews correlation increased for some mammal genomes, but were still clearly lower than in chickens. Conclusion Our results suggest that BSDT is an expressive visualization method for AT and CG skew and enabled the discovery of the very high skew correlation in bird genomes; this peculiarity is worth further study. Computational analysis indicated that this correlation might be a compositional characteristic

CyanoClust: comparative genome resources of cyanobacteria and plastids

OpenAIRE

Sasaki, Naobumi V.; Sato, Naoki

2010-01-01

Cyanobacteria, which perform oxygen-evolving photosynthesis as do chloroplasts of plants and algae, are one of the best-studied prokaryotic phyla and one from which many representative genomes have been sequenced. Lack of a suitable comparative genomic database has been a problem in cyanobacterial genomics because many proteins involved in physiological functions such as photosynthesis and nitrogen fixation are not catalogued in commonly used databases, such as Clusters of Orthologous Protein...

Draft genome sequence of Bacillus azotoformans MEV2011, a (Co-) denitrifying strain unable to grow with oxygen.

Science.gov (United States)

Nielsen, Maja; Schreiber, Lars; Finster, Kai; Schramm, Andreas

2015-01-01

Bacillus azotoformans MEV2011, isolated from soil, is a microaerotolerant obligate denitrifier, which can also produce N2 by co-denitrification. Oxygen is consumed but not growth-supportive. The draft genome has a size of 4.7 Mb and contains key genes for both denitrification and dissimilatory nitrate reduction to ammonium.

Identification of networks of co-occurring, tumor-related DNA copy number changes using a genome-wide scoring approach.

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Christiaan Klijn

2010-01-01

Full Text Available Tumorigenesis is a multi-step process in which normal cells transform into malignant tumors following the accumulation of genetic mutations that enable them to evade the growth control checkpoints that would normally suppress their growth or result in apoptosis. It is therefore important to identify those combinations of mutations that collaborate in cancer development and progression. DNA copy number alterations (CNAs are one of the ways in which cancer genes are deregulated in tumor cells. We hypothesized that synergistic interactions between cancer genes might be identified by looking for regions of co-occurring gain and/or loss. To this end we developed a scoring framework to separate truly co-occurring aberrations from passenger mutations and dominant single signals present in the data. The resulting regions of high co-occurrence can be investigated for between-region functional interactions. Analysis of high-resolution DNA copy number data from a panel of 95 hematological tumor cell lines correctly identified co-occurring recombinations at the T-cell receptor and immunoglobulin loci in T- and B-cell malignancies, respectively, showing that we can recover truly co-occurring genomic alterations. In addition, our analysis revealed networks of co-occurring genomic losses and gains that are enriched for cancer genes. These networks are also highly enriched for functional relationships between genes. We further examine sub-networks of these networks, core networks, which contain many known cancer genes. The core network for co-occurring DNA losses we find seems to be independent of the canonical cancer genes within the network. Our findings suggest that large-scale, low-intensity copy number alterations may be an important feature of cancer development or maintenance by affecting gene dosage of a large interconnected network of functionally related genes.

Co-Option and De Novo Gene Evolution Underlie Molluscan Shell Diversity

Science.gov (United States)

Aguilera, Felipe; McDougall, Carmel

2017-01-01

Abstract Molluscs fabricate shells of incredible diversity and complexity by localized secretions from the dorsal epithelium of the mantle. Although distantly related molluscs express remarkably different secreted gene products, it remains unclear if the evolution of shell structure and pattern is underpinned by the differential co-option of conserved genes or the integration of lineage-specific genes into the mantle regulatory program. To address this, we compare the mantle transcriptomes of 11 bivalves and gastropods of varying relatedness. We find that each species, including four Pinctada (pearl oyster) species that diverged within the last 20 Ma, expresses a unique mantle secretome. Lineage- or species-specific genes comprise a large proportion of each species’ mantle secretome. A majority of these secreted proteins have unique domain architectures that include repetitive, low complexity domains (RLCDs), which evolve rapidly, and have a proclivity to expand, contract and rearrange in the genome. There are also a large number of secretome genes expressed in the mantle that arose before the origin of gastropods and bivalves. Each species expresses a unique set of these more ancient genes consistent with their independent co-option into these mantle gene regulatory networks. From this analysis, we infer lineage-specific secretomes underlie shell diversity, and include both rapidly evolving RLCD-containing proteins, and the continual recruitment and loss of both ancient and recently evolved genes into the periphery of the regulatory network controlling gene expression in the mantle epithelium. PMID:28053006

Genome-scale reconstruction of the metabolic network in Yersinia pestis CO92

Science.gov (United States)

Navid, Ali; Almaas, Eivind

2007-03-01

The gram-negative bacterium Yersinia pestis is the causative agent of bubonic plague. Using publicly available genomic, biochemical and physiological data, we have developed a constraint-based flux balance model of metabolism in the CO92 strain (biovar Orientalis) of this organism. The metabolic reactions were appropriately compartmentalized, and the model accounts for the exchange of metabolites, as well as the import of nutrients and export of waste products. We have characterized the metabolic capabilities and phenotypes of this organism, after comparing the model predictions with available experimental observations to evaluate accuracy and completeness. We have also begun preliminary studies into how cellular metabolism affects virulence.

Positive Selection Driving Cytoplasmic Genome Evolution of the Medicinally Important Ginseng Plant Genus Panax.

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Jiang, Peng; Shi, Feng-Xue; Li, Ming-Rui; Liu, Bao; Wen, Jun; Xiao, Hong-Xing; Li, Lin-Feng

2018-01-01

Panax L. (the ginseng genus) is a shade-demanding group within the family Araliaceae and all of its species are of crucial significance in traditional Chinese medicine. Phylogenetic and biogeographic analyses demonstrated that two rounds of whole genome duplications accompanying with geographic and ecological isolations promoted the diversification of Panax species. However, contributions of the cytoplasmic genomes to the adaptive evolution of Panax species remained largely uninvestigated. In this study, we sequenced the chloroplast and mitochondrial genomes of 11 accessions belonging to seven Panax species. Our results show that heterogeneity in nucleotide substitution rate is abundant in both of the two cytoplasmic genomes, with the mitochondrial genome possessing more variants at the total level but the chloroplast showing higher sequence polymorphisms at the genic regions. Genome-wide scanning of positive selection identified five and 12 genes from the chloroplast and mitochondrial genomes, respectively. Functional analyses further revealed that these selected genes play important roles in plant development, cellular metabolism and adaptation. We therefore conclude that positive selection might be one of the potential evolutionary forces that shaped nucleotide variation pattern of these Panax species. In particular, the mitochondrial genes evolved under stronger selective pressure compared to the chloroplast genes.

The piRNAs forge an immune system for the genome

DEFF Research Database (Denmark)

Muller, Sébastian; Pandey, R.R.; Pillai, R.S.

2013-01-01

Genome integrity of germline is essential for the survival of any species. A dedicated defence mechanism based on small RNA called piRNA (PIWI-interacting RNA) has evolved to protect the germline from the deleterious effects of transposon mobility in genomes such as mutations, deletions or chromo...

A Computational Approach for Predicting Role of Human MicroRNAs in MERS-CoV Genome

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Md Mahmudul Hasan

2014-01-01

Full Text Available The new epidemic Middle East Respiratory Syndrome (MERS is caused by a type of human coronavirus called MERS-CoV which has global fatality rate of about 30%. We are investigating potential antiviral therapeutics against MERS-CoV by using host microRNAs (miRNAs which may downregulate viral gene expression to quell viral replication. We computationally predicted potential 13 cellular miRNAs from 11 potential hairpin sequences of MERS-CoV genome. Our study provided an interesting hypothesis that those miRNAs, that is, hsa-miR-628-5p, hsa-miR-6804-3p, hsa-miR-4289, hsa-miR-208a-3p, hsa-miR-510-3p, hsa-miR-18a-3p, hsa-miR-329-3p, hsa-miR-548ax, hsa-miR-3934-5p, hsa-miR-4474-5p, hsa-miR-7974, hsa-miR-6865-5p, and hsa-miR-342-3p, would be antiviral therapeutics against MERS-CoV infection.

Experimental Evaluation of Unicast and Multicast CoAP Group Communication

Directory of Open Access Journals (Sweden)

Isam Ishaq

2016-07-01

Full Text Available The Internet of Things (IoT is expanding rapidly to new domains in which embedded devices play a key role and gradually outnumber traditionally-connected devices. These devices are often constrained in their resources and are thus unable to run standard Internet protocols. The Constrained Application Protocol (CoAP is a new alternative standard protocol that implements the same principals as the Hypertext Transfer Protocol (HTTP, but is tailored towards constrained devices. In many IoT application domains, devices need to be addressed in groups in addition to being addressable individually. Two main approaches are currently being proposed in the IoT community for CoAP-based group communication. The main difference between the two approaches lies in the underlying communication type: multicast versus unicast. In this article, we experimentally evaluate those two approaches using two wireless sensor testbeds and under different test conditions. We highlight the pros and cons of each of them and propose combining these approaches in a hybrid solution to better suit certain use case requirements. Additionally, we provide a solution for multicast-based group membership management using CoAP.

The genomes and comparative genomics of Lactobacillus delbrueckii phages.

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Riipinen, Katja-Anneli; Forsman, Päivi; Alatossava, Tapani

2011-07-01

Lactobacillus delbrueckii phages are a great source of genetic diversity. Here, the genome sequences of Lb. delbrueckii phages LL-Ku, c5 and JCL1032 were analyzed in detail, and the genetic diversity of Lb. delbrueckii phages belonging to different taxonomic groups was explored. The lytic isometric group b phages LL-Ku (31,080 bp) and c5 (31,841 bp) showed a minimum nucleotide sequence identity of 90% over about three-fourths of their genomes. The genomic locations of their lysis modules were unique, and the genomes featured several putative overlapping transcription units of genes. LL-Ku and c5 virions displayed peptidoglycan hydrolytic activity associated with a ~36-kDa protein similar in size to the endolysin. Unexpectedly, the 49,433-bp genome of the prolate phage JCL1032 (temperate, group c) revealed a conserved gene order within its structural genes. Lb. delbrueckii phages representing groups a (a phage LL-H), b and c possessed only limited protein sequence homology. Genomic comparison of LL-Ku and c5 suggested that diversification of Lb. delbrueckii phages is mainly due to insertions, deletions and recombination. For the first time, the complete genome sequences of group b and c Lb. delbrueckii phages are reported.

Draft genome comparison of representatives of the three dominant genotype groups of dairy Bacillus licheniformis strains.

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Dhakal, Rajat; Seale, R Brent; Deeth, Hilton C; Craven, Heather; Turner, Mark S

2014-06-01

The spore-forming bacterium Bacillus licheniformis is a common contaminant of milk and milk products. Strains of this species isolated from dairy products can be differentiated into three major groups, namely, G, F1, and F2, using random amplification of polymorphic DNA (RAPD) analysis; however, little is known about the genomic differences between these groups and the identity of the fragments that make up their RAPD profiles. In this work we obtained high-quality draft genomes of representative strains from each of the three RAPD groups (designated strain G-1, strain F1-1, and strain F2-1) and compared them to each other and to B. licheniformis ATCC 14580 and Bacillus subtilis 168. Whole-genome comparison and multilocus sequence typing revealed that strain G-1 contains significant sequence variability and belongs to a lineage distinct from the group F strains. Strain G-1 was found to contain genes coding for a type I restriction modification system, urease production, and bacitracin synthesis, as well as the 8-kbp plasmid pFL7, and these genes were not present in strains F1-1 and F2-1. In agreement with this, all isolates of group G, but no group F isolates, were found to possess urease activity and antimicrobial activity against Micrococcus. Identification of RAPD band sequences revealed that differences in the RAPD profiles were due to differences in gene lengths, 3' ends of predicted primer binding sites, or gene presence or absence. This work provides a greater understanding of the phylogenetic and phenotypic differences observed within the B. licheniformis species.

A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae).

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Schoville, Sean D; Chen, Yolanda H; Andersson, Martin N; Benoit, Joshua B; Bhandari, Anita; Bowsher, Julia H; Brevik, Kristian; Cappelle, Kaat; Chen, Mei-Ju M; Childers, Anna K; Childers, Christopher; Christiaens, Olivier; Clements, Justin; Didion, Elise M; Elpidina, Elena N; Engsontia, Patamarerk; Friedrich, Markus; García-Robles, Inmaculada; Gibbs, Richard A; Goswami, Chandan; Grapputo, Alessandro; Gruden, Kristina; Grynberg, Marcin; Henrissat, Bernard; Jennings, Emily C; Jones, Jeffery W; Kalsi, Megha; Khan, Sher A; Kumar, Abhishek; Li, Fei; Lombard, Vincent; Ma, Xingzhou; Martynov, Alexander; Miller, Nicholas J; Mitchell, Robert F; Munoz-Torres, Monica; Muszewska, Anna; Oppert, Brenda; Palli, Subba Reddy; Panfilio, Kristen A; Pauchet, Yannick; Perkin, Lindsey C; Petek, Marko; Poelchau, Monica F; Record, Éric; Rinehart, Joseph P; Robertson, Hugh M; Rosendale, Andrew J; Ruiz-Arroyo, Victor M; Smagghe, Guy; Szendrei, Zsofia; Thomas, Gregg W C; Torson, Alex S; Vargas Jentzsch, Iris M; Weirauch, Matthew T; Yates, Ashley D; Yocum, George D; Yoon, June-Sun; Richards, Stephen

2018-01-31

The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.

Insights from the Genome Sequence of Acidovorax citrulli M6, a Group I Strain of the Causal Agent of Bacterial Fruit Blotch of Cucurbits.

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Eckshtain-Levi, Noam; Shkedy, Dafna; Gershovits, Michael; Da Silva, Gustavo M; Tamir-Ariel, Dafna; Walcott, Ron; Pupko, Tal; Burdman, Saul

2016-01-01

Acidovorax citrulli is a seedborne bacterium that causes bacterial fruit blotch of cucurbit plants including watermelon and melon. A. citrulli strains can be divided into two major groups based on DNA fingerprint analyses and biochemical properties. Group I strains have been generally isolated from non-watermelon cucurbits, while group II strains are closely associated with watermelon. In the present study, we report the genome sequence of M6, a group I model A. citrulli strain, isolated from melon. We used comparative genome analysis to investigate differences between the genome of strain M6 and the genome of the group II model strain AAC00-1. The draft genome sequence of A. citrulli M6 harbors 139 contigs, with an overall approximate size of 4.85 Mb. The genome of M6 is ∼500 Kb shorter than that of strain AAC00-1. Comparative analysis revealed that this size difference is mainly explained by eight fragments, ranging from ∼35-120 Kb and distributed throughout the AAC00-1 genome, which are absent in the M6 genome. In agreement with this finding, while AAC00-1 was found to possess 532 open reading frames (ORFs) that are absent in strain M6, only 123 ORFs in M6 were absent in AAC00-1. Most of these M6 ORFs are hypothetical proteins and most of them were also detected in two group I strains that were recently sequenced, tw6 and pslb65. Further analyses by PCR assays and coverage analyses with other A. citrulli strains support the notion that some of these fragments or significant portions of them are discriminative between groups I and II strains of A. citrulli. Moreover, GC content, effective number of codon values and cluster of orthologs' analyses indicate that these fragments were introduced into group II strains by horizontal gene transfer events. Our study reports the genome sequence of a model group I strain of A. citrulli, one of the most important pathogens of cucurbits. It also provides the first comprehensive comparison at the genomic level between the

The resurrection genome of Boea hygrometrica: A blueprint for survival of dehydration

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Xiao, Lihong; Yang, Ge; Zhang, Liechi; Yang, Xinhua; Zhao, Shuang; Ji, Zhongzhong; Zhou, Qing; Hu, Min; Wang, Yu; Chen, Ming; Xu, Yu; Jin, Haijing; Xiao, Xuan; Hu, Guipeng; Bao, Fang; Hu, Yong; Wan, Ping; Li, Legong; Deng, Xin; Kuang, Tingyun; Xiang, Chengbin; Zhu, Jian-Kang; Oliver, Melvin J.; He, Yikun

2015-01-01

“Drying without dying” is an essential trait in land plant evolution. Unraveling how a unique group of angiosperms, the Resurrection Plants, survive desiccation of their leaves and roots has been hampered by the lack of a foundational genome perspective. Here we report the ∼1,691-Mb sequenced genome of Boea hygrometrica, an important resurrection plant model. The sequence revealed evidence for two historical genome-wide duplication events, a compliment of 49,374 protein-coding genes, 29.15% of which are unique (orphan) to Boea and 20% of which (9,888) significantly respond to desiccation at the transcript level. Expansion of early light-inducible protein (ELIP) and 5S rRNA genes highlights the importance of the protection of the photosynthetic apparatus during drying and the rapid resumption of protein synthesis in the resurrection capability of Boea. Transcriptome analysis reveals extensive alternative splicing of transcripts and a focus on cellular protection strategies. The lack of desiccation tolerance-specific genome organizational features suggests the resurrection phenotype evolved mainly by an alteration in the control of dehydration response genes. PMID:25902549

Comparative genomics and evolution of eukaryotic phospholipidbiosynthesis

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Lykidis, Athanasios

2006-12-01

Phospholipid biosynthetic enzymes produce diverse molecular structures and are often present in multiple forms encoded by different genes. This work utilizes comparative genomics and phylogenetics for exploring the distribution, structure and evolution of phospholipid biosynthetic genes and pathways in 26 eukaryotic genomes. Although the basic structure of the pathways was formed early in eukaryotic evolution, the emerging picture indicates that individual enzyme families followed unique evolutionary courses. For example, choline and ethanolamine kinases and cytidylyltransferases emerged in ancestral eukaryotes, whereas, multiple forms of the corresponding phosphatidyltransferases evolved mainly in a lineage specific manner. Furthermore, several unicellular eukaryotes maintain bacterial-type enzymes and reactions for the synthesis of phosphatidylglycerol and cardiolipin. Also, base-exchange phosphatidylserine synthases are widespread and ancestral enzymes. The multiplicity of phospholipid biosynthetic enzymes has been largely generated by gene expansion in a lineage specific manner. Thus, these observations suggest that phospholipid biosynthesis has been an actively evolving system. Finally, comparative genomic analysis indicates the existence of novel phosphatidyltransferases and provides a candidate for the uncharacterized eukaryotic phosphatidylglycerol phosphate phosphatase.

Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits.

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Dessimoz, Christophe; Boeckmann, Brigitte; Roth, Alexander C J; Gonnet, Gaston H

2006-01-01

Correct orthology assignment is a critical prerequisite of numerous comparative genomics procedures, such as function prediction, construction of phylogenetic species trees and genome rearrangement analysis. We present an algorithm for the detection of non-orthologs that arise by mistake in current orthology classification methods based on genome-specific best hits, such as the COGs database. The algorithm works with pairwise distance estimates, rather than computationally expensive and error-prone tree-building methods. The accuracy of the algorithm is evaluated through verification of the distribution of predicted cases, case-by-case phylogenetic analysis and comparisons with predictions from other projects using independent methods. Our results show that a very significant fraction of the COG groups include non-orthologs: using conservative parameters, the algorithm detects non-orthology in a third of all COG groups. Consequently, sequence analysis sensitive to correct orthology assignments will greatly benefit from these findings.

Functional genomics of physiological plasticity and local adaptation in killifish.

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Whitehead, Andrew; Galvez, Fernando; Zhang, Shujun; Williams, Larissa M; Oleksiak, Marjorie F

2011-01-01

Evolutionary solutions to the physiological challenges of life in highly variable habitats can span the continuum from evolution of a cosmopolitan plastic phenotype to the evolution of locally adapted phenotypes. Killifish (Fundulus sp.) have evolved both highly plastic and locally adapted phenotypes within different selective contexts, providing a comparative system in which to explore the genomic underpinnings of physiological plasticity and adaptive variation. Importantly, extensive variation exists among populations and species for tolerance to a variety of stressors, and we exploit this variation in comparative studies to yield insights into the genomic basis of evolved phenotypic variation. Notably, species of Fundulus occupy the continuum of osmotic habitats from freshwater to marine and populations within Fundulus heteroclitus span far greater variation in pollution tolerance than across all species of fish. Here, we explore how transcriptome regulation underpins extreme physiological plasticity on osmotic shock and how genomic and transcriptomic variation is associated with locally evolved pollution tolerance. We show that F. heteroclitus quickly acclimate to extreme osmotic shock by mounting a dramatic rapid transcriptomic response including an early crisis control phase followed by a tissue remodeling phase involving many regulatory pathways. We also show that convergent evolution of locally adapted pollution tolerance involves complex patterns of gene expression and genome sequence variation, which is confounded with body-weight dependence for some genes. Similarly, exploiting the natural phenotypic variation associated with other established and emerging model organisms is likely to greatly accelerate the pace of discovery of the genomic basis of phenotypic variation.

Evolving spiking neural networks: a novel growth algorithm exhibits unintelligent design

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Schaffer, J. David

2015-06-01

Spiking neural networks (SNNs) have drawn considerable excitement because of their computational properties, believed to be superior to conventional von Neumann machines, and sharing properties with living brains. Yet progress building these systems has been limited because we lack a design methodology. We present a gene-driven network growth algorithm that enables a genetic algorithm (evolutionary computation) to generate and test SNNs. The genome for this algorithm grows O(n) where n is the number of neurons; n is also evolved. The genome not only specifies the network topology, but all its parameters as well. Experiments show the algorithm producing SNNs that effectively produce a robust spike bursting behavior given tonic inputs, an application suitable for central pattern generators. Even though evolution did not include perturbations of the input spike trains, the evolved networks showed remarkable robustness to such perturbations. In addition, the output spike patterns retain evidence of the specific perturbation of the inputs, a feature that could be exploited by network additions that could use this information for refined decision making if required. On a second task, a sequence detector, a discriminating design was found that might be considered an example of "unintelligent design"; extra non-functional neurons were included that, while inefficient, did not hamper its proper functioning.

Regulating genomics in the 21st century: from logos to pathos?

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Gottweis, Herbert

2005-03-01

There is currently an important change in the governance of genomics. In the past, much of the regulatory discussion about genomics has focused on issues of risk. Today, a new discussion is evolving that emphasizes the uncertainties involved in the development and diffusion of genomics into society. The increasing importance of emotional language and the focus on trust in the discussion about genomics reflects the attempt to substitute for the shortcomings of logos with ethos and pathos.

Sperm should evolve to make female meiosis fair.

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Brandvain, Yaniv; Coop, Graham

2015-04-01

Genomic conflicts arise when an allele gains an evolutionary advantage at a cost to organismal fitness. Oögenesis is inherently susceptible to such conflicts because alleles compete for inclusion into the egg. Alleles that distort meiosis in their favor (i.e., meiotic drivers) often decrease organismal fitness, and therefore indirectly favor the evolution of mechanisms to suppress meiotic drive. In this light, many facets of oögenesis and gametogenesis have been interpreted as mechanisms of protection against genomic outlaws. That females of many animal species do not complete meiosis until after fertilization, appears to run counter to this interpretation, because this delay provides an opportunity for sperm-acting alleles to meddle with the outcome of female meiosis and help like alleles drive in heterozygous females. Contrary to this perceived danger, the population genetic theory presented herein suggests that, in fact, sperm nearly always evolve to increase the fairness of female meiosis in the face of genomic conflicts. These results are consistent with the apparent sperm dependence of the best characterized female meiotic driversin animals. Rather than providing an opportunity for sperm collaboration in female meiotic drive, the "fertilization requirement" indirectly protects females from meiotic drivers by providing sperm an opportunity to suppress drive. © 2015 The Author(s).

Sperm should evolve to make female meiosis fair

Science.gov (United States)

Brandvain, Yaniv; Coop, Graham

2017-01-01

Genomic conflicts arise when an allele gains an evolutionary advantage at a cost to organismal fitness. Oögenesis is inherently susceptible to such conflicts because alleles compete for inclusion into the egg. Alleles that distort meiosis in their favor (i.e. meiotic drivers) often decrease organismal fitness, and therefore indirectly favor the evolution of mechanisms to suppress meiotic drive. In this light, many facets of oögenesis and gametogenesis have been interpreted as mechanisms of protection against genomic outlaws. That females of many animal species do not complete meiosis until after fertilization, appears to run counter to this interpretation, because this delay provides an opportunity for sperm-acting alleles to meddle with the outcome of female meiosis and help like alleles drive in heterozygous females. Contrary to this perceived danger, the population genetic theory presented herein suggests that, in fact, sperm nearly always evolve to increase the fairness of female meiosis in the face of genomic conflicts. These results are consistent with the apparent sperm dependence of the best characterized female meiotic drivers in animals. Rather than providing an opportunity for sperm collaboration in female meiotic drive, the ‘fertilization requirement’ indirectly protects females from meiotic drivers by providing sperm an opportunity to suppress drive. PMID:25662355

Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi.

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Knapp, Dániel G; Németh, Julianna B; Barry, Kerrie; Hainaut, Matthieu; Henrissat, Bernard; Johnson, Jenifer; Kuo, Alan; Lim, Joanne Hui Ping; Lipzen, Anna; Nolan, Matt; Ohm, Robin A; Tamás, László; Grigoriev, Igor V; Spatafora, Joseph W; Nagy, László G; Kovács, Gábor M

2018-04-20

Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes of two common DSE of semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced and analyzed with another 32 ascomycetes of different lifestyles. Cadophora sp. (Helotiales) and P. macrospinosa (Pleosporales) have genomes of 70.46 Mb and 54.99 Mb with 22,766 and 18,750 gene models, respectively. The majority of DSE-specific protein clusters lack functional annotation with no similarity to characterized proteins, implying that they have evolved unique genetic innovations. Both DSE possess an expanded number of carbohydrate active enzymes (CAZymes), including plant cell wall degrading enzymes (PCWDEs). Those were similar in three other DSE, and contributed a signal for the separation of root endophytes in principal component analyses of CAZymes, indicating shared genomic traits of DSE fungi. Number of secreted proteases and lipases, aquaporins, and genes linked to melanin synthesis were also relatively high in our fungi. In spite of certain similarities between our two DSE, we observed low levels of convergence in their gene family evolution. This suggests that, despite originating from the same habitat, these two fungi evolved along different evolutionary trajectories and display considerable functional differences within the endophytic lifestyle.

Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes.

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Chen, Yi; Gonzalez-Escalona, Narjol; Hammack, Thomas S; Allard, Marc W; Strain, Errol A; Brown, Eric W

2016-10-15

Many listeriosis outbreaks are caused by a few globally distributed clonal groups, designated clonal complexes or epidemic clones, of Listeria monocytogenes, several of which have been defined by classic multilocus sequence typing (MLST) schemes targeting 6 to 8 housekeeping or virulence genes. We have developed and evaluated core genome MLST (cgMLST) schemes and applied them to isolates from multiple clonal groups, including those associated with 39 listeriosis outbreaks. The cgMLST clusters were congruent with MLST-defined clonal groups, which had various degrees of diversity at the whole-genome level. Notably, cgMLST could distinguish among outbreak strains and epidemiologically unrelated strains of the same clonal group, which could not be achieved using classic MLST schemes. The precise selection of cgMLST gene targets may not be critical for the general identification of clonal groups and outbreak strains. cgMLST analyses further identified outbreak strains, including those associated with recent outbreaks linked to contaminated French-style cheese, Hispanic-style cheese, stone fruit, caramel apple, ice cream, and packaged leafy green salad, as belonging to major clonal groups. We further developed lineage-specific cgMLST schemes, which can include accessory genes when core genomes do not possess sufficient diversity, and this provided additional resolution over species-specific cgMLST. Analyses of isolates from different common-source listeriosis outbreaks revealed various degrees of diversity, indicating that the numbers of allelic differences should always be combined with cgMLST clustering and epidemiological evidence to define a listeriosis outbreak. Classic multilocus sequence typing (MLST) schemes targeting internal fragments of 6 to 8 genes that define clonal complexes or epidemic clones have been widely employed to study L. monocytogenes biodiversity and its relation to pathogenicity potential and epidemiology. We demonstrated that core genome MLST

Genome-wide analysis of the WRKY gene family in cotton.

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Dou, Lingling; Zhang, Xiaohong; Pang, Chaoyou; Song, Meizhen; Wei, Hengling; Fan, Shuli; Yu, Shuxun

2014-12-01

WRKY proteins are major transcription factors involved in regulating plant growth and development. Although many studies have focused on the functional identification of WRKY genes, our knowledge concerning many areas of WRKY gene biology is limited. For example, in cotton, the phylogenetic characteristics, global expression patterns, molecular mechanisms regulating expression, and target genes/pathways of WRKY genes are poorly characterized. Therefore, in this study, we present a genome-wide analysis of the WRKY gene family in cotton (Gossypium raimondii and Gossypium hirsutum). We identified 116 WRKY genes in G. raimondii from the completed genome sequence, and we cloned 102 WRKY genes in G. hirsutum. Chromosomal location analysis indicated that WRKY genes in G. raimondii evolved mainly from segmental duplication followed by tandem amplifications. Phylogenetic analysis of alga, bryophyte, lycophyta, monocot and eudicot WRKY domains revealed family member expansion with increasing complexity of the plant body. Microarray, expression profiling and qRT-PCR data revealed that WRKY genes in G. hirsutum may regulate the development of fibers, anthers, tissues (roots, stems, leaves and embryos), and are involved in the response to stresses. Expression analysis showed that most group II and III GhWRKY genes are highly expressed under diverse stresses. Group I members, representing the ancestral form, seem to be insensitive to abiotic stress, with low expression divergence. Our results indicate that cotton WRKY genes might have evolved by adaptive duplication, leading to sensitivity to diverse stresses. This study provides fundamental information to inform further analysis and understanding of WRKY gene functions in cotton species.

The complete genomic sequence of lytic bacteriophage gh-1 infecting Pseudomonas putida--evidence for close relationship to the T7 group

International Nuclear Information System (INIS)

Kovalyova, Irina V.; Kropinski, Andrew M.

2003-01-01

The genome of the lytic Pseudomonas putida bacteriophage gh-1 is linear double-stranded DNA containing 37,359 bp with 216-bp direct terminal repeats. Like other members of the T7 group, the gh-1 genome contains regions of high homology to T7 interspersed with nonhomologous regions that contain small open reading frames of unknown function. The genome shares 31 genes in common with other members of the T7 group, including RNA polymerase, and an additional 12 unique putative genes. A major difference between gh-1 and other members of this group is the absence of any open reading frames between the left direct terminal repeat and gene 1. Sequence analysis of the gh-1 genome also revealed the presence of 10 putative phage promoters with a consensus sequence similar to the promoters of T3 and phiYeO3-12 (consensus: TAAAAACCCTCACTRTGGCHSCM). P. putida mutants resistant to gh-1 were demonstrated to have an altered lipopolysaccharide structure, indicating that members of this group use lipopolysaccharide as their cellular receptor

Comparative genomics of Wolbachia and the bacterial species concept.

Directory of Open Access Journals (Sweden)

Kirsten Maren Ellegaard

2013-04-01

Full Text Available The importance of host-specialization to speciation processes in obligate host-associated bacteria is well known, as is also the ability of recombination to generate cohesion in bacterial populations. However, whether divergent strains of highly recombining intracellular bacteria, such as Wolbachia, can maintain their genetic distinctness when infecting the same host is not known. We first developed a protocol for the genome sequencing of uncultivable endosymbionts. Using this method, we have sequenced the complete genomes of the Wolbachia strains wHa and wNo, which occur as natural double infections in Drosophila simulans populations on the Seychelles and in New Caledonia. Taxonomically, wHa belong to supergroup A and wNo to supergroup B. A comparative genomics study including additional strains supported the supergroup classification scheme and revealed 24 and 33 group-specific genes, putatively involved in host-adaptation processes. Recombination frequencies were high for strains of the same supergroup despite different host-preference patterns, leading to genomic cohesion. The inferred recombination fragments for strains of different supergroups were of short sizes, and the genomes of the co-infecting Wolbachia strains wHa and wNo were not more similar to each other and did not share more genes than other A- and B-group strains that infect different hosts. We conclude that Wolbachia strains of supergroup A and B represent genetically distinct clades, and that strains of different supergroups can co-exist in the same arthropod host without converging into the same species. This suggests that the supergroups are irreversibly separated and that barriers other than host-specialization are able to maintain distinct clades in recombining endosymbiont populations. Acquiring a good knowledge of the barriers to genetic exchange in Wolbachia will advance our understanding of how endosymbiont communities are constructed from vertically and horizontally

Novel phage group infecting Lactobacillus delbrueckii subsp. lactis, as revealed by genomic and proteomic analysis of bacteriophage Ldl1.

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Casey, Eoghan; Mahony, Jennifer; Neve, Horst; Noben, Jean-Paul; Dal Bello, Fabio; van Sinderen, Douwe

2015-02-01

Ldl1 is a virulent phage infecting the dairy starter Lactobacillus delbrueckii subsp. lactis LdlS. Electron microscopy analysis revealed that this phage exhibits a large head and a long tail and bears little resemblance to other characterized phages infecting Lactobacillus delbrueckii. In vitro propagation of this phage revealed a latent period of 30 to 40 min and a burst size of 59.9 +/- 1.9 phage particles. Comparative genomic and proteomic analyses showed remarkable similarity between the genome of Ldl1 and that of Lactobacillus plantarum phage ATCC 8014-B2. The genomic and proteomic characteristics of Ldl1 demonstrate that this phage does not belong to any of the four previously recognized L. delbrueckii phage groups, necessitating the creation of a new group, called group e, thus adding to the knowledge on the diversity of phages targeting strains of this industrially important lactic acid bacterial species.

Identification of copy number variants defining genomic differences among major human groups.

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Lluís Armengol

Full Text Available BACKGROUND: Understanding the genetic contribution to phenotype variation of human groups is necessary to elucidate differences in disease predisposition and response to pharmaceutical treatments in different human populations. METHODOLOGY/PRINCIPAL FINDINGS: We have investigated the genome-wide profile of structural variation on pooled samples from the three populations studied in the HapMap project by comparative genome hybridization (CGH in different array platforms. We have identified and experimentally validated 33 genomic loci that show significant copy number differences from one population to the other. Interestingly, we found an enrichment of genes related to environment adaptation (immune response, lipid metabolism and extracellular space within these regions and the study of expression data revealed that more than half of the copy number variants (CNVs translate into gene-expression differences among populations, suggesting that they could have functional consequences. In addition, the identification of single nucleotide polymorphisms (SNPs that are in linkage disequilibrium with the copy number alleles allowed us to detect evidences of population differentiation and recent selection at the nucleotide variation level. CONCLUSIONS: Overall, our results provide a comprehensive view of relevant copy number changes that might play a role in phenotypic differences among major human populations, and generate a list of interesting candidates for future studies.

Genomic diversity and evolution of the head crest in the rock pigeon.

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Shapiro, Michael D; Kronenberg, Zev; Li, Cai; Domyan, Eric T; Pan, Hailin; Campbell, Michael; Tan, Hao; Huff, Chad D; Hu, Haofu; Vickrey, Anna I; Nielsen, Sandra C A; Stringham, Sydney A; Hu, Hao; Willerslev, Eske; Gilbert, M Thomas P; Yandell, Mark; Zhang, Guojie; Wang, Jun

2013-03-01

The geographic origins of breeds and the genetic basis of variation within the widely distributed and phenotypically diverse domestic rock pigeon (Columba livia) remain largely unknown. We generated a rock pigeon reference genome and additional genome sequences representing domestic and feral populations. We found evidence for the origins of major breed groups in the Middle East and contributions from a racing breed to North American feral populations. We identified the gene EphB2 as a strong candidate for the derived head crest phenotype shared by numerous breeds, an important trait in mate selection in many avian species. We also found evidence that this trait evolved just once and spread throughout the species, and that the crest originates early in development by the localized molecular reversal of feather bud polarity.

Predicting co-complexed protein pairs using genomic and proteomic data integration

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King Oliver D

2004-04-01

Full Text Available Abstract Background Identifying all protein-protein interactions in an organism is a major objective of proteomics. A related goal is to know which protein pairs are present in the same protein complex. High-throughput methods such as yeast two-hybrid (Y2H and affinity purification coupled with mass spectrometry (APMS have been used to detect interacting proteins on a genomic scale. However, both Y2H and APMS methods have substantial false-positive rates. Aside from high-throughput interaction screens, other gene- or protein-pair characteristics may also be informative of physical interaction. Therefore it is desirable to integrate multiple datasets and utilize their different predictive value for more accurate prediction of co-complexed relationship. Results Using a supervised machine learning approach – probabilistic decision tree, we integrated high-throughput protein interaction datasets and other gene- and protein-pair characteristics to predict co-complexed pairs (CCP of proteins. Our predictions proved more sensitive and specific than predictions based on Y2H or APMS methods alone or in combination. Among the top predictions not annotated as CCPs in our reference set (obtained from the MIPS complex catalogue, a significant fraction was found to physically interact according to a separate database (YPD, Yeast Proteome Database, and the remaining predictions may potentially represent unknown CCPs. Conclusions We demonstrated that the probabilistic decision tree approach can be successfully used to predict co-complexed protein (CCP pairs from other characteristics. Our top-scoring CCP predictions provide testable hypotheses for experimental validation.

Enforcing Co-expression Within a Brain-Imaging Genomics Regression Framework.

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Zille, Pascal; Calhoun, Vince D; Wang, Yu-Ping

2017-06-28

Among the challenges arising in brain imaging genetic studies, estimating the potential links between neurological and genetic variability within a population is key. In this work, we propose a multivariate, multimodal formulation for variable selection that leverages co-expression patterns across various data modalities. Our approach is based on an intuitive combination of two widely used statistical models: sparse regression and canonical correlation analysis (CCA). While the former seeks multivariate linear relationships between a given phenotype and associated observations, the latter searches to extract co-expression patterns between sets of variables belonging to different modalities. In the following, we propose to rely on a 'CCA-type' formulation in order to regularize the classical multimodal sparse regression problem (essentially incorporating both CCA and regression models within a unified formulation). The underlying motivation is to extract discriminative variables that are also co-expressed across modalities. We first show that the simplest formulation of such model can be expressed as a special case of collaborative learning methods. After discussing its limitation, we propose an extended, more flexible formulation, and introduce a simple and efficient alternating minimization algorithm to solve the associated optimization problem.We explore the parameter space and provide some guidelines regarding parameter selection. Both the original and extended versions are then compared on a simple toy dataset and a more advanced simulated imaging genomics dataset in order to illustrate the benefits of the latter. Finally, we validate the proposed formulation using single nucleotide polymorphisms (SNP) data and functional magnetic resonance imaging (fMRI) data from a population of adolescents (n = 362 subjects, age 16.9 ± 1.9 years from the Philadelphia Neurodevelopmental Cohort) for the study of learning ability. Furthermore, we carry out a significance

Group-Sequential Strategies in Clinical Trials with Multiple Co-Primary Outcomes

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Hamasaki, Toshimitsu; Asakura, Koko; Evans, Scott R; Sugimoto, Tomoyuki; Sozu, Takashi

2015-01-01

We discuss the decision-making frameworks for clinical trials with multiple co-primary endpoints in a group-sequential setting. The decision-making frameworks can account for flexibilities such as a varying number of analyses, equally or unequally spaced increments of information and fixed or adaptive Type I error allocation among endpoints. The frameworks can provide efficiency, i.e., potentially fewer trial participants, than the fixed sample size designs. We investigate the operating characteristics of the decision-making frameworks and provide guidance on constructing efficient group-sequential strategies in clinical trials with multiple co-primary endpoints. PMID:25844122

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system.

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Vonk, Freek J; Casewell, Nicholas R; Henkel, Christiaan V; Heimberg, Alysha M; Jansen, Hans J; McCleary, Ryan J R; Kerkkamp, Harald M E; Vos, Rutger A; Guerreiro, Isabel; Calvete, Juan J; Wüster, Wolfgang; Woods, Anthony E; Logan, Jessica M; Harrison, Robert A; Castoe, Todd A; de Koning, A P Jason; Pollock, David D; Yandell, Mark; Calderon, Diego; Renjifo, Camila; Currier, Rachel B; Salgado, David; Pla, Davinia; Sanz, Libia; Hyder, Asad S; Ribeiro, José M C; Arntzen, Jan W; van den Thillart, Guido E E J M; Boetzer, Marten; Pirovano, Walter; Dirks, Ron P; Spaink, Herman P; Duboule, Denis; McGlinn, Edwina; Kini, R Manjunatha; Richardson, Michael K

2013-12-17

Snakes are limbless predators, and many species use venom to help overpower relatively large, agile prey. Snake venoms are complex protein mixtures encoded by several multilocus gene families that function synergistically to cause incapacitation. To examine venom evolution, we sequenced and interrogated the genome of a venomous snake, the king cobra (Ophiophagus hannah), and compared it, together with our unique transcriptome, microRNA, and proteome datasets from this species, with data from other vertebrates. In contrast to the platypus, the only other venomous vertebrate with a sequenced genome, we find that snake toxin genes evolve through several distinct co-option mechanisms and exhibit surprisingly variable levels of gene duplication and directional selection that correlate with their functional importance in prey capture. The enigmatic accessory venom gland shows a very different pattern of toxin gene expression from the main venom gland and seems to have recruited toxin-like lectin genes repeatedly for new nontoxic functions. In addition, tissue-specific microRNA analyses suggested the co-option of core genetic regulatory components of the venom secretory system from a pancreatic origin. Although the king cobra is limbless, we recovered coding sequences for all Hox genes involved in amniote limb development, with the exception of Hoxd12. Our results provide a unique view of the origin and evolution of snake venom and reveal multiple genome-level adaptive responses to natural selection in this complex biological weapon system. More generally, they provide insight into mechanisms of protein evolution under strong selection.

Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci

DEFF Research Database (Denmark)

Rasmusen, L. H.; Dargis, R.; Iversen, Katrine Højholt

2016-01-01

observed in single gene analyses. Species identification based on single gene analysis showed their limitations when more strains were included. In contrast, analyses incorporating more sequence data, like MLSA, SNPs and core-genome analyses, provided more distinct clustering. The core-genome tree showed......Identification of Mitis group streptococci (MGS) to the species level is challenging for routine microbiology laboratories. Correct identification is crucial for the diagnosis of infective endocarditis, identification of treatment failure, and/or infection relapse. Eighty MGS from Danish patients...

Microeconomic principles explain an optimal genome size in bacteria.

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Ranea, Juan A G; Grant, Alastair; Thornton, Janet M; Orengo, Christine A

2005-01-01

Bacteria can clearly enhance their survival by expanding their genetic repertoire. However, the tight packing of the bacterial genome and the fact that the most evolved species do not necessarily have the biggest genomes suggest there are other evolutionary factors limiting their genome expansion. To clarify these restrictions on size, we studied those protein families contributing most significantly to bacterial-genome complexity. We found that all bacteria apply the same basic and ancestral 'molecular technology' to optimize their reproductive efficiency. The same microeconomics principles that define the optimum size in a factory can also explain the existence of a statistical optimum in bacterial genome size. This optimum is reached when the bacterial genome obtains the maximum metabolic complexity (revenue) for minimal regulatory genes (logistic cost).

Origin and Possible Genetic Recombination of the Middle East Respiratory Syndrome Coronavirus from the First Imported Case in China: Phylogenetics and Coalescence Analysis.

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Wang, Yanqun; Liu, Di; Shi, Weifeng; Lu, Roujian; Wang, Wenling; Zhao, Yanjie; Deng, Yao; Zhou, Weimin; Ren, Hongguang; Wu, Jun; Wang, Yu; Wu, Guizhen; Gao, George F; Tan, Wenjie

2015-09-08

The Middle East respiratory syndrome coronavirus (MERS-CoV) causes a severe acute respiratory tract infection with a high fatality rate in humans. Coronaviruses are capable of infecting multiple species and can evolve rapidly through recombination events. Here, we report the complete genomic sequence analysis of a MERS-CoV strain imported to China from South Korea. The imported virus, provisionally named ChinaGD01, belongs to group 3 in clade B in the whole-genome phylogenetic tree and also has a similar tree topology structure in the open reading frame 1a and -b (ORF1ab) gene segment but clusters with group 5 of clade B in the tree constructed using the S gene. Genetic recombination analysis and lineage-specific single-nucleotide polymorphism (SNP) comparison suggest that the imported virus is a recombinant comprising group 3 and group 5 elements. The time-resolved phylogenetic estimation indicates that the recombination event likely occurred in the second half of 2014. Genetic recombination events between group 3 and group 5 of clade B may have implications for the transmissibility of the virus. The recent outbreak of MERS-CoV in South Korea has attracted global media attention due to the speed of spread and onward transmission. Here, we present the complete genome of the first imported MERS-CoV case in China and demonstrate genetic recombination events between group 3 and group 5 of clade B that may have implications for the transmissibility of MERS-CoV. Copyright © 2015 Wang et al.

Yeast Sub1 and human PC4 are G-quadruplex binding proteins that suppress genome instability at co-transcriptionally formed G4 DNA.

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Lopez, Christopher R; Singh, Shivani; Hambarde, Shashank; Griffin, Wezley C; Gao, Jun; Chib, Shubeena; Yu, Yang; Ira, Grzegorz; Raney, Kevin D; Kim, Nayun

2017-06-02

G-quadruplex or G4 DNA is a non-B secondary DNA structure consisting of a stacked array of guanine-quartets that can disrupt critical cellular functions such as replication and transcription. When sequences that can adopt Non-B structures including G4 DNA are located within actively transcribed genes, the reshaping of DNA topology necessary for transcription process stimulates secondary structure-formation thereby amplifying the potential for genome instability. Using a reporter assay designed to study G4-induced recombination in the context of an actively transcribed locus in Saccharomyces cerevisiae, we tested whether co-transcriptional activator Sub1, recently identified as a G4-binding factor, contributes to genome maintenance at G4-forming sequences. Our data indicate that, upon Sub1-disruption, genome instability linked to co-transcriptionally formed G4 DNA in Top1-deficient cells is significantly augmented and that its highly conserved DNA binding domain or the human homolog PC4 is sufficient to suppress G4-associated genome instability. We also show that Sub1 interacts specifically with co-transcriptionally formed G4 DNA in vivo and that yeast cells become highly sensitivity to G4-stabilizing chemical ligands by the loss of Sub1. Finally, we demonstrate the physical and genetic interaction of Sub1 with the G4-resolving helicase Pif1, suggesting a possible mechanism by which Sub1 suppresses instability at G4 DNA. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genome Content and Phylogenomics Reveal both Ancestral and Lateral Evolutionary Pathways in Plant-Pathogenic Streptomyces Species

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Huguet-Tapia, Jose C.; Lefebure, Tristan; Badger, Jonathan H.; Guan, Dongli; Stanhope, Michael J.

2016-01-01

Streptomyces spp. are highly differentiated actinomycetes with large, linear chromosomes that encode an arsenal of biologically active molecules and catabolic enzymes. Members of this genus are well equipped for life in nutrient-limited environments and are common soil saprophytes. Out of the hundreds of species in the genus Streptomyces, a small group has evolved the ability to infect plants. The recent availability of Streptomyces genome sequences, including four genomes of pathogenic species, provided an opportunity to characterize the gene content specific to these pathogens and to study phylogenetic relationships among them. Genome sequencing, comparative genomics, and phylogenetic analysis enabled us to discriminate pathogenic from saprophytic Streptomyces strains; moreover, we calculated that the pathogen-specific genome contains 4,662 orthologs. Phylogenetic reconstruction suggested that Streptomyces scabies and S. ipomoeae share an ancestor but that their biosynthetic clusters encoding the required virulence factor thaxtomin have diverged. In contrast, S. turgidiscabies and S. acidiscabies, two relatively unrelated pathogens, possess highly similar thaxtomin biosynthesis clusters, which suggests that the acquisition of these genes was through lateral gene transfer. PMID:26826232

Mammalian-specific genomic functions: Newly acquired traits generated by genomic imprinting and LTR retrotransposon-derived genes in mammals.

Science.gov (United States)

Kaneko-Ishino, Tomoko; Ishino, Fumitoshi

2015-01-01

Mammals, including human beings, have evolved a unique viviparous reproductive system and a highly developed central nervous system. How did these unique characteristics emerge in mammalian evolution, and what kinds of changes did occur in the mammalian genomes as evolution proceeded? A key conceptual term in approaching these issues is "mammalian-specific genomic functions", a concept covering both mammalian-specific epigenetics and genetics. Genomic imprinting and LTR retrotransposon-derived genes are reviewed as the representative, mammalian-specific genomic functions that are essential not only for the current mammalian developmental system, but also mammalian evolution itself. First, the essential roles of genomic imprinting in mammalian development, especially related to viviparous reproduction via placental function, as well as the emergence of genomic imprinting in mammalian evolution, are discussed. Second, we introduce the novel concept of "mammalian-specific traits generated by mammalian-specific genes from LTR retrotransposons", based on the finding that LTR retrotransposons served as a critical driving force in the mammalian evolution via generating mammalian-specific genes.

Evolved stars in the Local Group galaxies - II. AGB, RSG stars and dust production in IC10

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Dell'Agli, F.; Di Criscienzo, M.; Ventura, P.; Limongi, M.; García-Hernández, D. A.; Marini, E.; Rossi, C.

2018-06-01

We study the evolved stellar population of the Local Group galaxy IC10, with the aim of characterizing the individual sources observed and to derive global information on the galaxy, primarily the star formation history and the dust production rate. To this aim, we use evolutionary sequences of low- and intermediate-mass (M account for 40% of the sources brighter than the tip of the red giant branch. Most of these stars descend from ˜1.1 - 1.3 M⊙ progenitors, formed during the major epoch of star formation, which occurred ˜2.5 Gyr ago. The presence of a significant number of bright stars indicates that IC10 has been site of significant star formation in recent epochs and currently hosts a group of massive stars in the core helium-burning phase. Dust production in this galaxy is largely dominated by carbon stars; the overall dust production rate estimated is 7 × 10-6 M⊙/yr.

A rapidly evolving secretome builds and patterns a sea shell

Directory of Open Access Journals (Sweden)

Green Kathryn

2006-11-01

Full Text Available Abstract Background Instructions to fabricate mineralized structures with distinct nanoscale architectures, such as seashells and coral and vertebrate skeletons, are encoded in the genomes of a wide variety of animals. In mollusks, the mantle is responsible for the extracellular production of the shell, directing the ordered biomineralization of CaCO3 and the deposition of architectural and color patterns. The evolutionary origins of the ability to synthesize calcified structures across various metazoan taxa remain obscure, with only a small number of protein families identified from molluskan shells. The recent sequencing of a wide range of metazoan genomes coupled with the analysis of gene expression in non-model animals has allowed us to investigate the evolution and process of biomineralization in gastropod mollusks. Results Here we show that over 25% of the genes expressed in the mantle of the vetigastropod Haliotis asinina encode secreted proteins, indicating that hundreds of proteins are likely to be contributing to shell fabrication and patterning. Almost 85% of the secretome encodes novel proteins; remarkably, only 19% of these have identifiable homologues in the full genome of the patellogastropod Lottia scutum. The spatial expression profiles of mantle genes that belong to the secretome is restricted to discrete mantle zones, with each zone responsible for the fabrication of one of the structural layers of the shell. Patterned expression of a subset of genes along the length of the mantle is indicative of roles in shell ornamentation. For example, Has-sometsuke maps precisely to pigmentation patterns in the shell, providing the first case of a gene product to be involved in molluskan shell pigmentation. We also describe the expression of two novel genes involved in nacre (mother of pearl deposition. Conclusion The unexpected complexity and evolvability of this secretome and the modular design of the molluskan mantle enables

The Small Nuclear Genomes of Selaginella Are Associated with a Low Rate of Genome Size Evolution.

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Baniaga, Anthony E; Arrigo, Nils; Barker, Michael S

2016-06-03

The haploid nuclear genome size (1C DNA) of vascular land plants varies over several orders of magnitude. Much of this observed diversity in genome size is due to the proliferation and deletion of transposable elements. To date, all vascular land plant lineages with extremely small nuclear genomes represent recently derived states, having ancestors with much larger genome sizes. The Selaginellaceae represent an ancient lineage with extremely small genomes. It is unclear how small nuclear genomes evolved in Selaginella We compared the rates of nuclear genome size evolution in Selaginella and major vascular plant clades in a comparative phylogenetic framework. For the analyses, we collected 29 new flow cytometry estimates of haploid genome size in Selaginella to augment publicly available data. Selaginella possess some of the smallest known haploid nuclear genome sizes, as well as the lowest rate of genome size evolution observed across all vascular land plants included in our analyses. Additionally, our analyses provide strong support for a history of haploid nuclear genome size stasis in Selaginella Our results indicate that Selaginella, similar to other early diverging lineages of vascular land plants, has relatively low rates of genome size evolution. Further, our analyses highlight that a rapid transition to a small genome size is only one route to an extremely small genome. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The Genome Biology of Effector Gene Evolution in Filamentous Plant Pathogens.

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Sánchez-Vallet, Andrea; Fouché, Simone; Fudal, Isabelle; Hartmann, Fanny E; Soyer, Jessica L; Tellier, Aurélien; Croll, Daniel

2018-05-16

Filamentous pathogens, including fungi and oomycetes, pose major threats to global food security. Crop pathogens cause damage by secreting effectors that manipulate the host to the pathogen's advantage. Genes encoding such effectors are among the most rapidly evolving genes in pathogen genomes. Here, we review how the major characteristics of the emergence, function, and regulation of effector genes are tightly linked to the genomic compartments where these genes are located in pathogen genomes. The presence of repetitive elements in these compartments is associated with elevated rates of point mutations and sequence rearrangements with a major impact on effector diversification. The expression of many effectors converges on an epigenetic control mediated by the presence of repetitive elements. Population genomics analyses showed that rapidly evolving pathogens show high rates of turnover at effector loci and display a mosaic in effector presence-absence polymorphism among strains. We conclude that effective pathogen containment strategies require a thorough understanding of the effector genome biology and the pathogen's potential for rapid adaptation. Expected final online publication date for the Annual Review of Phytopathology Volume 56 is August 25, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Evolved Gas Analyses of the Murray Formation in Gale Crater, Mars: Results of the Curiosity Rover's Sample Analysis at Mars (SAM) Instrument

Science.gov (United States)

Sutter, B.; McAdam, A. C.; Rampe, E. B.; Thompson, L. M.; Ming, D. W.; Mahaffy, P. R.; Navarro-Gonzalez, R.; Stern, J. C.; Eigenbrode, J. L.; Archer, P. D.

2017-01-01

The Sample Analysis at Mars (SAM) instrument aboard the Mars Science Laboratory rover has analyzed 13 samples from Gale Crater. All SAM-evolved gas analyses have yielded a multitude of volatiles (e.g., H2O, SO2, H2S, CO2, CO, NO, O2, HCl) [1- 6]. The objectives of this work are to 1) Characterize recent evolved SO2, CO2, O2, and NO gas traces of the Murray formation mudstone, 2) Constrain sediment mineralogy/composition based on SAM evolved gas analysis (SAM-EGA), and 3) Discuss the implications of these results relative to understanding the geological history of Gale Crater.

The evolving definition of systemic arterial hypertension.

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Ram, C Venkata S; Giles, Thomas D

2010-05-01

Systemic hypertension is an important risk factor for premature cardiovascular disease. Hypertension also contributes to excessive morbidity and mortality. Whereas excellent therapeutic options are available to treat hypertension, there is an unsettled issue about the very definition of hypertension. At what level of blood pressure should we treat hypertension? Does the definition of hypertension change in the presence of co-morbid conditions? This article covers in detail the evolving concepts in the diagnosis and management of hypertension.

Evolution and genome architecture in fungal plant pathogens.

Science.gov (United States)

Möller, Mareike; Stukenbrock, Eva H

2017-12-01

The fungal kingdom comprises some of the most devastating plant pathogens. Sequencing the genomes of fungal pathogens has shown a remarkable variability in genome size and architecture. Population genomic data enable us to understand the mechanisms and the history of changes in genome size and adaptive evolution in plant pathogens. Although transposable elements predominantly have negative effects on their host, fungal pathogens provide prominent examples of advantageous associations between rapidly evolving transposable elements and virulence genes that cause variation in virulence phenotypes. By providing homogeneous environments at large regional scales, managed ecosystems, such as modern agriculture, can be conducive for the rapid evolution and dispersal of pathogens. In this Review, we summarize key examples from fungal plant pathogen genomics and discuss evolutionary processes in pathogenic fungi in the context of molecular evolution, population genomics and agriculture.

Genomic analysis of expressed sequence tags in American black bear Ursus americanus

Science.gov (United States)

2010-01-01

Background Species of the bear family (Ursidae) are important organisms for research in molecular evolution, comparative physiology and conservation biology, but relatively little genetic sequence information is available for this group. Here we report the development and analyses of the first large scale Expressed Sequence Tag (EST) resource for the American black bear (Ursus americanus). Results Comprehensive analyses of molecular functions, alternative splicing, and tissue-specific expression of 38,757 black bear EST sequences were conducted using the dog genome as a reference. We identified 18 genes, involved in functions such as lipid catabolism, cell cycle, and vesicle-mediated transport, that are showing rapid evolution in the bear lineage Three genes, Phospholamban (PLN), cysteine glycine-rich protein 3 (CSRP3) and Troponin I type 3 (TNNI3), are related to heart contraction, and defects in these genes in humans lead to heart disease. Two genes, biphenyl hydrolase-like (BPHL) and CSRP3, contain positively selected sites in bear. Global analysis of evolution rates of hibernation-related genes in bear showed that they are largely conserved and slowly evolving genes, rather than novel and fast-evolving genes. Conclusion We provide a genomic resource for an important mammalian organism and our study sheds new light on the possible functions and evolution of bear genes. PMID:20338065

Genomic analysis of expressed sequence tags in American black bear Ursus americanus.

Science.gov (United States)

Zhao, Sen; Shao, Chunxuan; Goropashnaya, Anna V; Stewart, Nathan C; Xu, Yichi; Tøien, Øivind; Barnes, Brian M; Fedorov, Vadim B; Yan, Jun

2010-03-26

Species of the bear family (Ursidae) are important organisms for research in molecular evolution, comparative physiology and conservation biology, but relatively little genetic sequence information is available for this group. Here we report the development and analyses of the first large scale Expressed Sequence Tag (EST) resource for the American black bear (Ursus americanus). Comprehensive analyses of molecular functions, alternative splicing, and tissue-specific expression of 38,757 black bear EST sequences were conducted using the dog genome as a reference. We identified 18 genes, involved in functions such as lipid catabolism, cell cycle, and vesicle-mediated transport, that are showing rapid evolution in the bear lineage Three genes, Phospholamban (PLN), cysteine glycine-rich protein 3 (CSRP3) and Troponin I type 3 (TNNI3), are related to heart contraction, and defects in these genes in humans lead to heart disease. Two genes, biphenyl hydrolase-like (BPHL) and CSRP3, contain positively selected sites in bear. Global analysis of evolution rates of hibernation-related genes in bear showed that they are largely conserved and slowly evolving genes, rather than novel and fast-evolving genes. We provide a genomic resource for an important mammalian organism and our study sheds new light on the possible functions and evolution of bear genes.

Polyploidy: adaptation to the genomic environment.

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Hollister, Jesse D

2015-02-01

Genomic evidence of ancestral whole genome duplication (WGD) and polyploidy is widespread among eukaryotic species, and especially among plants. WGD is thought to provide the raw material for adaptation in the form of duplicated genes, and polyploids are thought to benefit from both physiological and genetic buffering. Comparatively little attention has focused on the genomic challenge of polyploidy, however, although much evidence exists that polyploidy severely perturbs important cellular functions. Here, I review recent progress in the study of the re-establishment of stable meiosis in recently evolved polyploids, focusing on four plant species. This work has yielded an insight into the mechanisms underlying stabilization of genome transmission in polyploids, and is revealing remarkable parallels among diverse taxa. Importantly, these studies also provide a road map for investigating how polyploids respond to the challenge of WGD.

Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling.

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Junha Shin

Full Text Available Phylogenetic profiling, a network inference method based on gene inheritance profiles, has been widely used to construct functional gene networks in microbes. However, its utility for network inference in higher eukaryotes has been limited. An improved algorithm with an in-depth understanding of pathway evolution may overcome this limitation. In this study, we investigated the effects of taxonomic structures on co-inheritance analysis using 2,144 reference species in four query species: Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens. We observed three clusters of reference species based on a principal component analysis of the phylogenetic profiles, which correspond to the three domains of life-Archaea, Bacteria, and Eukaryota-suggesting that pathways inherit primarily within specific domains or lower-ranked taxonomic groups during speciation. Hence, the co-inheritance pattern within a taxonomic group may be eroded by confounding inheritance patterns from irrelevant taxonomic groups. We demonstrated that co-inheritance analysis within domains substantially improved network inference not only in microbe species but also in the higher eukaryotes, including humans. Although we observed two sub-domain clusters of reference species within Eukaryota, co-inheritance analysis within these sub-domain taxonomic groups only marginally improved network inference. Therefore, we conclude that co-inheritance analysis within domains is the optimal approach to network inference with the given reference species. The construction of a series of human gene networks with increasing sample sizes of the reference species for each domain revealed that the size of the high-accuracy networks increased as additional reference species genomes were included, suggesting that within-domain co-inheritance analysis will continue to expand human gene networks as genomes of additional species are sequenced. Taken together, we propose that co

Complete genome sequence of the bioleaching bacterium Leptospirillum sp. group II strain CF-1.

Science.gov (United States)

Ferrer, Alonso; Bunk, Boyke; Spröer, Cathrin; Biedendieck, Rebekka; Valdés, Natalia; Jahn, Martina; Jahn, Dieter; Orellana, Omar; Levicán, Gloria

2016-03-20

We describe the complete genome sequence of Leptospirillum sp. group II strain CF-1, an acidophilic bioleaching bacterium isolated from an acid mine drainage (AMD). This work provides data to gain insights about adaptive response of Leptospirillum spp. to the extreme conditions of bioleaching environments. Copyright © 2016 Elsevier B.V. All rights reserved.

Distinguishing friends, foes, and freeloaders in giant genomes.

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Bennetzen, Jeffrey L; Park, Minkyu

2018-04-01

Most annotations of large eukaryotic genomes initially find transposable elements (TEs) and other repeats, then mask them so that subsequent efforts can be concentrated on the annotation and study of non-TE genes. However, TEs often contribute to host biology, and their community biologies are of intrinsic interest. This review discusses the challenges, rationale and technologies for comprehensive TE annotation in the commonly giant genomes of animals and plants. Complete discovery of the TEs in a fully sequenced genome is laborious, but feasible, with current strategies in the hands of a careful researcher. These deep TE studies have begun to provide important perspectives on how genomes evolve and the degree to which genome changes do and do not affect eukaryotic biology. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Evolvability Search: Directly Selecting for Evolvability in order to Study and Produce It

DEFF Research Database (Denmark)

Mengistu, Henok; Lehman, Joel Anthony; Clune, Jeff

2016-01-01

of evolvable digital phenotypes. Although some types of selection in evolutionary computation indirectly encourage evolvability, one unexplored possibility is to directly select for evolvability. To do so, we estimate an individual's future potential for diversity by calculating the behavioral diversity of its...... immediate offspring, and select organisms with increased offspring variation. While the technique is computationally expensive, we hypothesized that direct selection would better encourage evolvability than indirect methods. Experiments in two evolutionary robotics domains confirm this hypothesis: in both...... domains, such Evolvability Search produces solutions with higher evolvability than those produced with Novelty Search or traditional objective-based search algorithms. Further experiments demonstrate that the higher evolvability produced by Evolvability Search in a training environment also generalizes...

Triplet transitions of neutral CO in the spectra of comets and the abundance of CO2 or molecules containing the CO group in comets

International Nuclear Information System (INIS)

Biermann, L.

1976-03-01

The high-dispersion spectra of comet Mrkos (1957 V) taken at Mt. Palomar by J. L. Greenstein and remeasured by A. Woszczyk contain many unidentified weak lines. The possibility that some of these lines belong to transitions between triplet levels of neutral CO molecules is investigated. Their presence would suggest excitation related to the dissociative recombination of a parent containing the CO group, which is first ionized by solar uv. Of 31 CO lines (of the Asundi and Triplet systems), 14 are masked by known or by questionably identified lines as statistically expected. Of the remaining 17, 13 coincide within a few tenths of an Angstrom with an unidentified line and 4 do not. These results are contrary to statistical expectations. (Some members of the third positive system of CO, which might be present, have not been included in the figures.) Although these figures strongly favor the identification proposed, the numbers are not large enough to support entirely the argument of a small statistical probability (0.2 percent) of the observed state. Also, the rotational structure of the CO bands for the triplet systems needs further investigation. C. F. Lillie's observations of comet Bennett (1970 II) between 1200 and 1800 A, especially of the fourth positive system of CO, seem to favor a cometary atmosphere characterized by a large relative abundance of CO 2 and/or molecules containing the CO group. A model outlined for comet Bennett at 0.8 a.u. seems to be approximately consistent with observations. The chemical aspects, however, especially need further consideration. New observations, particularly of the Cameron bands of CO, are needed to settle the questions raised

Expansion of CORE-SINEs in the genome of the Tasmanian devil.

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Nilsson, Maria A; Janke, Axel; Murchison, Elizabeth P; Ning, Zemin; Hallström, Björn M

2012-05-06

The genome of the carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii, Order: Dasyuromorphia), was sequenced in the hopes of finding a cure for or gaining a better understanding of the contagious devil facial tumor disease that is threatening the species' survival. To better understand the Tasmanian devil genome, we screened it for transposable elements and investigated the dynamics of short interspersed element (SINE) retroposons. The temporal history of Tasmanian devil SINEs, elucidated using a transposition in transposition analysis, indicates that WSINE1, a CORE-SINE present in around 200,000 copies, is the most recently active element. Moreover, we discovered a new subtype of WSINE1 (WSINE1b) that comprises at least 90% of all Tasmanian devil WSINE1s. The frequencies of WSINE1 subtypes differ in the genomes of two of the other Australian marsupial orders. A co-segregation analysis indicated that at least 66 subfamilies of WSINE1 evolved during the evolution of Dasyuromorphia. Using a substitution rate derived from WSINE1 insertions, the ages of the subfamilies were estimated and correlated with a newly established phylogeny of Dasyuromorphia. Phylogenetic analyses and divergence time estimates of mitochondrial genome data indicate a rapid radiation of the Tasmanian devil and the closest relative the quolls (Dasyurus) around 14 million years ago. The radiation and abundance of CORE-SINEs in marsupial genomes indicates that they may be a major player in the evolution of marsupials. It is evident that the early phases of evolution of the carnivorous marsupial order Dasyuromorphia was characterized by a burst of SINE activity. A correlation between a speciation event and a major burst of retroposon activity is for the first time shown in a marsupial genome.

Expansion of CORE-SINEs in the genome of the Tasmanian devil

Directory of Open Access Journals (Sweden)

Nilsson Maria A

2012-05-01

Full Text Available Abstract Background The genome of the carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii, Order: Dasyuromorphia, was sequenced in the hopes of finding a cure for or gaining a better understanding of the contagious devil facial tumor disease that is threatening the species’ survival. To better understand the Tasmanian devil genome, we screened it for transposable elements and investigated the dynamics of short interspersed element (SINE retroposons. Results The temporal history of Tasmanian devil SINEs, elucidated using a transposition in transposition analysis, indicates that WSINE1, a CORE-SINE present in around 200,000 copies, is the most recently active element. Moreover, we discovered a new subtype of WSINE1 (WSINE1b that comprises at least 90% of all Tasmanian devil WSINE1s. The frequencies of WSINE1 subtypes differ in the genomes of two of the other Australian marsupial orders. A co-segregation analysis indicated that at least 66 subfamilies of WSINE1 evolved during the evolution of Dasyuromorphia. Using a substitution rate derived from WSINE1 insertions, the ages of the subfamilies were estimated and correlated with a newly established phylogeny of Dasyuromorphia. Phylogenetic analyses and divergence time estimates of mitochondrial genome data indicate a rapid radiation of the Tasmanian devil and the closest relative the quolls (Dasyurus around 14 million years ago. Conclusions The radiation and abundance of CORE-SINEs in marsupial genomes indicates that they may be a major player in the evolution of marsupials. It is evident that the early phases of evolution of the carnivorous marsupial order Dasyuromorphia was characterized by a burst of SINE activity. A correlation between a speciation event and a major burst of retroposon activity is for the first time shown in a marsupial genome.

Small groups and long memories promote cooperation.

Science.gov (United States)

Stewart, Alexander J; Plotkin, Joshua B

2016-06-01

Complex social behaviors lie at the heart of many of the challenges facing evolutionary biology, sociology, economics, and beyond. For evolutionary biologists the question is often how group behaviors such as collective action, or decision making that accounts for memories of past experience, can emerge and persist in an evolving system. Evolutionary game theory provides a framework for formalizing these questions and admitting them to rigorous study. Here we develop such a framework to study the evolution of sustained collective action in multi-player public-goods games, in which players have arbitrarily long memories of prior rounds of play and can react to their experience in an arbitrary way. We construct a coordinate system for memory-m strategies in iterated n-player games that permits us to characterize all cooperative strategies that resist invasion by any mutant strategy, and stabilize cooperative behavior. We show that, especially when groups are small, longer-memory strategies make cooperation easier to evolve, by increasing the number of ways to stabilize cooperation. We also explore the co-evolution of behavior and memory. We find that even when memory has a cost, longer-memory strategies often evolve, which in turn drives the evolution of cooperation, even when the benefits for cooperation are low.

UK Natural Analogue Co-Ordinating Group: first annual progress report

International Nuclear Information System (INIS)

Hooker, P.J.; Chapman, N.A.

1987-11-01

The British Geological Survey is reponsible for co-ordinating the Department of the Environment's programme of natural analogue studies of radionuclide migration, a research programme that involved both UK and overseas sites. Co-ordination is achieved through the UK Natural Analogue Co-ordinating Group (NACG) which was established in October 1986. It has met three times to date and its function is to ensure that the different research projects have an integrated purpose aimed at improving and applying our understanding of natural geochemical processes in a way that will increase our confidence in long-term modelling predictions. Improved modelling prediction of radionuclide transport in the geosphere will directly benefit the performance and safety assessments of proposed radioactive waste repositories. (author)

Characterization of CoPK02, a Ca2+/calmodulin-dependent protein kinase in mushroom Coprinopsis cinerea.

Science.gov (United States)

Yamashita, Masashi; Sueyoshi, Noriyuki; Yamada, Hiroki; Katayama, Syouichi; Senga, Yukako; Takenaka, Yasuhiro; Ishida, Atsuhiko; Kameshita, Isamu; Shigeri, Yasushi

2018-04-20

We surveyed genome sequences from the basidiomycetous mushroom Coprinopsis cinerea and isolated a cDNA homologous to CMKA, a calmodulin-dependent protein kinase (CaMK) in Aspergillus nidulans. We designated this sequence, encoding 580 amino acids with a molecular weight of 63,987, as CoPK02. CoPK02 possessed twelve subdomains specific to protein kinases and exhibited 43, 35, 40% identity with rat CaMKI, CaMKII, CaMKIV, respectively, and 40% identity with CoPK12, one of the CaMK orthologs in C. cinerea. CoPK02 showed significant autophosphorylation activity and phosphorylated exogenous proteins in the presence of Ca 2+ /CaM. By the CaM-overlay assay we confirmed that the C-terminal sequence (Trp346-Arg358) was the calmodulin-binding site, and that the binding of Ca 2+ /CaM to CoPK02 was reduced by the autophosphorylation of CoPK02. Since CoPK02 evolved in a different clade from CoPK12, and showed different gene expression compared to that of CoPK32, which is homologous to mitogen-activated protein kinase-activated protein kinase, CoPK02 and CoPK12 might cooperatively regulate Ca 2+ -signaling in C. cinerea.

The chromosomal distributions of Ty1-copia group retrotransposable elements in higher plants and their implications for genome evolution

Science.gov (United States)

J.S. (Pat) Heslop-Harrison; Andrea Brandes; Shin Taketa; Thomas Schmidt; Alexander V. Vershinin; Elena G. Alkhimova; Anette Kamm; Robert L. Doudrick; . [and others

1997-01-01

Retrotransposons make up a major fraction - sometimes more than 40% - of all plant genomes investigated so far. We have isolated the reverse transcriptase domains of theTyl-copia group elements from several species, ranging in genome size from some 100 Mbp to 23,000 Mbp, and determined the distribution patterns of these retrotransposons on metaphase chromosomes and...

Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs

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David Juan

2016-02-01

Full Text Available Summary: Epigenetic communication through histone and cytosine modifications is essential for gene regulation and cell identity. Here, we propose a framework that is based on a chromatin communication model to get insight on the function of epigenetic modifications in ESCs. The epigenetic communication network was inferred from genome-wide location data plus extensive manual annotation. Notably, we found that 5-hydroxymethylcytosine (5hmC is the most-influential hub of this network, connecting DNA demethylation to nucleosome remodeling complexes and to key transcription factors of pluripotency. Moreover, an evolutionary analysis revealed a central role of 5hmC in the co-evolution of chromatin-related proteins. Further analysis of regions where 5hmC co-localizes with specific interactors shows that each interaction points to chromatin remodeling, stemness, differentiation, or metabolism. Our results highlight the importance of cytosine modifications in the epigenetic communication of ESCs. : 5-hydroxymethylcytosine (5hmC plays a key role in the epigenomic communication network of embryonic stem cells. Juan et al. build a communication network based in co-localization of epigenomic data and literature. The analysis of the network and its components reveals that proteins reading and editing 5hmC co-evolve and serve as links between diverse molecular processes.

Natural co-infection of Solanum tuberosum crops by the Potato yellow vein virus and potyvirus in Colombia

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Angela Villamil-Garzón

2014-08-01

Full Text Available The Potato yellow vein virus (PYVV, a Crinivirus with an RNA tripartite genome, is the causal agent of the potato yellow vein disease, reported in Colombian since 1950, with yield reductions of up to 50%. Co-infection of two or more viruses is common in nature and can be associated with differences in virus accumulation and symptom expression. No evidence of mixed infection between PYVV and other viruses has been reported. In this study, eight plants showing yellowing PYVV symptoms: four Solanum tuberosum Group Phureja (P and four Group Andigena (A, were collected in Cundinamarca, Colombia to detect mixed infection in the isolates using next generation sequencing (NGS. The Potato virus Y (PVY complete genome (similar to N strain and the Potato virus V (PVV partial genomes were detected using NGS and re-confirmed by RT-PCR. Preliminary field screening in a large sample showed that PYVV and PVY co-infect potato plants with a prevalence of 21% within the P group and 23% within the A group. This is the first report of co-infection of PYVV and potyvirus in Colombia and with the use of NGS. Considering that potyviruses enhance symptom severity and/or yield reductions in mixed infections, our results may be relevant for disease diagnosis, breeding programs and tuber certification.

Unleashing the genome of Brassica rapa

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Haibao eTang

2012-07-01

Full Text Available The completion and release of the Brassica rapa genome is of great benefit to researchers of the Brassicas, Arabidopsis, and genome evolution. While its lineage is closely related to the model organism Arabidopsis thaliana, the Brassicas experienced a whole genome triplication subsequent to their divergence. This event contemporaneously created three copies of its ancestral genome, which had diploidized through the process of homeologous gene loss known as fractionation. By the fractionation of homeologous gene content and genetic regulatory binding sites, Brassica’s genome is well placed to use comparative genomic techniques to identify syntenic regions, homeologous gene duplications, and putative regulatory sequences. Here, we use the comparative genomics platform CoGe to perform several different genomic analyses with which to study structural changes of its genome and dynamics of various genetic elements. Starting with whole genome comparisons, the Brassica paleohexaploidy is characterized, syntenic regions with Arabidopsis thaliana are identified, and the TOC1 gene in the circadian rhythm pathway from Arabidopsis thaliana is used to find duplicated orthologs in Brassica rapa. These TOC1 genes are further analyzed to identify conserved noncoding sequences that contain cis-acting regulatory elements and promoter sequences previously implicated in circadian rhythmicity. Each 'cookbook style' analysis includes a step-by-step walkthrough with links to CoGe to quickly reproduce each step of the analytical process.

Managing the genomic revolution in cancer diagnostics.

Science.gov (United States)

Nguyen, Doreen; Gocke, Christopher D

2017-08-01

Molecular tumor profiling is now a routine part of patient care, revealing targetable genomic alterations and molecularly distinct tumor subtypes with therapeutic and prognostic implications. The widespread adoption of next-generation sequencing technologies has greatly facilitated clinical implementation of genomic data and opened the door for high-throughput multigene-targeted sequencing. Herein, we discuss the variability of cancer genetic profiling currently offered by clinical laboratories, the challenges of applying rapidly evolving medical knowledge to individual patients, and the need for more standardized population-based molecular profiling.

Differential expression of genome in the progeny doubling 40 generations of normal human liver cells irradiated by 60Co γ rays

International Nuclear Information System (INIS)

Zuo Yahui; Wang Fang; Geng Xiaohua; Wang Xiaoli; Li Jianguo; Wang Zhongwen; Tong Jian

2008-01-01

In order to investigate the differential expression of genome in nomal human liver cell irradiated by 60 Co γ rays, cDNA chip was applied to assay the alterations of transcriptional profile of nomal human liver cell'rogeny exposed to 4 Gy and 8 Gy of γ ray from 60 Co. Then Quantitative real-time PCR was used to confirm the commonly changed genes including VTN and INSIG1. The results demonstrated that the transcription level of 58 genes changed in the progeny of survival cells irradiated by 4 Gy γ rays, while 882 genes changed in the progeny of survival cells irradiated by 8 Gy γ rays. 16 genes changed in these cells irradiated by both 4 and 8 Gy γ rays. The transcription level was correlated to the original irradiation dose. Most of the genes were associated with transduction, cell cycle regulation, cellular immunity, cytoskeleton and movement, cell replication and repair mechanism, etc. The changed transcriptional level was further confirmed by RT-PCR assay for some of these genes. The results showed that differential expression of genome irradiated by different doses of γ rays. These results offer the fundamental materials for the research of genomic instability induced by radiation on the molecular level. (authors)

Facilitating value co-creation in networks

DEFF Research Database (Denmark)

Rasmussen, Mette Apollo

participants in varied ways come to grasp the meaning of networking. The dissertation draws on insights from the Service-Dominant (S-D) Logic to explain how networks can be seen as spheres for value co-creation. Co-creation as a theoretical construct has evolved from varied streams of service marketing...... of networking. The concept of “imaginative value” (Beckert, 2011) is used to explain the oscillating behaviors observed in the two networks. Imaginative value can be defined as symbolic value that actors ascribe to an object, in this case the network. I argue that the group practices in the networks led......The dissertation investigates through two ethnographic case studies how value co-creation takes place in inter-organizational networks that have been facilitated by a municipality. The contribution of the study to business network research is the emphasis on development phases of networks...

The founding charter of the Genomic Observatories Network.

Science.gov (United States)

Davies, Neil; Field, Dawn; Amaral-Zettler, Linda; Clark, Melody S; Deck, John; Drummond, Alexei; Faith, Daniel P; Geller, Jonathan; Gilbert, Jack; Glöckner, Frank Oliver; Hirsch, Penny R; Leong, Jo-Ann; Meyer, Chris; Obst, Matthias; Planes, Serge; Scholin, Chris; Vogler, Alfried P; Gates, Ruth D; Toonen, Rob; Berteaux-Lecellier, Véronique; Barbier, Michèle; Barker, Katherine; Bertilsson, Stefan; Bicak, Mesude; Bietz, Matthew J; Bobe, Jason; Bodrossy, Levente; Borja, Angel; Coddington, Jonathan; Fuhrman, Jed; Gerdts, Gunnar; Gillespie, Rosemary; Goodwin, Kelly; Hanson, Paul C; Hero, Jean-Marc; Hoekman, David; Jansson, Janet; Jeanthon, Christian; Kao, Rebecca; Klindworth, Anna; Knight, Rob; Kottmann, Renzo; Koo, Michelle S; Kotoulas, Georgios; Lowe, Andrew J; Marteinsson, Viggó Thór; Meyer, Folker; Morrison, Norman; Myrold, David D; Pafilis, Evangelos; Parker, Stephanie; Parnell, John Jacob; Polymenakou, Paraskevi N; Ratnasingham, Sujeevan; Roderick, George K; Rodriguez-Ezpeleta, Naiara; Schonrogge, Karsten; Simon, Nathalie; Valette-Silver, Nathalie J; Springer, Yuri P; Stone, Graham N; Stones-Havas, Steve; Sansone, Susanna-Assunta; Thibault, Kate M; Wecker, Patricia; Wichels, Antje; Wooley, John C; Yahara, Tetsukazu; Zingone, Adriana

2014-03-07

The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington (DC, USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expressed here are ours alone as individual scientists, and do not necessarily represent those of the institutions with which we are affiliated.

Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome.

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Jian Li

Full Text Available The hotspots of structural polymorphisms and structural mutability in the human genome remain to be explained mechanistically. We examine associations of structural mutability with germline DNA methylation and with non-allelic homologous recombination (NAHR mediated by low-copy repeats (LCRs. Combined evidence from four human sperm methylome maps, human genome evolution, structural polymorphisms in the human population, and previous genomic and disease studies consistently points to a strong association of germline hypomethylation and genomic instability. Specifically, methylation deserts, the ~1% fraction of the human genome with the lowest methylation in the germline, show a tenfold enrichment for structural rearrangements that occurred in the human genome since the branching of chimpanzee and are highly enriched for fast-evolving loci that regulate tissue-specific gene expression. Analysis of copy number variants (CNVs from 400 human samples identified using a custom-designed array comparative genomic hybridization (aCGH chip, combined with publicly available structural variation data, indicates that association of structural mutability with germline hypomethylation is comparable in magnitude to the association of structural mutability with LCR-mediated NAHR. Moreover, rare CNVs occurring in the genomes of individuals diagnosed with schizophrenia, bipolar disorder, and developmental delay and de novo CNVs occurring in those diagnosed with autism are significantly more concentrated within hypomethylated regions. These findings suggest a new connection between the epigenome, selective mutability, evolution, and human disease.

Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium

DEFF Research Database (Denmark)

Freschi, Luca; Jeukens, Julie; Kukavica-Ibrulj, Irena

2015-01-01

The International Pseudomonas aeruginosa Consortium is sequencing over 1000 genomes and building an analysis pipeline for the study of Pseudomonas genome evolution, antibiotic resistance and virulence genes. Metadata, including genomic and phenotypic data for each isolate of the collection, are a...... implicated in human and animal infections, understand how patients become infected and how the infection evolves over time as well as identify prognostic markers for better evidence-based decisions on patient care....

Multiple groups of endogenous epsilon-like retroviruses conserved across primates.

Science.gov (United States)

Brown, Katherine; Emes, Richard D; Tarlinton, Rachael E

2014-11-01

Several types of cancer in fish are caused by retroviruses, including those responsible for major outbreaks of disease, such as walleye dermal sarcoma virus and salmon swim bladder sarcoma virus. These viruses form a phylogenetic group often described as the epsilonretrovirus genus. Epsilon-like retroviruses have become endogenous retroviruses (ERVs) on several occasions, integrating into germ line cells to become part of the host genome, and sections of fish and amphibian genomes are derived from epsilon-like retroviruses. However, epsilon-like ERVs have been identified in very few mammals. We have developed a pipeline to screen full genomes for ERVs, and using this pipeline, we have located over 800 endogenous epsilon-like ERV fragments in primate genomes. Genomes from 32 species of mammals and birds were screened, and epsilon-like ERV fragments were found in all primate and tree shrew genomes but no others. These viruses appear to have entered the genome of a common ancestor of Old and New World monkeys between 42 million and 65 million years ago. Based on these results, there is an ancient evolutionary relationship between epsilon-like retroviruses and primates. Clearly, these viruses had the potential to infect the ancestors of primates and were at some point a common pathogen in these hosts. Therefore, this result raises questions about the potential of epsilonretroviruses to infect humans and other primates and about the evolutionary history of these retroviruses. Epsilonretroviruses are a group of retroviruses that cause several important diseases in fish. Retroviruses have the ability to become a permanent part of the DNA of their host by entering the germ line as endogenous retroviruses (ERVs), where they lose their infectivity over time but can be recognized as retroviruses for millions of years. Very few mammals are known to have epsilon-like ERVs; however, we have identified over 800 fragments of endogenous epsilon-like ERVs in the genomes of all major

Culture independent genomic comparisons reveal environmental adaptations for Altiarchaeales

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Jordan T Bird

2016-08-01

Full Text Available The recently proposed candidatus order Altiarchaeales remains an uncultured archaeal lineage composed of genetically diverse, globally widespread organisms frequently observed in anoxic subsurface environments. In spite of 15 years of studies on the psychrophilic biofilm-producing Candidatus (Ca. Altiarchaeum hamiconexum and its close relatives, very little is known about the phylogenetic and functional diversity of the widespread free-living marine members of this taxon. From methanogenic sediments in the White Oak River Estuary, NC, we sequenced a single cell amplified genome (SAG, WOR_SCG_SM1, and used it to identify and refine two high-quality genomes from metagenomes, WOR_79 and WOR_86-2, from the same site in a different year. These three genomic reconstructions form a monophyletic group which also includes three previously published genomes from metagenomes from terrestrial springs and a SAG from Sakinaw Lake in a group previously designated as pMC2A384. A synapomorphic mutation in the Altiarchaeales tRNA synthetase β subunit, pheT, causes the protein to be encoded as two subunits at distant loci. Consistent with the terrestrial spring clades, our estuarine genomes contain a near-complete autotrophic metabolism, H2 or CO as potential electron donors, a reductive acetyl-CoA pathway for carbon fixation, and methylotroph-like NADP(H-dependent dehydrogenase. Phylogenies based on 16S rRNA genes and concatenated conserved proteins identify two distinct sub-clades of Altiarchaeales, Alti-1 populated by organisms from actively flowing springs, and Alti-2 which is more widespread, diverse, and not associated with visible mats. The core Alti-1 genome supports Alti-1 as adapted for the stream environment, with lipopolysaccharide production capacity, extracellular hami structures. The core Alti-2 genome members of this clade are free-living, with distinct mechanisms for energy maintenance, motility, osmoregulation, and sulfur redox reactions. These

A synergism between adaptive effects and evolvability drives whole genome duplication to fixation

NARCIS (Netherlands)

Cuypers, Thomas D; Hogeweg, Paulien; Hogeweg, P.

Whole genome duplication has shaped eukaryotic evolutionary history and has been associated with drastic environmental change and species radiation. While the most common fate of WGD duplicates is a return to single copy, retained duplicates have been found enriched for highly interacting genes.

Avian papillomaviruses: the parrot Psittacus erithacus papillomavirus (PePV genome has a unique organization of the early protein region and is phylogenetically related to the chaffinch papillomavirus

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Jenson A Bennett

2002-07-01

Full Text Available Abstract Background An avian papillomavirus genome has been cloned from a cutaneous exophytic papilloma from an African grey parrot (Psittacus erithacus. The nucleotide sequence, genome organization, and phylogenetic position of the Psittacus erithacus papillomavirus (PePV were determined. This PePV sequence represents the first complete avian papillomavirus genome defined. Results The PePV genome (7304 basepairs differs from other papillomaviruses, in that it has a unique organization of the early protein region lacking classical E6 and E7 open reading frames. Phylogenetic comparison of the PePV sequence with partial E1 and L1 sequences of the chaffinch (Fringilla coelebs papillomavirus (FPV reveals that these two avian papillomaviruses form a monophyletic cluster with a common branch that originates near the unresolved center of the papillomavirus evolutionary tree. Conclusions The PePV genome has a unique layout of the early protein region which represents a novel prototypic genomic organization for avian papillomaviruses. The close relationship between PePV and FPV, and between their Psittaciformes and Passeriformes hosts, supports the hypothesis that papillomaviruses have co-evolved and speciated together with their host species throughout evolution.

Proliferation of group II introns in the chloroplast genome of the green alga Oedocladium carolinianum (Chlorophyceae

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Jean-Simon Brouard

2016-10-01

Full Text Available Background The chloroplast genome sustained extensive changes in architecture during the evolution of the Chlorophyceae, a morphologically and ecologically diverse class of green algae belonging to the Chlorophyta; however, the forces driving these changes are poorly understood. The five orders recognized in the Chlorophyceae form two major clades: the CS clade consisting of the Chlamydomonadales and Sphaeropleales, and the OCC clade consisting of the Oedogoniales, Chaetophorales, and Chaetopeltidales. In the OCC clade, considerable variations in chloroplast DNA (cpDNA structure, size, gene order, and intron content have been observed. The large inverted repeat (IR, an ancestral feature characteristic of most green plants, is present in Oedogonium cardiacum (Oedogoniales but is lacking in the examined members of the Chaetophorales and Chaetopeltidales. Remarkably, the Oedogonium 35.5-kb IR houses genes that were putatively acquired through horizontal DNA transfer. To better understand the dynamics of chloroplast genome evolution in the Oedogoniales, we analyzed the cpDNA of a second representative of this order, Oedocladium carolinianum. Methods The Oedocladium cpDNA was sequenced and annotated. The evolutionary distances separating Oedocladium and Oedogonium cpDNAs and two other pairs of chlorophycean cpDNAs were estimated using a 61-gene data set. Phylogenetic analysis of an alignment of group IIA introns from members of the OCC clade was performed. Secondary structures and insertion sites of oedogonialean group IIA introns were analyzed. Results The 204,438-bp Oedocladium genome is 7.9 kb larger than the Oedogonium genome, but its repertoire of conserved genes is remarkably similar and gene order differs by only one reversal. Although the 23.7-kb IR is missing the putative foreign genes found in Oedogonium, it contains sequences coding for a putative phage or bacterial DNA primase and a hypothetical protein. Intergenic sequences are 1.5-fold

Evolvable synthetic neural system

Science.gov (United States)

Curtis, Steven A. (Inventor)

2009-01-01

An evolvable synthetic neural system includes an evolvable neural interface operably coupled to at least one neural basis function. Each neural basis function includes an evolvable neural interface operably coupled to a heuristic neural system to perform high-level functions and an autonomic neural system to perform low-level functions. In some embodiments, the evolvable synthetic neural system is operably coupled to one or more evolvable synthetic neural systems in a hierarchy.

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system

Science.gov (United States)

Vonk, Freek J.; Casewell, Nicholas R.; Henkel, Christiaan V.; Heimberg, Alysha M.; Jansen, Hans J.; McCleary, Ryan J. R.; Kerkkamp, Harald M. E.; Vos, Rutger A.; Guerreiro, Isabel; Calvete, Juan J.; Wüster, Wolfgang; Woods, Anthony E.; Logan, Jessica M.; Harrison, Robert A.; Castoe, Todd A.; de Koning, A. P. Jason; Pollock, David D.; Yandell, Mark; Calderon, Diego; Renjifo, Camila; Currier, Rachel B.; Salgado, David; Pla, Davinia; Sanz, Libia; Hyder, Asad S.; Ribeiro, José M. C.; Arntzen, Jan W.; van den Thillart, Guido E. E. J. M.; Boetzer, Marten; Pirovano, Walter; Dirks, Ron P.; Spaink, Herman P.; Duboule, Denis; McGlinn, Edwina; Kini, R. Manjunatha; Richardson, Michael K.

2013-01-01

Snakes are limbless predators, and many species use venom to help overpower relatively large, agile prey. Snake venoms are complex protein mixtures encoded by several multilocus gene families that function synergistically to cause incapacitation. To examine venom evolution, we sequenced and interrogated the genome of a venomous snake, the king cobra (Ophiophagus hannah), and compared it, together with our unique transcriptome, microRNA, and proteome datasets from this species, with data from other vertebrates. In contrast to the platypus, the only other venomous vertebrate with a sequenced genome, we find that snake toxin genes evolve through several distinct co-option mechanisms and exhibit surprisingly variable levels of gene duplication and directional selection that correlate with their functional importance in prey capture. The enigmatic accessory venom gland shows a very different pattern of toxin gene expression from the main venom gland and seems to have recruited toxin-like lectin genes repeatedly for new nontoxic functions. In addition, tissue-specific microRNA analyses suggested the co-option of core genetic regulatory components of the venom secretory system from a pancreatic origin. Although the king cobra is limbless, we recovered coding sequences for all Hox genes involved in amniote limb development, with the exception of Hoxd12. Our results provide a unique view of the origin and evolution of snake venom and reveal multiple genome-level adaptive responses to natural selection in this complex biological weapon system. More generally, they provide insight into mechanisms of protein evolution under strong selection. PMID:24297900

SUBJECTIVE DISTRESS CAUSED BY CO-SPEAKERS’ REACTIONS – REDUCTION DURING STATIONARY GROUP TREATMENT

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Jelena TADIKJ

2010-04-01

Full Text Available Stuttering is a disorder that represents multifunctional problem. It probably exists since the beginning of mankind. Its’ frequency and severity are influenced by different factors. Among the most significant ones are the complexity of statement, speaking speed, and speakers’ emotional reaction to the whole speech situation and other co-speakers. Goal: To present the results of two-weeks intensive group stationary treatment of adults who stutter, especially stuttering severity and level of subjective distress caused by co-speakers’ reactions in the beginning and at the end of the treatment. Subjects: A group of 25 adults who stutter. Methodology: At the beginning and at the end of the group stationary treatment speech status was taken, consisting of counting, enumerating, repeating the sentences, reading a 100-word tale, retelling the read text, and conversation on a free subject. In the same time, subjective distress caused by 13 different co-speakers reactions was estimated. Results show that very positive results are achieved in the reduction of speech disfluences, as well as moderate reduction of subjective distress caused by co-speakers’ reactions. In the paper the results are shown in more details, and, subsequently, implications for further research and treatment.

Mitochondrial genome sequences reveal deep divergences among Anopheles punctulatus sibling species in Papua New Guinea

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Logue Kyle

2013-02-01

Full Text Available Abstract Background Members of the Anopheles punctulatus group (AP group are the primary vectors of human malaria in Papua New Guinea. The AP group includes 13 sibling species, most of them morphologically indistinguishable. Understanding why only certain species are able to transmit malaria requires a better comprehension of their evolutionary history. In particular, understanding relationships and divergence times among Anopheles species may enable assessing how malaria-related traits (e.g. blood feeding behaviours, vector competence have evolved. Methods DNA sequences of 14 mitochondrial (mt genomes from five AP sibling species and two species of the Anopheles dirus complex of Southeast Asia were sequenced. DNA sequences from all concatenated protein coding genes (10,770 bp were then analysed using a Bayesian approach to reconstruct phylogenetic relationships and date the divergence of the AP sibling species. Results Phylogenetic reconstruction using the concatenated DNA sequence of all mitochondrial protein coding genes indicates that the ancestors of the AP group arrived in Papua New Guinea 25 to 54 million years ago and rapidly diverged to form the current sibling species. Conclusion Through evaluation of newly described mt genome sequences, this study has revealed a divergence among members of the AP group in Papua New Guinea that would significantly predate the arrival of humans in this region, 50 thousand years ago. The divergence observed among the mtDNA sequences studied here may have resulted from reproductive isolation during historical changes in sea-level through glacial minima and maxima. This leads to a hypothesis that the AP sibling species have evolved independently for potentially thousands of generations. This suggests that the evolution of many phenotypes, such as insecticide resistance will arise independently in each of the AP sibling species studied here.

Influencing governance of a public-private partnership in plant genomics: The societal interface group as a new instrument for public involvement

NARCIS (Netherlands)

Hanssen, L.; Gremmen, B.

2013-01-01

The Centre for BioSystems Genomics (CBSG) is a Dutch public-private partnership in plant genomics active in potato and tomato research and exploitation. Its Societal Interface Group (SIG) has been developed to inform its communication strategy and governance practice. This new instrument identifies

Improvement of Xylose Fermentation Ability under Heat and Acid Co-Stress in Saccharomyces cerevisiae Using Genome Shuffling Technique

Directory of Open Access Journals (Sweden)

Kentaro Inokuma

2017-12-01

Full Text Available Xylose-assimilating yeasts with tolerance to both fermentation inhibitors (such as weak organic acids and high temperature are required for cost-effective simultaneous saccharification and cofermentation (SSCF of lignocellulosic materials. Here, we demonstrate the construction of a novel xylose-utilizing Saccharomyces cerevisiae strain with improved fermentation ability under heat and acid co-stress using the drug resistance marker-aided genome shuffling technique. The mutagenized genome pools derived from xylose-utilizing diploid yeasts with thermotolerance or acid tolerance were shuffled by sporulation and mating. The shuffled strains were then subjected to screening under co-stress conditions of heat and acids, and the hybrid strain Hyb-8 was isolated. The hybrid strain displayed enhanced xylose fermentation ability in comparison to both parental strains under co-stress conditions of heat and acids. Hyb-8 consumed 33.1 ± 0.6 g/L xylose and produced 11.1 ± 0.4 g/L ethanol after 72 h of fermentation at 38°C with 20 mM acetic acid and 15 mM formic acid. We also performed transcriptomic analysis of the hybrid strain and its parental strains to screen for key genes for multiple stress tolerances. We found that 13 genes, including 5 associated with cellular transition metal ion homeostasis, were significantly upregulated in Hyb-8 compared to levels in both parental strains under co-stress conditions. The hybrid strain Hyb-8 has strong potential for cost-effective SSCF of lignocellulosic materials. Moreover, the transcriptome data gathered in this study will be useful for understanding the mechanisms of multiple tolerance to high temperature and acids in yeast and facilitate the development of robust yeast strains for SSCF.

Phylogenetic Structure of Plant Communities: Are Polyploids Distantly Related to Co-occurring Diploids?

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Michelle L. Gaynor

2018-04-01

Full Text Available Polyploidy is widely acknowledged to have played an important role in the evolution and diversification of vascular plants. However, the influence of genome duplication on population-level dynamics and its cascading effects at the community level remain unclear. In part, this is due to persistent uncertainties over the extent of polyploid phenotypic variation, and the interactions between polyploids and co-occurring species, and highlights the need to integrate polyploid research at the population and community level. Here, we investigate how community-level patterns of phylogenetic relatedness might influence escape from minority cytotype exclusion, a classic population genetics hypothesis about polyploid establishment, and population-level species interactions. Focusing on two plant families in which polyploidy has evolved multiple times, Brassicaceae and Rosaceae, we build upon the hypothesis that the greater allelic and phenotypic diversity of polyploids allow them to successfully inhabit a different geographic range compared to their diploid progenitor and close relatives. Using a phylogenetic framework, we specifically test (1 whether polyploid species are more distantly related to diploids within the same community than co-occurring diploids are to one another, and (2 if polyploid species tend to exhibit greater ecological success than diploids, using species abundance in communities as an indicator of successful establishment. Overall, our results suggest that the effects of genome duplication on community structure are not clear-cut. We find that polyploid species tend to be more distantly related to co-occurring diploids than diploids are to each other. However, we do not find a consistent pattern of polyploid species being more abundant than diploid species, suggesting polyploids are not uniformly more ecologically successful than diploids. While polyploidy appears to have some important influences on species co-occurrence in

A non-classical phase diagram for virus-bacterial co-evolution mediated by CRISPR

Science.gov (United States)

Han, Pu; Deem, Michael

CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. Due to the cost of CRISPR, bacteria can lose the acquired immunity. We will show an intriguing phase diagram of the virus extinction probability, which when the rate of losing the acquired immunity is small, is more complex than that of the classic predator-prey model. As the CRISPR incorporates genetic material, viruses are under pressure to evolve to escape the recognition by CRISPR, and this co-evolution leads to a non-trivial phase structure that cannot be explained by the classical predator-prey model.

"Orphan" retrogenes in the human genome.

Science.gov (United States)

Ciomborowska, Joanna; Rosikiewicz, Wojciech; Szklarczyk, Damian; Makałowski, Wojciech; Makałowska, Izabela

2013-02-01

Gene duplicates generated via retroposition were long thought to be pseudogenized and consequently decayed. However, a significant number of these genes escaped their evolutionary destiny and evolved into functional genes. Despite multiple studies, the number of functional retrogenes in human and other genomes remains unclear. We performed a comparative analysis of human, chicken, and worm genomes to identify "orphan" retrogenes, that is, retrogenes that have replaced their progenitors. We located 25 such candidates in the human genome. All of these genes were previously known, and the majority has been intensively studied. Despite this, they have never been recognized as retrogenes. Analysis revealed that the phenomenon of replacing parental genes with their retrocopies has been taking place over the entire span of animal evolution. This process was often species specific and contributed to interspecies differences. Surprisingly, these retrogenes, which should evolve in a more relaxed mode, are subject to a very strong purifying selection, which is, on average, two and a half times stronger than other human genes. Also, for retrogenes, they do not show a typical overall tendency for a testis-specific expression. Notably, seven of them are associated with human diseases. Recognizing them as "orphan" retrocopies, which have different regulatory machinery than their parents, is important for any disease studies in model organisms, especially when discoveries made in one species are transferred to humans.

Co-Creating Tourism Research

NARCIS (Netherlands)

Ren, Carina; Jóhannesson, Gunnar Thór; Duim, van der V.R.

2018-01-01

Co-creation has become a buzzword in many social science disciplines, in business and in tourism studies. Given the prominence of co-creation, surprisingly little discussion has evolved around its implications for research practices and knowledge production as well as what challenges there are for

A PLSPM-Based Test Statistic for Detecting Gene-Gene Co-Association in Genome-Wide Association Study with Case-Control Design

Science.gov (United States)

Zhang, Xiaoshuai; Yang, Xiaowei; Yuan, Zhongshang; Liu, Yanxun; Li, Fangyu; Peng, Bin; Zhu, Dianwen; Zhao, Jinghua; Xue, Fuzhong

2013-01-01

For genome-wide association data analysis, two genes in any pathway, two SNPs in the two linked gene regions respectively or in the two linked exons respectively within one gene are often correlated with each other. We therefore proposed the concept of gene-gene co-association, which refers to the effects not only due to the traditional interaction under nearly independent condition but the correlation between two genes. Furthermore, we constructed a novel statistic for detecting gene-gene co-association based on Partial Least Squares Path Modeling (PLSPM). Through simulation, the relationship between traditional interaction and co-association was highlighted under three different types of co-association. Both simulation and real data analysis demonstrated that the proposed PLSPM-based statistic has better performance than single SNP-based logistic model, PCA-based logistic model, and other gene-based methods. PMID:23620809

Vertebrate Genome Evolution in the Light of Fish Cytogenomics and rDNAomics

Science.gov (United States)

Howell, W. Mike

2018-01-01

To understand the cytogenomic evolution of vertebrates, we must first unravel the complex genomes of fishes, which were the first vertebrates to evolve and were ancestors to all other vertebrates. We must not forget the immense time span during which the fish genomes had to evolve. Fish cytogenomics is endowed with unique features which offer irreplaceable insights into the evolution of the vertebrate genome. Due to the general DNA base compositional homogeneity of fish genomes, fish cytogenomics is largely based on mapping DNA repeats that still represent serious obstacles in genome sequencing and assembling, even in model species. Localization of repeats on chromosomes of hundreds of fish species and populations originating from diversified environments have revealed the biological importance of this genomic fraction. Ribosomal genes (rDNA) belong to the most informative repeats and in fish, they are subject to a more relaxed regulation than in higher vertebrates. This can result in formation of a literal ‘rDNAome’ consisting of more than 20,000 copies with their high proportion employed in extra-coding functions. Because rDNA has high rates of transcription and recombination, it contributes to genome diversification and can form reproductive barrier. Our overall knowledge of fish cytogenomics grows rapidly by a continuously increasing number of fish genomes sequenced and by use of novel sequencing methods improving genome assembly. The recently revealed exceptional compositional heterogeneity in an ancient fish lineage (gars) sheds new light on the compositional genome evolution in vertebrates generally. We highlight the power of synergy of cytogenetics and genomics in fish cytogenomics, its potential to understand the complexity of genome evolution in vertebrates, which is also linked to clinical applications and the chromosomal backgrounds of speciation. We also summarize the current knowledge on fish cytogenomics and outline its main future avenues. PMID

PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes

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Wasnick Michael

2008-03-01

Full Text Available Abstract Background The conservation of gene order among prokaryotic genomes can provide valuable insight into gene function, protein interactions, or events by which genomes have evolved. Although some tools are available for visualizing and comparing the order of genes between genomes of study, few support an efficient and organized analysis between large numbers of genomes. The Prokaryotic Sequence homology Analysis Tool (PSAT is a web tool for comparing gene neighborhoods among multiple prokaryotic genomes. Results PSAT utilizes a database that is preloaded with gene annotation, BLAST hit results, and gene-clustering scores designed to help identify regions of conserved gene order. Researchers use the PSAT web interface to find a gene of interest in a reference genome and efficiently retrieve the sequence homologs found in other bacterial genomes. The tool generates a graphic of the genomic neighborhood surrounding the selected gene and the corresponding regions for its homologs in each comparison genome. Homologs in each region are color coded to assist users with analyzing gene order among various genomes. In contrast to common comparative analysis methods that filter sequence homolog data based on alignment score cutoffs, PSAT leverages gene context information for homologs, including those with weak alignment scores, enabling a more sensitive analysis. Features for constraining or ordering results are designed to help researchers browse results from large numbers of comparison genomes in an organized manner. PSAT has been demonstrated to be useful for helping to identify gene orthologs and potential functional gene clusters, and detecting genome modifications that may result in loss of function. Conclusion PSAT allows researchers to investigate the order of genes within local genomic neighborhoods of multiple genomes. A PSAT web server for public use is available for performing analyses on a growing set of reference genomes through any

A Feast of Malaria Parasite Genomes.

Science.gov (United States)

Carlton, Jane M; Sullivan, Steven A

2017-03-08

The Plasmodium genus has evolved over time and across hosts, complexifying our understanding of malaria. In a recent Nature paper, Rutledge et al. (2017) describe the genome sequences of three major human malaria parasite species, providing insight into Plasmodium evolution and raising the question of how many species there are. Copyright © 2017 Elsevier Inc. All rights reserved.

Genomics and metagenomics in medical microbiology.

Science.gov (United States)

Padmanabhan, Roshan; Mishra, Ajay Kumar; Raoult, Didier; Fournier, Pierre-Edouard

2013-12-01

Over the last two decades, sequencing tools have evolved from laborious time-consuming methodologies to real-time detection and deciphering of genomic DNA. Genome sequencing, especially using next generation sequencing (NGS) has revolutionized the landscape of microbiology and infectious disease. This deluge of sequencing data has not only enabled advances in fundamental biology but also helped improve diagnosis, typing of pathogen, virulence and antibiotic resistance detection, and development of new vaccines and culture media. In addition, NGS also enabled efficient analysis of complex human micro-floras, both commensal, and pathological, through metagenomic methods, thus helping the comprehension and management of human diseases such as obesity. This review summarizes technological advances in genomics and metagenomics relevant to the field of medical microbiology. Copyright © 2013 Elsevier B.V. All rights reserved.

Genome-wide analysis of protein-protein interactions and involvement of viral proteins in SARS-CoV replication.

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Ji'an Pan

Full Text Available Analyses of viral protein-protein interactions are an important step to understand viral protein functions and their underlying molecular mechanisms. In this study, we adopted a mammalian two-hybrid system to screen the genome-wide intraviral protein-protein interactions of SARS coronavirus (SARS-CoV and therefrom revealed a number of novel interactions which could be partly confirmed by in vitro biochemical assays. Three pairs of the interactions identified were detected in both directions: non-structural protein (nsp 10 and nsp14, nsp10 and nsp16, and nsp7 and nsp8. The interactions between the multifunctional nsp10 and nsp14 or nsp16, which are the unique proteins found in the members of Nidovirales with large RNA genomes including coronaviruses and toroviruses, may have important implication for the mechanisms of replication/transcription complex assembly and functions of these viruses. Using a SARS-CoV replicon expressing a luciferase reporter under the control of a transcription regulating sequence, it has been shown that several viral proteins (N, X and SUD domains of nsp3, and nsp12 provided in trans stimulated the replicon reporter activity, indicating that these proteins may regulate coronavirus replication and transcription. Collectively, our findings provide a basis and platform for further characterization of the functions and mechanisms of coronavirus proteins.

Antagonistic parent-offspring co-adaptation.

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Mathias Kölliker

2010-01-01

Full Text Available In species across taxa, offspring have means to influence parental investment (PI. PI thus evolves as an interacting phenotype and indirect genetic effects may strongly affect the co-evolutionary dynamics of offspring and parental behaviors. Evolutionary theory focused on explaining how exaggerated offspring solicitation can be understood as resolution of parent-offspring conflict, but the evolutionary origin and diversification of different forms of family interactions remains unclear.In contrast to previous theory that largely uses a static approach to predict how "offspring individuals" and "parental individuals" should interact given conflict over PI, we present a dynamic theoretical framework of antagonistic selection on the PI individuals obtain/take as offspring and the PI they provide as parents to maximize individual lifetime reproductive success; we analyze a deterministic and a stochastic version of this dynamic framework. We show that a zone for equivalent co-adaptation outcomes exists in which stable levels of PI can evolve and be maintained despite fast strategy transitions and ongoing co-evolutionary dynamics. Under antagonistic co-adaptation, cost-free solicitation can evolve as an adaptation to emerging preferences in parents.We show that antagonistic selection across the offspring and parental life-stage of individuals favors co-adapted offspring and parental behavior within a zone of equivalent outcomes. This antagonistic parent-offspring co-adaptation does not require solicitation to be costly, allows for rapid divergence and evolutionary novelty and potentially explains the origin and diversification of the observed provisioning forms in family life.

Co-creating tourism research

DEFF Research Database (Denmark)

Co-creation has become a buzzword in many social science disciplines, in business and in tourism studies. Given the prominence of co-creation, surprisingly little discussion has evolved around its implications for research practices and knowledge production as well as what challenges there are fo......Co-creation has become a buzzword in many social science disciplines, in business and in tourism studies. Given the prominence of co-creation, surprisingly little discussion has evolved around its implications for research practices and knowledge production as well as what challenges...... there are for fulfilling the promise of co-creation in tourism research. This book aims to contribute to this discussion by addressing how tourism research comes together as a collaborative achievement and by exploring different ways of collaborative knowledge production in tourism research. It is structured to offer......, on one hand, an introduction to the ontological basis for collaborative research and, on the other hand, a set of empirical examples of how collaborative knowledge creation can inform tourism design, management, policy and education. The theoretical accounts and empirical cases of this book display how...

Complete mitochondrial DNA sequences of the threadfin cichlid (Petrochromis trewavasae and the blunthead cichlid (Tropheus moorii and patterns of mitochondrial genome evolution in cichlid fishes.

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Christoph Fischer

Full Text Available The cichlid fishes of the East African Great Lakes represent a model especially suited to study adaptive radiation and speciation. With several African cichlid genome projects being in progress, a promising set of closely related genomes is emerging, which is expected to serve as a valuable data base to solve questions on genotype-phenotype relations. The mitochondrial (mt genomes presented here are the first results of the assembly and annotation process for two closely related but eco-morphologically highly distinct Lake Tanganyika cichlids, Petrochromis trewavasae and Tropheus moorii. The genomic sequences comprise 16,588 bp (P. trewavasae and 16,590 bp (T. moorii, and exhibit the typical mitochondrial structure, with 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a non-coding control region. Analyses confirmed that the two species are very closely related with an overall sequence similarity of 96%. We analyzed the newly generated sequences in the phylogenetic context of 21 published labroid fish mitochondrial genomes. Consistent with other vertebrates, the D-loop region was found to evolve faster than protein-coding genes, which in turn are followed by the rRNAs; the tRNAs vary greatly in the rate of sequence evolution, but on average evolve the slowest. Within the group of coding genes, ND6 evolves most rapidly. Codon usage is similar among examined cichlid tribes and labroid families; although a slight shift in usage patterns down the gene tree could be observed. Despite having a clearly different nucleotide composition, ND6 showed a similar codon usage. C-terminal ends of Cox1 exhibit variations, where the varying number of amino acids is related to the structure of the obtained phylogenetic tree. This variation may be of functional relevance for Cox1 synthesis.

Recurrent emergence of structural variants of LTR retrotransposon CsRn1 evolving novel expression strategy and their selective expansion in a carcinogenic liver fluke, Clonorchis sinensis.

Science.gov (United States)

Kim, Seon-Hee; Kong, Yoon; Bae, Young-An

2017-06-01

Autonomous retrotransposons, in which replication and transcription are coupled, encode the essential gag and pol genes as a fusion or separate overlapping form(s) that are expressed in single transcripts regulated by a common upstream promoter. The element-specific expression strategies have driven development of relevant translational recoding mechanisms including ribosomal frameshifting to satisfy the protein stoichiometry critical for the assembly of infectious virus-like particles. Retrotransposons with different recoding strategies exhibit a mosaic distribution pattern across the diverse families of reverse transcribing elements, even though their respective distributions are substantially skewed towards certain family groups. However, only a few investigations to date have focused on the emergence of retrotransposons evolving novel expression strategy and causal genetic drivers of the structural variants. In this study, the bulk of genomic and transcribed sequences of a Ty3/gypsy-like CsRn1 retrotransposon in Clonorchis sinensis were analyzed for the comprehensive examination of its expression strategy. Our results demonstrated that structural variants with single open reading frame (ORF) have recurrently emerged from precedential CsRn1 copies encoding overlapping gag-pol ORFs by a single-nucleotide insertion in an upstream region of gag stop codon. In the parasite genome, some of the newly evolved variants appeared to undergo proliferative burst as active master lineages together with their ancestral copies. The genetic event was similarly observed in Opisthorchis viverrini, the closest neighbor of C. sinensis, whereas the resulting structural variants might have failed to overcome purifying selection and comprised minor remnant copies in the Opisthorchis genome. Copyright © 2017 Elsevier B.V. All rights reserved.

Phylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation

Science.gov (United States)

2013-01-01

Background The Streptococcus Anginosus Group (SAG) represents three closely related species of the viridans group streptococci recognized as commensal bacteria of the oral, gastrointestinal and urogenital tracts. The SAG also cause severe invasive infections, and are pathogens during cystic fibrosis (CF) pulmonary exacerbation. Little genomic information or description of virulence mechanisms is currently available for SAG. We conducted intra and inter species whole-genome comparative analyses with 59 publically available Streptococcus genomes and seven in-house closed high quality finished SAG genomes; S. constellatus (3), S. intermedius (2), and S. anginosus (2). For each SAG species, we sequenced at least one numerically dominant strain from CF airways recovered during acute exacerbation and an invasive, non-lung isolate. We also evaluated microevolution that occurred within two isolates that were cultured from one individual one year apart. Results The SAG genomes were most closely related to S. gordonii and S. sanguinis, based on shared orthologs and harbor a similar number of proteins within each COG category as other Streptococcus species. Numerous characterized streptococcus virulence factor homologs were identified within the SAG genomes including; adherence, invasion, spreading factors, LPxTG cell wall proteins, and two component histidine kinases known to be involved in virulence gene regulation. Mobile elements, primarily integrative conjugative elements and bacteriophage, account for greater than 10% of the SAG genomes. S. anginosus was the most variable species sequenced in this study, yielding both the smallest and the largest SAG genomes containing multiple genomic rearrangements, insertions and deletions. In contrast, within the S. constellatus and S. intermedius species, there was extensive continuous synteny, with only slight differences in genome size between strains. Within S. constellatus we were able to determine important SNPs and changes in

Patient-controlled encrypted genomic data: an approach to advance clinical genomics

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Trakadis Yannis J

2012-07-01

Full Text Available Abstract Background The revolution in DNA sequencing technologies over the past decade has made it feasible to sequence an individual’s whole genome at a relatively low cost. The potential value of the information generated by genomic technologies for medicine and society is enormous. However, in order for exome sequencing, and eventually whole genome sequencing, to be implemented clinically, a number of major challenges need to be overcome. For instance, obtaining meaningful informed-consent, managing incidental findings and the great volume of data generated (including multiple findings with uncertain clinical significance, re-interpreting the genomic data and providing additional counselling to patients as genetic knowledge evolves are issues that need to be addressed. It appears that medical genetics is shifting from the present “phenotype-first” medical model to a “data-first” model which leads to multiple complexities. Discussion This manuscript discusses the different challenges associated with integrating genomic technologies into clinical practice and describes a “phenotype-first” approach, namely, “Individualized Mutation-weighed Phenotype Search”, and its benefits. The proposed approach allows for a more efficient prioritization of the genes to be tested in a clinical lab based on both the patient’s phenotype and his/her entire genomic data. It simplifies “informed-consent” for clinical use of genomic technologies and helps to protect the patient’s autonomy and privacy. Overall, this approach could potentially render widespread use of genomic technologies, in the immediate future, practical, ethical and clinically useful. Summary The “Individualized Mutation-weighed Phenotype Search” approach allows for an incremental integration of genomic technologies into clinical practice. It ensures that we do not over-medicalize genomic data but, rather, continue our current medical model which is based on serving

Genomic analysis of Melioribacter roseus, facultatively anaerobic organotrophic bacterium representing a novel deep lineage within Bacteriodetes/Chlorobi group.

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Vitaly V Kadnikov

Full Text Available Melioribacter roseus is a moderately thermophilic facultatively anaerobic organotrophic bacterium representing a novel deep branch within Bacteriodetes/Chlorobi group. To better understand the metabolic capabilities and possible ecological functions of M. roseus and get insights into the evolutionary history of this bacterial lineage, we sequenced the genome of the type strain P3M-2(T. A total of 2838 open reading frames was predicted from its 3.30 Mb genome. The whole proteome analysis supported phylum-level classification of M. roseus since most of the predicted proteins had closest matches in Bacteriodetes, Proteobacteria, Chlorobi, Firmicutes and deeply-branching bacterium Caldithrix abyssi, rather than in one particular phylum. Consistent with the ability of the bacterium to grow on complex carbohydrates, the genome analysis revealed more than one hundred glycoside hydrolases, glycoside transferases, polysaccharide lyases and carbohydrate esterases. The reconstructed central metabolism revealed pathways enabling the fermentation of complex organic substrates, as well as their complete oxidation through aerobic and anaerobic respiration. Genes encoding the photosynthetic and nitrogen-fixation machinery of green sulfur bacteria, as well as key enzymes of autotrophic carbon fixation pathways, were not identified. The M. roseus genome supports its affiliation to a novel phylum Ignavibateriae, representing the first step on the evolutionary pathway from heterotrophic ancestors of Bacteriodetes/Chlorobi group towards anaerobic photoautotrophic Chlorobi.

Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta.

Science.gov (United States)

McNeal, Joel R; Kuehl, Jennifer V; Boore, Jeffrey L; de Pamphilis, Claude W

2007-10-24

Plastid genome content and protein sequence are highly conserved across land plants and their closest algal relatives. Parasitic plants, which obtain some or all of their nutrition through an attachment to a host plant, are often a striking exception. Heterotrophy can lead to relaxed constraint on some plastid genes or even total gene loss. We sequenced plastid genomes of two species in the parasitic genus Cuscuta along with a non-parasitic relative, Ipomoea purpurea, to investigate changes in the plastid genome that may result from transition to the parasitic lifestyle. Aside from loss of all ndh genes, Cuscuta exaltata retains photosynthetic and photorespiratory genes that evolve under strong selective constraint. Cuscuta obtusiflora has incurred substantially more change to its plastid genome, including loss of all genes for the plastid-encoded RNA polymerase. Despite extensive change in gene content and greatly increased rate of overall nucleotide substitution, C. obtusiflora also retains all photosynthetic and photorespiratory genes with only one minor exception. Although Epifagus virginiana, the only other parasitic plant with its plastid genome sequenced to date, has lost a largely overlapping set of transfer-RNA and ribosomal genes as Cuscuta, it has lost all genes related to photosynthesis and maintains a set of genes which are among the most divergent in Cuscuta. Analyses demonstrate photosynthetic genes are under the highest constraint of any genes within the plastid genomes of Cuscuta, indicating a function involving RuBisCo and electron transport through photosystems is still the primary reason for retention of the plastid genome in these species.

Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta

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Kuehl Jennifer V

2007-10-01

Full Text Available Abstract Background Plastid genome content and protein sequence are highly conserved across land plants and their closest algal relatives. Parasitic plants, which obtain some or all of their nutrition through an attachment to a host plant, are often a striking exception. Heterotrophy can lead to relaxed constraint on some plastid genes or even total gene loss. We sequenced plastid genomes of two species in the parasitic genus Cuscuta along with a non-parasitic relative, Ipomoea purpurea, to investigate changes in the plastid genome that may result from transition to the parasitic lifestyle. Results Aside from loss of all ndh genes, Cuscuta exaltata retains photosynthetic and photorespiratory genes that evolve under strong selective constraint. Cuscuta obtusiflora has incurred substantially more change to its plastid genome, including loss of all genes for the plastid-encoded RNA polymerase. Despite extensive change in gene content and greatly increased rate of overall nucleotide substitution, C. obtusiflora also retains all photosynthetic and photorespiratory genes with only one minor exception. Conclusion Although Epifagus virginiana, the only other parasitic plant with its plastid genome sequenced to date, has lost a largely overlapping set of transfer-RNA and ribosomal genes as Cuscuta, it has lost all genes related to photosynthesis and maintains a set of genes which are among the most divergent in Cuscuta. Analyses demonstrate photosynthetic genes are under the highest constraint of any genes within the plastid genomes of Cuscuta, indicating a function involving RuBisCo and electron transport through photosystems is still the primary reason for retention of the plastid genome in these species.

Manipulating or superseding host recombination functions: a dilemma that shapes phage evolvability.

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Louis-Marie Bobay

Full Text Available Phages, like many parasites, tend to have small genomes and may encode autonomous functions or manipulate those of their hosts'. Recombination functions are essential for phage replication and diversification. They are also nearly ubiquitous in bacteria. The E. coli genome encodes many copies of an octamer (Chi motif that upon recognition by RecBCD favors repair of double strand breaks by homologous recombination. This might allow self from non-self discrimination because RecBCD degrades DNA lacking Chi. Bacteriophage Lambda, an E. coli parasite, lacks Chi motifs, but escapes degradation by inhibiting RecBCD and encoding its own autonomous recombination machinery. We found that only half of 275 lambdoid genomes encode recombinases, the remaining relying on the host's machinery. Unexpectedly, we found that some lambdoid phages contain extremely high numbers of Chi motifs concentrated between the phage origin of replication and the packaging site. This suggests a tight association between replication, packaging and RecBCD-mediated recombination in these phages. Indeed, phages lacking recombinases strongly over-represent Chi motifs. Conversely, phages encoding recombinases and inhibiting host recombination machinery select for the absence of Chi motifs. Host and phage recombinases use different mechanisms and the latter are more tolerant to sequence divergence. Accordingly, we show that phages encoding their own recombination machinery have more mosaic genomes resulting from recent recombination events and have more diverse gene repertoires, i.e. larger pan genomes. We discuss the costs and benefits of superseding or manipulating host recombination functions and how this decision shapes phage genome structure and evolvability.

Genome-wide evolutionary dynamics of influenza B viruses on a global scale.

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Pinky Langat

2017-12-01

Full Text Available The global-scale epidemiology and genome-wide evolutionary dynamics of influenza B remain poorly understood compared with influenza A viruses. We compiled a spatio-temporally comprehensive dataset of influenza B viruses, comprising over 2,500 genomes sampled worldwide between 1987 and 2015, including 382 newly-sequenced genomes that fill substantial gaps in previous molecular surveillance studies. Our contributed data increase the number of available influenza B virus genomes in Europe, Africa and Central Asia, improving the global context to study influenza B viruses. We reveal Yamagata-lineage diversity results from co-circulation of two antigenically-distinct groups that also segregate genetically across the entire genome, without evidence of intra-lineage reassortment. In contrast, Victoria-lineage diversity stems from geographic segregation of different genetic clades, with variability in the degree of geographic spread among clades. Differences between the lineages are reflected in their antigenic dynamics, as Yamagata-lineage viruses show alternating dominance between antigenic groups, while Victoria-lineage viruses show antigenic drift of a single lineage. Structural mapping of amino acid substitutions on trunk branches of influenza B gene phylogenies further supports these antigenic differences and highlights two potential mechanisms of adaptation for polymerase activity. Our study provides new insights into the epidemiological and molecular processes shaping influenza B virus evolution globally.

Genome-wide evolutionary dynamics of influenza B viruses on a global scale

Science.gov (United States)

Langat, Pinky; Bowden, Thomas A.; Edwards, Stephanie; Gall, Astrid; Rambaut, Andrew; Daniels, Rodney S.; Russell, Colin A.; Pybus, Oliver G.; McCauley, John

2017-01-01

The global-scale epidemiology and genome-wide evolutionary dynamics of influenza B remain poorly understood compared with influenza A viruses. We compiled a spatio-temporally comprehensive dataset of influenza B viruses, comprising over 2,500 genomes sampled worldwide between 1987 and 2015, including 382 newly-sequenced genomes that fill substantial gaps in previous molecular surveillance studies. Our contributed data increase the number of available influenza B virus genomes in Europe, Africa and Central Asia, improving the global context to study influenza B viruses. We reveal Yamagata-lineage diversity results from co-circulation of two antigenically-distinct groups that also segregate genetically across the entire genome, without evidence of intra-lineage reassortment. In contrast, Victoria-lineage diversity stems from geographic segregation of different genetic clades, with variability in the degree of geographic spread among clades. Differences between the lineages are reflected in their antigenic dynamics, as Yamagata-lineage viruses show alternating dominance between antigenic groups, while Victoria-lineage viruses show antigenic drift of a single lineage. Structural mapping of amino acid substitutions on trunk branches of influenza B gene phylogenies further supports these antigenic differences and highlights two potential mechanisms of adaptation for polymerase activity. Our study provides new insights into the epidemiological and molecular processes shaping influenza B virus evolution globally. PMID:29284042

Supplementary data: A complete mitochondrial genome of wheat ...

Indian Academy of Sciences (India)

Supplementary data: A complete mitochondrial genome of wheat (Triticum aestivum cv. Chinese Yumai), and fast evolving mitochondrial genes in higher plants. Peng Cui, Huitao Liu, Qiang Lin, Feng Ding, Guoyin Zhuo, Songnian Hu, Dongcheng Liu, Wenlong Yang, Kehui Zhan,. Aimin Zhang and Jun Yu. J. Genet.

Mitochondrial genome sequencing helps show the evolutionary mechanism of mitochondrial genome formation in Brassica

Science.gov (United States)

2011-01-01

Background Angiosperm mitochondrial genomes are more complex than those of other organisms. Analyses of the mitochondrial genome sequences of at least 11 angiosperm species have showed several common properties; these cannot easily explain, however, how the diverse mitotypes evolved within each genus or species. We analyzed the evolutionary relationships of Brassica mitotypes by sequencing. Results We sequenced the mitotypes of cam (Brassica rapa), ole (B. oleracea), jun (B. juncea), and car (B. carinata) and analyzed them together with two previously sequenced mitotypes of B. napus (pol and nap). The sizes of whole single circular genomes of cam, jun, ole, and car are 219,747 bp, 219,766 bp, 360,271 bp, and 232,241 bp, respectively. The mitochondrial genome of ole is largest as a resulting of the duplication of a 141.8 kb segment. The jun mitotype is the result of an inherited cam mitotype, and pol is also derived from the cam mitotype with evolutionary modifications. Genes with known functions are conserved in all mitotypes, but clear variation in open reading frames (ORFs) with unknown functions among the six mitotypes was observed. Sequence relationship analysis showed that there has been genome compaction and inheritance in the course of Brassica mitotype evolution. Conclusions We have sequenced four Brassica mitotypes, compared six Brassica mitotypes and suggested a mechanism for mitochondrial genome formation in Brassica, including evolutionary events such as inheritance, duplication, rearrangement, genome compaction, and mutation. PMID:21988783

New Insights into the genetic diversity of Clostridium botulinum Group III through extensive genome exploration

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Cédric eWoudstra

2016-05-01

Full Text Available Animal botulism is caused by group III Clostridium botulinum strains producing type C and D toxins, or their chimeric forms C/D and D/C. Animal botulism is considered an emerging disease in Europe, notably in poultry production. Before our study, 14 genomes from different countries were available in the public database, but none were from France. In order to investigate the genetic relationship of French strains with different geographical areas and find new potential typing targets, 17 strains of C. botulinum group III were sequenced (16 from France and one from New Caledonia. Fourteen were type C/D strains isolated from chickens, ducks, guinea fowl and turkeys and three were type D/C strains isolated from cattle. The New Caledonian strain was a type D/C strain. Whole genome sequence analysis showed the French strains to be closely related to European strains from C. botulinum group III lineages Ia and Ib. The investigation of CRISPR sequences as genetic targets for differentiating strains in group III proved to be irrelevant for type C/D due to a deficient CRISPR/Cas mechanism, but not for type D/C. Conversely, the extrachromosomal elements of type C/D strains could be used to generate a genetic ID card. The highest level of discrimination was achieved with SNP core phylogeny, which allowed differentiation up to strain level and provide the most relevant information for genetic epidemiology studies and discrimination.

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

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Liu, Shengyi; Liu, Yumei; Yang, Xinhua; Tong, Chaobo; Edwards, David; Parkin, Isobel A. P.; Zhao, Meixia; Ma, Jianxin; Yu, Jingyin; Huang, Shunmou; Wang, Xiyin; Wang, Junyi; Lu, Kun; Fang, Zhiyuan; Bancroft, Ian; Yang, Tae-Jin; Hu, Qiong; Wang, Xinfa; Yue, Zhen; Li, Haojie; Yang, Linfeng; Wu, Jian; Zhou, Qing; Wang, Wanxin; King, Graham J; Pires, J. Chris; Lu, Changxin; Wu, Zhangyan; Sampath, Perumal; Wang, Zhuo; Guo, Hui; Pan, Shengkai; Yang, Limei; Min, Jiumeng; Zhang, Dong; Jin, Dianchuan; Li, Wanshun; Belcram, Harry; Tu, Jinxing; Guan, Mei; Qi, Cunkou; Du, Dezhi; Li, Jiana; Jiang, Liangcai; Batley, Jacqueline; Sharpe, Andrew G; Park, Beom-Seok; Ruperao, Pradeep; Cheng, Feng; Waminal, Nomar Espinosa; Huang, Yin; Dong, Caihua; Wang, Li; Li, Jingping; Hu, Zhiyong; Zhuang, Mu; Huang, Yi; Huang, Junyan; Shi, Jiaqin; Mei, Desheng; Liu, Jing; Lee, Tae-Ho; Wang, Jinpeng; Jin, Huizhe; Li, Zaiyun; Li, Xun; Zhang, Jiefu; Xiao, Lu; Zhou, Yongming; Liu, Zhongsong; Liu, Xuequn; Qin, Rui; Tang, Xu; Liu, Wenbin; Wang, Yupeng; Zhang, Yangyong; Lee, Jonghoon; Kim, Hyun Hee; Denoeud, France; Xu, Xun; Liang, Xinming; Hua, Wei; Wang, Xiaowu; Wang, Jun; Chalhoub, Boulos; Paterson, Andrew H

2014-01-01

Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear. Brassica is an ideal model to increase knowledge of polyploid evolution. Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes. Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B. oleracea. This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus. PMID:24852848

Coevolution of aah: A dps-Like Gene with the Host Bacterium Revealed by Comparative Genomic Analysis

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Liyan Ping

2012-01-01

Full Text Available A protein named AAH was isolated from the bacterium Microbacterium arborescens SE14, a gut commensal of the lepidopteran larvae. It showed not only a high sequence similarity to Dps-like proteins (DNA-binding proteins from starved cell but also reversible hydrolase activity. A comparative genomic analysis was performed to gain more insights into its evolution. The GC profile of the aah gene indicated that it was evolved from a low GC ancestor. Its stop codon usage was also different from the general pattern of Actinobacterial genomes. The phylogeny of dps-like proteins showed strong correlation with the phylogeny of host bacteria. A conserved genomic synteny was identified in some taxonomically related Actinobacteria, suggesting that the ancestor genes had incorporated into the genome before the divergence of Micrococcineae from other families. The aah gene had evolved new function but still retained the typical dodecameric structure.

A phylogenomic gene cluster resource: The phylogeneticallyinferred groups (PhlGs) database

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Dehal, Paramvir S.; Boore, Jeffrey L.

2005-08-25

We present here the PhIGs database, a phylogenomic resource for sequenced genomes. Although many methods exist for clustering gene families, very few attempt to create truly orthologous clusters sharing descent from a single ancestral gene across a range of evolutionary depths. Although these non-phylogenetic gene family clusters have been used broadly for gene annotation, errors are known to be introduced by the artifactual association of slowly evolving paralogs and lack of annotation for those more rapidly evolving. A full phylogenetic framework is necessary for accurate inference of function and for many studies that address pattern and mechanism of the evolution of the genome. The automated generation of evolutionary gene clusters, creation of gene trees, determination of orthology and paralogy relationships, and the correlation of this information with gene annotations, expression information, and genomic context is an important resource to the scientific community.

Admixture patterns and genetic differentiation in negrito groups from West Malaysia estimated from genome-wide SNP data.

Science.gov (United States)

Jinam, Timothy A; Phipps, Maude E; Saitou, Naruya

2013-01-01

Southeast Asia houses various culturally and linguistically diverse ethnic groups. In Malaysia, where the Malay, Chinese, and Indian ethnic groups form the majority, there exist minority groups such as the "negritos" who are believed to be descendants of the earliest settlers of Southeast Asia. Here we report patterns of genetic substructure and admixture in two Malaysian negrito populations (Jehai and Kensiu), using ~50,000 genome-wide single-nucleotide polymorphism (SNP) data. We found traces of recent admixture in both the negrito populations, particularly in the Jehai, with the Malay through principal component analysis and STRUCTURE analysis software, which suggested that the admixture was as recent as one generation ago. We also identified significantly differentiated nonsynonymous SNPs and haplotype blocks related to intracellular transport, metabolic processes, and detection of stimulus. These results highlight the different levels of admixture experienced by the two Malaysian negritos. Delineating admixture and differentiated genomic regions should be of importance in designing and interpretation of molecular anthropology and disease association studies. Copyright © 2013 Wayne State University Press, Detroit, Michigan 48201-1309.

IMG 4 version of the integrated microbial genomes comparative analysis system

Science.gov (United States)

Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Woyke, Tanja; Huntemann, Marcel; Anderson, Iain; Billis, Konstantinos; Varghese, Neha; Mavromatis, Konstantinos; Pati, Amrita; Ivanova, Natalia N.; Kyrpides, Nikos C.

2014-01-01

The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG provides tools for analyzing and reviewing the structural and functional annotations of genomes in a comparative context. IMG’s data content and analytical capabilities have increased continuously since its first version released in 2005. Since the last report published in the 2012 NAR Database Issue, IMG’s annotation and data integration pipelines have evolved while new tools have been added for recording and analyzing single cell genomes, RNA Seq and biosynthetic cluster data. Different IMG datamarts provide support for the analysis of publicly available genomes (IMG/W: http://img.jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu). PMID:24165883

IMG 4 version of the integrated microbial genomes comparative analysis system

Energy Technology Data Exchange (ETDEWEB)

Markowitz, Victor M. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center. Computational Research Division; Chen, I-Min A. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center. Computational Research Division; Palaniappan, Krishna [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center. Computational Research Division; Chu, Ken [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center. Computational Research Division; Szeto, Ernest [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center. Computational Research Division; Pillay, Manoj [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center. Computational Research Division; Ratner, Anna [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center. Computational Research Division; Huang, Jinghua [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center. Computational Research Division; Woyke, Tanja [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Microbial Genome and Metagenome Program; Huntemann, Marcel [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Microbial Genome and Metagenome Program; Anderson, Iain [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Microbial Genome and Metagenome Program; Billis, Konstantinos [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Microbial Genome and Metagenome Program; Varghese, Neha [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Microbial Genome and Metagenome Program; Mavromatis, Konstantinos [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Microbial Genome and Metagenome Program; Pati, Amrita [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Microbial Genome and Metagenome Program; Ivanova, Natalia N. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Microbial Genome and Metagenome Program; Kyrpides, Nikos C. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Microbial Genome and Metagenome Program

2013-10-27

The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG provides tools for analyzing and reviewing the structural and functional annotations of genomes in a comparative context. IMG’s data content and analytical capabilities have increased continuously since its first version released in 2005. Since the last report published in the 2012 NAR Database Issue, IMG’s annotation and data integration pipelines have evolved while new tools have been added for recording and analyzing single cell genomes, RNA Seq and biosynthetic cluster data. Finally, different IMG datamarts provide support for the analysis of publicly available genomes (IMG/W: http://img.jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu).

Friends Drinking Together: Young Adults' Evolving Support Practices

Science.gov (United States)

Dresler, Emma; Anderson, Margaret

2018-01-01

Purpose: Young adult's drinking is about pleasure, a communal practice of socialising together in a friendship group. The purpose of this paper is to investigate the evolving support practices of drinking groups for better targeting of health communications messages. Design/methodology/approach: This qualitative descriptive study examined the…

Cross-species genome-wide identification of evolutionary conserved microproteins

DEFF Research Database (Denmark)

Straub, Daniel; Wenkel, Stephan

2017-01-01

Protein concept beyond transcription factors to other protein families. Here, we reveal potential microProtein candidates in several plant and animal reference genomes. A large number of these microProteins are species-specific while others evolved early and are evolutionary highly conserved. Most known micro...... act in plant transcriptional regulation, signal transduction and anatomical structure development. MiPFinder is freely available to find microProteins in any genome and will aid in the identification of novel microProteins in plants and animals....

Analysis tools for the interplay between genome layout and regulation.

Science.gov (United States)

Bouyioukos, Costas; Elati, Mohamed; Képès, François

2016-06-06

Genome layout and gene regulation appear to be interdependent. Understanding this interdependence is key to exploring the dynamic nature of chromosome conformation and to engineering functional genomes. Evidence for non-random genome layout, defined as the relative positioning of either co-functional or co-regulated genes, stems from two main approaches. Firstly, the analysis of contiguous genome segments across species, has highlighted the conservation of gene arrangement (synteny) along chromosomal regions. Secondly, the study of long-range interactions along a chromosome has emphasised regularities in the positioning of microbial genes that are co-regulated, co-expressed or evolutionarily correlated. While one-dimensional pattern analysis is a mature field, it is often powerless on biological datasets which tend to be incomplete, and partly incorrect. Moreover, there is a lack of comprehensive, user-friendly tools to systematically analyse, visualise, integrate and exploit regularities along genomes. Here we present the Genome REgulatory and Architecture Tools SCAN (GREAT:SCAN) software for the systematic study of the interplay between genome layout and gene expression regulation. SCAN is a collection of related and interconnected applications currently able to perform systematic analyses of genome regularities as well as to improve transcription factor binding sites (TFBS) and gene regulatory network predictions based on gene positional information. We demonstrate the capabilities of these tools by studying on one hand the regular patterns of genome layout in the major regulons of the bacterium Escherichia coli. On the other hand, we demonstrate the capabilities to improve TFBS prediction in microbes. Finally, we highlight, by visualisation of multivariate techniques, the interplay between position and sequence information for effective transcription regulation.

Mining genome sequencing data to identify the genomic features linked to breast cancer histopathology

Science.gov (United States)

Ping, Zheng; Siegal, Gene P.; Almeida, Jonas S.; Schnitt, Stuart J.; Shen, Dejun

2014-01-01

Background: Genetics and genomics have radically altered our understanding of breast cancer progression. However, the genomic basis of various histopathologic features of breast cancer is not yet well-defined. Materials and Methods: The Cancer Genome Atlas (TCGA) is an international database containing a large collection of human cancer genome sequencing data. cBioPortal is a web tool developed for mining these sequencing data. We performed mining of TCGA sequencing data in an attempt to characterize the genomic features correlated with breast cancer histopathology. We first assessed the quality of the TCGA data using a group of genes with known alterations in various cancers. Both genome-wide gene mutation and copy number changes as well as a group of genes with a high frequency of genetic changes were then correlated with various histopathologic features of invasive breast cancer. Results: Validation of TCGA data using a group of genes with known alterations in breast cancer suggests that the TCGA has accurately documented the genomic abnormalities of multiple malignancies. Further analysis of TCGA breast cancer sequencing data shows that accumulation of specific genomic defects is associated with higher tumor grade, larger tumor size and receptor negativity. Distinct groups of genomic changes were found to be associated with the different grades of invasive ductal carcinoma. The mutator role of the TP53 gene was validated by genomic sequencing data of invasive breast cancer and TP53 mutation was found to play a critical role in defining high tumor grade. Conclusions: Data mining of the TCGA genome sequencing data is an innovative and reliable method to help characterize the genomic abnormalities associated with histopathologic features of invasive breast cancer. PMID:24672738

Mining genome sequencing data to identify the genomic features linked to breast cancer histopathology

Directory of Open Access Journals (Sweden)

Zheng Ping

2014-01-01

Full Text Available Background: Genetics and genomics have radically altered our understanding of breast cancer progression. However, the genomic basis of various histopathologic features of breast cancer is not yet well-defined. Materials and Methods: The Cancer Genome Atlas (TCGA is an international database containing a large collection of human cancer genome sequencing data. cBioPortal is a web tool developed for mining these sequencing data. We performed mining of TCGA sequencing data in an attempt to characterize the genomic features correlated with breast cancer histopathology. We first assessed the quality of the TCGA data using a group of genes with known alterations in various cancers. Both genome-wide gene mutation and copy number changes as well as a group of genes with a high frequency of genetic changes were then correlated with various histopathologic features of invasive breast cancer. Results: Validation of TCGA data using a group of genes with known alterations in breast cancer suggests that the TCGA has accurately documented the genomic abnormalities of multiple malignancies. Further analysis of TCGA breast cancer sequencing data shows that accumulation of specific genomic defects is associated with higher tumor grade, larger tumor size and receptor negativity. Distinct groups of genomic changes were found to be associated with the different grades of invasive ductal carcinoma. The mutator role of the TP53 gene was validated by genomic sequencing data of invasive breast cancer and TP53 mutation was found to play a critical role in defining high tumor grade. Conclusions: Data mining of the TCGA genome sequencing data is an innovative and reliable method to help characterize the genomic abnormalities associated with histopathologic features of invasive breast cancer.

Cell size, genome size and the dominance of Angiosperms

Science.gov (United States)

Simonin, K. A.; Roddy, A. B.

2016-12-01

Angiosperms are capable of maintaining the highest rates of photosynthetic gas exchange of all land plants. High rates of photosynthesis depends mechanistically both on efficiently transporting water to the sites of evaporation in the leaf and on regulating the loss of that water to the atmosphere as CO2 diffuses into the leaf. Angiosperm leaves are unique in their ability to sustain high fluxes of liquid and vapor phase water transport due to high vein densities and numerous, small stomata. Despite the ubiquity of studies characterizing the anatomical and physiological adaptations that enable angiosperms to maintain high rates of photosynthesis, the underlying mechanism explaining why they have been able to develop such high leaf vein densities, and such small and abundant stomata, is still incomplete. Here we ask whether the scaling of genome size and cell size places a fundamental constraint on the photosynthetic metabolism of land plants, and whether genome downsizing among the angiosperms directly contributed to their greater potential and realized primary productivity relative to the other major groups of terrestrial plants. Using previously published data we show that a single relationship can predict guard cell size from genome size across the major groups of terrestrial land plants (e.g. angiosperms, conifers, cycads and ferns). Similarly, a strong positive correlation exists between genome size and both stomatal density and vein density that together ultimately constrains maximum potential (gs, max) and operational stomatal conductance (gs, op). Further the difference in the slopes describing the covariation between genome size and both gs, max and gs, op suggests that genome downsizing brings gs, op closer to gs, max. Taken together the data presented here suggests that the smaller genomes of angiosperms allow their final cell sizes to vary more widely and respond more directly to environmental conditions and in doing so bring operational photosynthetic

Elucidation of Operon Structures across Closely Related Bacterial Genomes

Science.gov (United States)

Li, Guojun

2014-01-01

About half of the protein-coding genes in prokaryotic genomes are organized into operons to facilitate co-regulation during transcription. With the evolution of genomes, operon structures are undergoing changes which could coordinate diverse gene expression patterns in response to various stimuli during the life cycle of a bacterial cell. Here we developed a graph-based model to elucidate the diversity of operon structures across a set of closely related bacterial genomes. In the constructed graph, each node represents one orthologous gene group (OGG) and a pair of nodes will be connected if any two genes, from the corresponding two OGGs respectively, are located in the same operon as immediate neighbors in any of the considered genomes. Through identifying the connected components in the above graph, we found that genes in a connected component are likely to be functionally related and these identified components tend to form treelike topology, such as paths and stars, corresponding to different biological mechanisms in transcriptional regulation as follows. Specifically, (i) a path-structure component integrates genes encoding a protein complex, such as ribosome; and (ii) a star-structure component not only groups related genes together, but also reflects the key functional roles of the central node of this component, such as the ABC transporter with a transporter permease and substrate-binding proteins surrounding it. Most interestingly, the genes from organisms with highly diverse living environments, i.e., biomass degraders and animal pathogens of clostridia in our study, can be clearly classified into different topological groups on some connected components. PMID:24959722

From genomes to metabolomes: Understanding mechanisms of symbiosis and cell-cell signaling using the archaeal system Ignicoccus-Nanoarchaeum

Energy Technology Data Exchange (ETDEWEB)

Podar, Mircea [Univ. of Tennessee, Knoxville, TN (United States). Biosciences Division; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Hettich, Robert [Univ. of Tennessee, Knoxville, TN (United States). Biosciences Division; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Copie, Valerie [Montana State Univ., Bozeman, MT (United States). Dept. of Chemistry and Biochemistry; Bothner, Brian [Montana State Univ., Bozeman, MT (United States). Dept. of Chemistry and Biochemistry

2016-12-16

The main objective of this project was to use symbiotic Nanoarchaeaota, a group of thermophilic Archaea that are obligate symbionts/parasites on other Archaea, to develop an integrated multi-omic approach to study inter-species interactions as well as to understand fundamental mechanism that enable such relationships. As part of this grant we have achieved a number of important milestone on both technical and scientific levels. On the technical side, we developed immunofluorescence labeling and tracking methods to follow Nanoarchaeota in cultures and in environmental samples, we applied such methods in conjunction with flow cytometry to quantify and isolate uncultured representatives from the environment and characterized them by single cell genomics. On the proteomics side, we developed a more efficient and sensitive method to recover and semi-quantitatively measure membrane proteins, while achieving high total cellular proteome coverage (70-80% of the predicted proteome). Metabolomic analyses used complementary NMR and LC/GC mass spectrometry and led to the identification of novel lipids in these organisms as well as quantification of some of the major metabolites. Importantly, using several informatics approaches we were also able to integrate the transcriptomic, proteomic and metabolomic datasets, revealing aspects of the interspecies interaction that were not evident in the single omic analyses (manuscript in review). On the science side we determined that N. equitans and I. hospitalis are metabolically coupled and that N. equitans is strictly dependent on its host both for metabolic precursors and energetic needs. The actual mechanism by which small molecules move across the cell membrane remains unknown. The Ignicoccus host responds to the metabolic and energetic burned by upregulating of key primary metabolism steps and ATP synthesis. The two species have co-evolved, aspect that we determined by comparative genomics with other species of Ignicoccus

Reciprocal genomic evolution in the ant-fungus agricultural symbiosis

DEFF Research Database (Denmark)

Nygaard, Sanne; Hu, Haofu; Li, Cai

2016-01-01

The attine ant-fungus agricultural symbiosis evolved over tens of millions of years, producing complex societies with industrial-scale farming analogous to that of humans. Here we document reciprocal shifts in the genomes and transcriptomes of seven fungus-farming ant species and their fungal...

Characterization of a group of MITEs with unusual features from two coral genomes.

Directory of Open Access Journals (Sweden)

Shi Wang

Full Text Available BACKGROUND: Miniature inverted-repeat transposable elements (MITEs, which are common in eukaryotic genomes, are small non-coding elements that transpose by utilizing transposases encoded by autonomous transposons. Recent genome-wide analyses and cross-mobilization assays have greatly improved our knowledge on MITE proliferation, however, specific mechanisms for the origin and evolution of MITEs are still unclear. PRINCIPAL FINDINGS: A group of coral MITEs called CMITE were identified from two corals, Acropora millepora and Acropora palmata. CMITEs conform to many common characteristics of MITEs, but also present several unusual features. The most unusual feature of CMITEs is conservation of the internal region, which is more conserved between MITE families than the TIRs. The origin of this internal region remains unknown, although we found one CMITE family that seems to be derived from a piggyBac-like transposon in A. millepora. CMITEs can form tandem arrays, suggesting an unconventional way for MITEs to increase copy numbers. We also describe a case in which a novel transposable element was created by a CMITE insertion event. CONCLUSIONS: To our knowledge, this is the first report of identification of MITEs from coral genomes. Proliferation of CMITEs seems to be related to the transposition machinery of piggyBac-like autonomous transposons. The highly conserved internal region of CMITEs suggests a potential role for this region in their successful transposition. However, the origin of these unusual features in CMITEs remains unclear, and thus represents an intriguing topic for future investigations.

Characterization of a group of MITEs with unusual features from two coral genomes.

Science.gov (United States)

Wang, Shi; Zhang, Lingling; Meyer, Eli; Matz, Mikhail V

2010-05-18

Miniature inverted-repeat transposable elements (MITEs), which are common in eukaryotic genomes, are small non-coding elements that transpose by utilizing transposases encoded by autonomous transposons. Recent genome-wide analyses and cross-mobilization assays have greatly improved our knowledge on MITE proliferation, however, specific mechanisms for the origin and evolution of MITEs are still unclear. A group of coral MITEs called CMITE were identified from two corals, Acropora millepora and Acropora palmata. CMITEs conform to many common characteristics of MITEs, but also present several unusual features. The most unusual feature of CMITEs is conservation of the internal region, which is more conserved between MITE families than the TIRs. The origin of this internal region remains unknown, although we found one CMITE family that seems to be derived from a piggyBac-like transposon in A. millepora. CMITEs can form tandem arrays, suggesting an unconventional way for MITEs to increase copy numbers. We also describe a case in which a novel transposable element was created by a CMITE insertion event. To our knowledge, this is the first report of identification of MITEs from coral genomes. Proliferation of CMITEs seems to be related to the transposition machinery of piggyBac-like autonomous transposons. The highly conserved internal region of CMITEs suggests a potential role for this region in their successful transposition. However, the origin of these unusual features in CMITEs remains unclear, and thus represents an intriguing topic for future investigations.

Temporal genomic evolution of bird sex chromosomes

DEFF Research Database (Denmark)

Wang, Zongji; Zhang, Jilin; Yang, Wei

2014-01-01

BACKGROUND: Sex chromosomes exhibit many unusual patterns in sequence and gene expression relative to autosomes. Birds have evolved a female heterogametic sex system (male ZZ, female ZW), through stepwise suppression of recombination between chrZ and chrW. To address the broad patterns and complex...... driving forces of Z chromosome evolution, we analyze here 45 newly available bird genomes and four species' transcriptomes, over their course of recombination loss between the sex chromosomes. RESULTS: We show Z chromosomes in general have a significantly higher substitution rate in introns and synonymous...... ('fast-Z' evolution). And species with a lower level of intronic heterozygosities tend to evolve even faster on the Z chromosome. Further analysis of fast-evolving genes' enriched functional categories and sex-biased expression patterns support that, fast-Z evolution in birds is mainly driven by genetic...

CoLIde

Science.gov (United States)

Mohorianu, Irina; Stocks, Matthew Benedict; Wood, John; Dalmay, Tamas; Moulton, Vincent

2013-01-01

Small RNAs (sRNAs) are 20–25 nt non-coding RNAs that act as guides for the highly sequence-specific regulatory mechanism known as RNA silencing. Due to the recent increase in sequencing depth, a highly complex and diverse population of sRNAs in both plants and animals has been revealed. However, the exponential increase in sequencing data has also made the identification of individual sRNA transcripts corresponding to biological units (sRNA loci) more challenging when based exclusively on the genomic location of the constituent sRNAs, hindering existing approaches to identify sRNA loci.   To infer the location of significant biological units, we propose an approach for sRNA loci detection called CoLIde (Co-expression based sRNA Loci Identification) that combines genomic location with the analysis of other information such as variation in expression levels (expression pattern) and size class distribution. For CoLIde, we define a locus as a union of regions sharing the same pattern and located in close proximity on the genome. Biological relevance, detected through the analysis of size class distribution, is also calculated for each locus. CoLIde can be applied on ordered (e.g., time-dependent) or un-ordered (e.g., organ, mutant) series of samples both with or without biological/technical replicates. The method reliably identifies known types of loci and shows improved performance on sequencing data from both plants (e.g., A. thaliana, S. lycopersicum) and animals (e.g., D. melanogaster) when compared with existing locus detection techniques. CoLIde is available for use within the UEA Small RNA Workbench which can be downloaded from: http://srna-workbench.cmp.uea.ac.uk. PMID:23851377

In Silico Genomic Fingerprints of the Bacillus anthracis Group Obtained by Virtual Hybridization

Directory of Open Access Journals (Sweden)

Hueman Jaimes-Díaz

2015-02-01

Full Text Available In this study we evaluate the capacity of Virtual Hybridization to identify between highly related bacterial strains. Eight genomic fingerprints were obtained by virtual hybridization for the Bacillus anthracis genome set, and a set of 15,264 13-nucleotide short probes designed to produce genomic fingerprints unique for each organism. The data obtained from each genomic fingerprint were used to obtain hybridization patterns simulating a DNA microarray. Two virtual hybridization methods were used: the Direct and the Extended method to identify the number of potential hybridization sites and thus determine the minimum sensitivity value to discriminate between genomes with 99.9% similarity. Genomic fingerprints were compared using both methods and phylogenomic trees were constructed to verify that the minimum detection value is 0.000017. Results obtained from the genomic fingerprints suggest that the distribution in the trees is correct, as compared to other taxonomic methods. Specific virtual hybridization sites for each of the genomes studied were also identified.

Metabolic Environments and Genomic Features Associated with Pathogenic and Mutualistic Interactions between Bacteria and Plants is accepted for publication in MPMI

Energy Technology Data Exchange (ETDEWEB)

Karpinets, Tatiana V [ORNL; Park, Byung H [ORNL; Syed, Mustafa H [ORNL; Klotz, Martin G [University of North Carolina, Charlotte; Uberbacher, Edward C [ORNL

2014-01-01

Most bacterial symbionts of plants are phenotypically characterized by their parasitic or matualistic relationship with the host; however, the genomic characteristics that likely discriminate mutualistic symbionts from pathogens of plants are poorly understood. This study comparatively analyzed the genomes of 54 plant-symbiontic bacteria, 27 mutualists and 27 pathogens, to discover genomic determinants of their parasitic and mutualistic nature in terms of protein family domains, KEGG orthologous groups, metabolic pathways and families of carbohydrate-active enzymes (CAZymes). We further used all bacteria with sequenced genomesl, published microarrays and transcriptomics experimental datasets, and literature to validate and to explore results of the comparison. The analysis revealed that genomes of mutualists are larger in size and higher in GC content and encode greater molecular, functional and metabolic diversity than the investigated genomes of pathogens. This enriched molecular and functional enzyme diversity included constructive biosynthetic signatures of CAZymes and metabolic pathways in genomes of mutualists compared with catabolic signatures dominant in the genomes of pathogens. Another discriminative characteristic of mutualists is the co-occurence of gene clusters required for the expression and function of nitrogenase and RuBisCO. Analysis of previously published experimental data indicate that nitrogen-fixing mutualists may employ Rubisco to fix CO2 not in the canonical Calvin-Benson-Basham cycle but in a novel metabolic pathway, here called Rubisco-based glycolysis , to increase efficiency of sugar utilization during the symbiosis with plants. An important discriminative characteristic of plant pathogenic bacteria is two groups of genes likely encoding effector proteins involved in host invasion and a genomic locus encoding a putative secretion system that includes a DUF1525 domain protein conserved in pathogens of plants and of other organisms. The

Genomic insights into the fungal lignocellulolytic system of Myceliophthora thermophila

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Anthi eKarnaouri

2014-06-01

Full Text Available The microbial conversion of solid cellulosic biomass to liquid biofuels may provide a renewable energy source for transportation fuels. Cellulolytic fungi represent a promising group of organisms, as they have evolved complex systems for adaptation to their natural habitat. The filamentous fungus Myceliophthora thermophila constitutes an exceptionally powerful cellulolytic microorganism that synthesizes a complete set of enzymes necessary for the breakdown of plant cell wall. The genome of this fungus has been recently sequenced and annotated, allowing systematic examination and identification of enzymes required for the degradation of lignocellulosic biomass. The genomic analysis revealed the existence of an expanded enzymatic repertoire including numerous cellulases, hemicellulases and enzymes with auxiliary activities, covering the most of the recognized CAZy families. Most of them were predicted to possess a secretion signal and undergo through post translational glycosylation modifications. These data offer a better understanding of activities embedded in fungal lignocellulose decomposition mechanisms and suggest that M. thermophila could be made usable as an industrial production host for cellulolytic and hemicellulolytic enzymes.

Genome-wide detection of selection and other evolutionary forces

DEFF Research Database (Denmark)

Xu, Zhuofei; Zhou, Rui

2015-01-01

As is well known, pathogenic microbes evolve rapidly to escape from the host immune system and antibiotics. Genetic variations among microbial populations occur frequently during the long-term pathogen–host evolutionary arms race, and individual mutation beneficial for the fitness can be fixed...... to scan genome-wide alignments for evidence of positive Darwinian selection, recombination, and other evolutionary forces operating on the coding regions. In this chapter, we describe an integrative analysis pipeline and its application to tracking featured evolutionary trajectories on the genome...

Opportunities and challenges associated with clinical diagnostic genome sequencing: a report of the Association for Molecular Pathology.

Science.gov (United States)

Schrijver, Iris; Aziz, Nazneen; Farkas, Daniel H; Furtado, Manohar; Gonzalez, Andrea Ferreira; Greiner, Timothy C; Grody, Wayne W; Hambuch, Tina; Kalman, Lisa; Kant, Jeffrey A; Klein, Roger D; Leonard, Debra G B; Lubin, Ira M; Mao, Rong; Nagan, Narasimhan; Pratt, Victoria M; Sobel, Mark E; Voelkerding, Karl V; Gibson, Jane S

2012-11-01

This report of the Whole Genome Analysis group of the Association for Molecular Pathology illuminates the opportunities and challenges associated with clinical diagnostic genome sequencing. With the reality of clinical application of next-generation sequencing, technical aspects of molecular testing can be accomplished at greater speed and with higher volume, while much information is obtained. Although this testing is a next logical step for molecular pathology laboratories, the potential impact on the diagnostic process and clinical correlations is extraordinary and clinical interpretation will be challenging. We review the rapidly evolving technologies; provide application examples; discuss aspects of clinical utility, ethics, and consent; and address the analytic, postanalytic, and professional implications. Copyright © 2012 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Water Contact Angle Dependence with Hydroxyl Functional Groups on Silica Surfaces under CO2 Sequestration Conditions.

Science.gov (United States)

Chen, Cong; Zhang, Ning; Li, Weizhong; Song, Yongchen

2015-12-15

Functional groups on silica surfaces under CO2 sequestration conditions are complex due to reactions among supercritical CO2, brine and silica. Molecular dynamics simulations have been performed to investigate the effects of hydroxyl functional groups on wettability. It has been found that wettability shows a strong dependence on functional groups on silica surfaces: silanol number density, space distribution, and deprotonation/protonation degree. For neutral silica surfaces with crystalline structure (Q(3), Q(3)/Q(4), Q(4)), as silanol number density decreases, contact angle increases from 33.5° to 146.7° at 10.5 MPa and 318 K. When Q(3) surface changes to an amorphous structure, water contact angle increases 20°. Water contact angle decreases about 12° when 9% of silanol groups on Q(3) surface are deprotonated. When the deprotonation degree increases to 50%, water contact angle decreases to 0. The dependence of wettability on silica surface functional groups was used to analyze contact angle measurement ambiguity in literature. The composition of silica surfaces is complicated under CO2 sequestration conditions, the results found in this study may help to better understand wettability of CO2/brine/silica system.

Bioelectrochemical conversion of CO2 to chemicals

NARCIS (Netherlands)

Bajracharya, Suman; Vanbroekhoven, Karolien; Buisman, Cees J.N.; Strik, David P.B.T.B.; Pant, Deepak

2017-01-01

The recent concept of microbial electrosynthesis (MES) has evolved as an electricity-driven production technology for chemicals from low-value carbon dioxide (CO2) using micro-organisms as biocatalysts. MES from CO2 comprises bioelectrochemical reduction of CO2 to multi-carbon organic compounds

Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda) revealed from complete mitochondrial genomes.

Science.gov (United States)

Lin, Feng-Jiau; Liu, Yuan; Sha, Zhongli; Tsang, Ling Ming; Chu, Ka Hou; Chan, Tin-Yam; Liu, Ruiyu; Cui, Zhaoxia

2012-11-16

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. 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. Phylogenetic analyses on the mt genome sequences and the distinct gene orders provide further

Holistic Nursing in the Genetic/Genomic Era.

Science.gov (United States)

Sharoff, Leighsa

2016-06-01

Holistic nursing practice is an ever-evolving transformative process with core values that require continued growth, professional leadership, and advocacy. Holistic nurses are required to stay current with all new required competencies, such as the Core Competencies in Genetics for Health Professional, and, as such, be adept at translating scientific evidence relating to genetics/genomics in the clinical setting. Knowledge of genetics/genomics in relation to nursing practice, policy, utilization, and research influence nurses' responsibilities. In addition to holistic nursing competencies, the holistic nurse must have basic knowledge and skills to integrate genetics/genomics aspects. It is important for holistic nurses to enhance their overall knowledge foundation, skills, and attitudes about genetics to prepare for the transformation in health care that is already underway. Holistic nurses can provide an important perspective to the application of genetics and genomics, focusing on health promotion, caring, and understanding the relationship between caring and families, community, and society. Yet there may be a lack of genetic and genomic knowledge to fully participate in the current genomic era. This article will explore the required core competencies for all health care professionals, share linkage of holistic nurses in practice with genetic/genomic conditions, and provide resources to further one's knowledge base. © The Author(s) 2015.

Summary report of working group I CO{sub 2} capture, fixation/utilization, and disposal

Energy Technology Data Exchange (ETDEWEB)

NONE

1993-12-31

The topics of our working group were divided into four key areas: CO{sub 2} Capture, Utilization/Fixation, Ocean Disposal, and Land Disposal. Fourteen presentations were made as follows: CO{sub 2} Capture: Toshikatsu Hakuta (Japan) and Rod Judkins, Bruce St. John, and Alan Wolsky (US). Utilization/Fixation: Hironori Arakawa, Yasuo Asada, and Takashi lbusuki (Japan) and Ed Lipinsky (US). Ocean Disposal: Yuji Shindo (Japan) and Eric Adams, Gerard Nihous, and Wheeler North (US). Land Disposal: Shoichi Tanaka (Japan) and Roger Bailey (US/Canada). Co-chairs for this working group were Toshikatsu Hakuta (Japan) and Howard Herzog (US). This document contains only a summary outline of research needs in the area of CO{sub 2} capture and sequestration. It should be used in conjunction with other assessments made in this area. For the U.S., a DOE report entitled A Research Needs Assessment for the Capture, Utilization and Disposal of Carbon Dioxide from Fossil Fuel-Fired Power Plants will be forthcoming in 1993.

Genomic characterization, phylogenetic comparison and differential expression of the cyclic nucleotide-gated channels gene family in pear (Pyrus bretchneideri Rehd.).

Science.gov (United States)

Chen, Jianqing; Yin, Hao; Gu, Jinping; Li, Leiting; Liu, Zhe; Jiang, Xueting; Zhou, Hongsheng; Wei, Shuwei; Zhang, Shaoling; Wu, Juyou

2015-01-01

The cyclic nucleotide-gated channel (CNGC) family is involved in the uptake of various cations, such as Ca(2+), to regulate plant growth and respond to biotic and abiotic stresses. However, there is far less information about this family in woody plants such as pear. Here, we provided a genome-wide identification and analysis of the CNGC gene family in pear. Phylogenetic analysis showed that the 21 pear CNGC genes could be divided into five groups (I, II, III, IVA and IVB). The majority of gene duplications in pear appeared to have been caused by segmental duplication and occurred 32.94-39.14 million years ago. Evolutionary analysis showed that positive selection had driven the evolution of pear CNGCs. Motif analyses showed that Group I CNGCs generally contained 26 motifs, which was the greatest number of motifs in all CNGC groups. Among these, eight motifs were shared by each group, suggesting that these domains play a conservative role in CNGC activity. Tissue-specific expression analysis indicated that functional diversification of the duplicated CNGC genes was a major feature of long-term evolution. Our results also suggested that the P-S6 and PBC & hinge domains had co-evolved during the evolution. These results provide valuable information to increase our understanding of the function, evolution and expression analyses of the CNGC gene family in higher plants. Copyright © 2014 Elsevier Inc. All rights reserved.

Citrobacter rodentium is an unstable pathogen showing evidence of significant genomic flux.

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Nicola K Petty

2011-04-01

Full Text Available Citrobacter rodentium is a natural mouse pathogen that causes attaching and effacing (A/E lesions. It shares a common virulence strategy with the clinically significant human A/E pathogens enteropathogenic E. coli (EPEC and enterohaemorrhagic E. coli (EHEC and is widely used to model this route of pathogenesis. We previously reported the complete genome sequence of C. rodentium ICC168, where we found that the genome displayed many characteristics of a newly evolved pathogen. In this study, through PFGE, sequencing of isolates showing variation, whole genome transcriptome analysis and examination of the mobile genetic elements, we found that, consistent with our previous hypothesis, the genome of C. rodentium is unstable as a result of repeat-mediated, large-scale genome recombination and because of active transposition of mobile genetic elements such as the prophages. We sequenced an additional C. rodentium strain, EX-33, to reveal that the reference strain ICC168 is representative of the species and that most of the inactivating mutations were common to both isolates and likely to have occurred early on in the evolution of this pathogen. We draw parallels with the evolution of other bacterial pathogens and conclude that C. rodentium is a recently evolved pathogen that may have emerged alongside the development of inbred mice as a model for human disease.

Genetic addiction: selfish gene's strategy for symbiosis in the genome.

Science.gov (United States)

Mochizuki, Atsushi; Yahara, Koji; Kobayashi, Ichizo; Iwasa, Yoh

2006-02-01

The evolution and maintenance of the phenomenon of postsegregational host killing or genetic addiction are paradoxical. In this phenomenon, a gene complex, once established in a genome, programs death of a host cell that has eliminated it. The intact form of the gene complex would survive in other members of the host population. It is controversial as to why these genetic elements are maintained, due to the lethal effects of host killing, or perhaps some other properties are beneficial to the host. We analyzed their population dynamics by analytical methods and computer simulations. Genetic addiction turned out to be advantageous to the gene complex in the presence of a competitor genetic element. The advantage is, however, limited in a population without spatial structure, such as that in a well-mixed liquid culture. In contrast, in a structured habitat, such as the surface of a solid medium, the addiction gene complex can increase in frequency, irrespective of its initial density. Our demonstration that genomes can evolve through acquisition of addiction genes has implications for the general question of how a genome can evolve as a community of potentially selfish genes.

Signatures of adaptation in the weedy rice genome

Science.gov (United States)

Weedy rice is a common problem of by product of domestication that has evolved multiple times from cultivated and wild rice relatives. Here we use whole genome sequences to examine the origin and adaptation of the two major US weedy red rice strains, with a comparison to Chinese weedy red rice. We f...

Spirochaetes as intestinal pathogens: Lessons from a Brachyspira genome

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Hampson David J

2009-05-01

Full Text Available Abstract Anaerobic spirochaetes of the genus Brachyspira have long been known as important gut pathogens of pigs, but increasingly they are recognised as causing disease in birds and other animal species, including human beings. The genome sequence of the major swine pathogen Brachyspira hyodysenteriae was recently published, and this revealed extensive genome optimisation that leads to adaptation to the complex environment of the colon. The genome sequences of other pathogenic and non-pathogenic Brachyspira species are becoming available, and this data will help to reveal how these species have evolved and adapted to varied lifestyles in the large intestines of different species, and why some but not others can induce colitis and diarrhoea.

Quality of diabetes care in Dutch care groups: no differences between diabetes patients with and without co-morbidity

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Simone R de Bruin

2013-12-01

Full Text Available Objective: To evaluate the relationship between presence and nature of co-morbidity and quality of care for diabetes patients enrolled in diabetes disease management programmes provided by care groups.Methods: We performed an observational study within eight Dutch diabetes care groups. Data from patient record systems of care groups and patient questionnaires were used to determine quality of care. Quality of care was measured as provision of the recommended diabetes care, patients’ achievement of recommended clinical outcomes and patients’ perception of coordination and integration of care.Results: 527 diabetes patients without and 1187 diabetes patients with co-morbidity were included. Of the co-morbid patients, 7.8% had concordant co-morbid conditions only, 63.8% had discordant co-morbid diseases only and 28.4% had both types of conditions. Hardly any differences were observed between patients with and without co-morbidity in terms of provided care, achievement of clinical outcomes and perceived coordination and integration of care.Conclusions: Our study implies that care groups are able to provide similar quality of diabetes care for diabetes patients with and without co-morbidity. Considering the expected developments regarding additional disease management programmes in care groups, it is of importance to monitor quality of care, including patient experiences, for all chronic diseases. It will then become clear whether accountable provider-led organisations such as care groups are able to ensure quality of care for the increasing number of patients with multiple chronic conditions.

The possible evolution and future of CO2-concentrating mechanisms.

Science.gov (United States)

Raven, John A; Beardall, John; Sánchez-Baracaldo, Patricia

2017-06-01

CO2-concentrating mechanisms (CCMs), based either on active transport of inorganic carbon (biophysical CCMs) or on biochemistry involving supplementary carbon fixation into C4 acids (C4 and CAM), play a major role in global primary productivity. However, the ubiquitous CO2-fixing enzyme in autotrophs, Rubisco, evolved at a time when atmospheric CO2 levels were very much higher than today and O2 was very low and, as CO2 and O2 approached (by no means monotonically), today's levels, at some time subsequently many organisms evolved a CCM that increased the supply of CO2 and decreased Rubisco oxygenase activity. Given that CO2 levels and other environmental factors have altered considerably between when autotrophs evolved and the present day, and are predicted to continue to change into the future, we here examine the drivers for, and possible timing of, evolution of CCMs. CCMs probably evolved when CO2 fell to 2-16 times the present atmospheric level, depending on Rubisco kinetics. We also assess the effects of other key environmental factors such as temperature and nutrient levels on CCM activity and examine the evidence for evolutionary changes in CCM activity and related cellular processes as well as limitations on continuity of CCMs through environmental variations. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Genomic sequence of 'Candidatus Liberibacter solanacearum' haplotype C and its comparison with haplotype A and B genomes.

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Jinhui Wang

Full Text Available Haplotypes A and B of 'Candidatus Liberibacter solanacearum' (CLso are associated with diseases of solanaceous plants, especially Zebra chip disease of potato, and haplotypes C, D and E are associated with symptoms on apiaceous plants. To date, one complete genome of haplotype B and two high quality draft genomes of haplotype A have been obtained for these unculturable bacteria using metagenomics from the psyllid vector Bactericera cockerelli. Here, we present the first genomic sequences obtained for the carrot-associated CLso. These two genomic sequences of haplotype C, FIN114 (1.24 Mbp and FIN111 (1.20 Mbp, were obtained from carrot psyllids (Trioza apicalis harboring CLso. Genomic comparisons between the haplotypes A, B and C revealed that the genome organization differs between these haplotypes, due to large inversions and other recombinations. Comparison of protein-coding genes indicated that the core genome of CLso consists of 885 ortholog groups, with the pan-genome consisting of 1327 ortholog groups. Twenty-seven ortholog groups are unique to CLso haplotype C, whilst 11 ortholog groups shared by the haplotypes A and B, are not found in the haplotype C. Some of these ortholog groups that are not part of the core genome may encode functions related to interactions with the different host plant and psyllid species.

A synergism between adaptive effects and evolvability drives whole genome duplication to fixation

OpenAIRE

Cuypers, Thomas D; Hogeweg, Paulien; Hogeweg, P.

2014-01-01

Whole genome duplication has shaped eukaryotic evolutionary history and has been associated with drastic environmental change and species radiation. While the most common fate of WGD duplicates is a return to single copy, retained duplicates have been found enriched for highly interacting genes. This pattern has been explained by a neutral process of subfunctionalization and more recently, dosage balance selection. However, much about the relationship between environmental change, WGD and ada...

A synergism between adaptive effects and evolvability drives whole genome duplication to fixation.

OpenAIRE

Thomas D Cuypers; Paulien Hogeweg

2014-01-01

Whole genome duplication has shaped eukaryotic evolutionary history and has been associated with drastic environmental change and species radiation. While the most common fate of WGD duplicates is a return to single copy, retained duplicates have been found enriched for highly interacting genes. This pattern has been explained by a neutral process of subfunctionalization and more recently, dosage balance selection. However, much about the relationship between environmental change, WGD and ada...

Qualitative Functional Decomposition Analysis of Evolved Neuromorphic Flight Controllers

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Sanjay K. Boddhu

2012-01-01

Full Text Available In the previous work, it was demonstrated that one can effectively employ CTRNN-EH (a neuromorphic variant of EH method methodology to evolve neuromorphic flight controllers for a flapping wing robot. This paper describes a novel frequency grouping-based analysis technique, developed to qualitatively decompose the evolved controllers into explainable functional control blocks. A summary of the previous work related to evolving flight controllers for two categories of the controller types, called autonomous and nonautonomous controllers, is provided, and the applicability of the newly developed decomposition analysis for both controller categories is demonstrated. Further, the paper concludes with appropriate discussion of ongoing work and implications for possible future work related to employing the CTRNN-EH methodology and the decomposition analysis techniques presented in this paper.

Perspectives of Integrative Cancer Genomics in Next Generation Sequencing Era

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So Mee Kwon

2012-06-01

Full Text Available The explosive development of genomics technologies including microarrays and next generation sequencing (NGS has provided comprehensive maps of cancer genomes, including the expression of mRNAs and microRNAs, DNA copy numbers, sequence variations, and epigenetic changes. These genome-wide profiles of the genetic aberrations could reveal the candidates for diagnostic and/or prognostic biomarkers as well as mechanistic insights into tumor development and progression. Recent efforts to establish the huge cancer genome compendium and integrative omics analyses, so-called "integromics", have extended our understanding on the cancer genome, showing its daunting complexity and heterogeneity. However, the challenges of the structured integration, sharing, and interpretation of the big omics data still remain to be resolved. Here, we review several issues raised in cancer omics data analysis, including NGS, focusing particularly on the study design and analysis strategies. This might be helpful to understand the current trends and strategies of the rapidly evolving cancer genomics research.

Influencing governance of a public-private partnership in plant genomics: The societal interface group as a new instrument for public involvement.

Science.gov (United States)

Hanssen, Lucien; Gremmen, Bart

2013-08-01

The Centre for BioSystems Genomics (CBSG) is a Dutch public-private partnership in plant genomics active in potato and tomato research and exploitation. Its Societal Interface Group (SIG) has been developed to inform its communication strategy and governance practice. This new instrument identifies and discusses early signals from society by bringing together people from different societal backgrounds with members of CBSG management. This interactive learning process facilitates the inclusion of public concerns and needs in scientific developments in the field of plant genomics, and simultaneously enables genomics scientists to search for more societal aims, meanings, and starting points for their research agenda. Analysis of the SIG sessions revealed that the input of public expertise is not threatening or irrational, but provides the opportunity to harness the creative potential of future users highly relevant for the development of societal practices in which plant genomics plays a role.

Evolved Gas Analyses of Sedimentary Materials in Gale Crater, Mars: Results of the Curiosity Rover's Sample Analysis at Mars (SAM) Instrument from Yellowknife Bay to the Stimson Formation

Science.gov (United States)

Sutter, B.; McAdam, A. C.; Rampe, E. B.; Ming, D. W.; Mahaffy, P. R.; Navarro-Gonzalez, R.; Stern, J. C.; Eigenbrode, J. L.; Archer, P. D.

2016-01-01

The Sample Analysis at Mars (SAM) instrument aboard the Mars Science Laboratory rover has analyzed 10 samples from Gale Crater. All SAM evolved gas analyses have yielded a multitude of volatiles (e.g, H2O, SO2, H2S, CO2, CO, NO, O2, HC1). The objectives of this work are to 1) Characterize the evolved H2O, SO2, CO2, and O2 gas traces of sediments analyzed by SAM through sol 1178, 2) Constrain sediment mineralogy/composition based on SAM evolved gas analysis (SAM-EGA), and 3) Discuss the implications of these results releative to understanding the geochemical history of Gale Crater.

Co-residence patterns in hunter-gatherer societies show unique human social structure.

Science.gov (United States)

Hill, Kim R; Walker, Robert S; Bozicević, Miran; Eder, James; Headland, Thomas; Hewlett, Barry; Hurtado, A Magdalena; Marlowe, Frank; Wiessner, Polly; Wood, Brian

2011-03-11

Contemporary humans exhibit spectacular biological success derived from cumulative culture and cooperation. The origins of these traits may be related to our ancestral group structure. Because humans lived as foragers for 95% of our species' history, we analyzed co-residence patterns among 32 present-day foraging societies (total n = 5067 individuals, mean experienced band size = 28.2 adults). We found that hunter-gatherers display a unique social structure where (i) either sex may disperse or remain in their natal group, (ii) adult brothers and sisters often co-reside, and (iii) most individuals in residential groups are genetically unrelated. These patterns produce large interaction networks of unrelated adults and suggest that inclusive fitness cannot explain extensive cooperation in hunter-gatherer bands. However, large social networks may help to explain why humans evolved capacities for social learning that resulted in cumulative culture.

Codon based co-occurrence network motifs in human mitochondria

Directory of Open Access Journals (Sweden)

Pramod Shinde

2017-10-01

Full Text Available The nucleotide polymorphism in human mitochondrial genome (mtDNA tolled by codon position bias plays an indispensable role in human population dispersion and expansion. Herein, we constructed genome-wide nucleotide co-occurrence networks using a massive data consisting of five different geographical regions and around 3000 samples for each region. We developed a powerful network model to describe complex mitochondrial evolutionary patterns between codon and non-codon positions. It was interesting to report a different evolution of Asian genomes than those of the rest which is divulged by network motifs. We found evidence that mtDNA undergoes substantial amounts of adaptive evolution, a finding which was supported by a number of previous studies. The dominance of higher order motifs indicated the importance of long-range nucleotide co-occurrence in genomic diversity. Most notably, codon motifs apparently underpinned the preferences among codon positions for co-evolution which is probably highly biased during the origin of the genetic code. Our analyses manifested that codon position co-evolution is very well conserved across human sub-populations and independently maintained within human sub-populations implying the selective role of evolutionary processes on codon position co-evolution. Ergo, this study provided a framework to investigate cooperative genomic interactions which are critical in underlying complex mitochondrial evolution.

Fat: an evolving issue

Directory of Open Access Journals (Sweden)

John R. Speakman

2012-09-01

Work on obesity is evolving, and obesity is a consequence of our evolutionary history. In the space of 50 years, we have become an obese species. The reasons why can be addressed at a number of different levels. These include separating between whether the primary cause lies on the food intake or energy expenditure side of the energy balance equation, and determining how genetic and environmental effects contribute to weight variation between individuals. Opinion on whether increased food intake or decreased energy expenditure drives the obesity epidemic is still divided, but recent evidence favours the idea that food intake, rather than altered expenditure, is most important. There is more of a consensus that genetics explains most (probably around 65% of weight variation between individuals. Recent advances in genome-wide association studies have identified many polymorphisms that are linked to obesity, yet much of the genetic variance remains unexplained. Finding the causes of this unexplained variation will be an impetus of genetic and epigenetic research on obesity over the next decade. Many environmental factors – including gut microbiota, stress and endocrine disruptors – have been linked to the risk of developing obesity. A better understanding of gene-by-environment interactions will also be key to understanding obesity in the years to come.

Evolving a photosynthetic organelle

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Nakayama Takuro

2012-04-01

Full Text Available Abstract The evolution of plastids from cyanobacteria is believed to represent a singularity in the history of life. The enigmatic amoeba Paulinella and its 'recently' acquired photosynthetic inclusions provide a fascinating system through which to gain fresh insight into how endosymbionts become organelles. The plastids, or chloroplasts, of algae and plants evolved from cyanobacteria by endosymbiosis. This landmark event conferred on eukaryotes the benefits of photosynthesis - the conversion of solar energy into chemical energy - and in so doing had a huge impact on the course of evolution and the climate of Earth 1. From the present state of plastids, however, it is difficult to trace the evolutionary steps involved in this momentous development, because all modern-day plastids have fully integrated into their hosts. Paulinella chromatophora is a unicellular eukaryote that bears photosynthetic entities called chromatophores that are derived from cyanobacteria and has thus received much attention as a possible example of an organism in the early stages of organellogenesis. Recent studies have unlocked the genomic secrets of its chromatophore 23 and provided concrete evidence that the Paulinella chromatophore is a bona fide photosynthetic organelle 4. The question is how Paulinella can help us to understand the process by which an endosymbiont is converted into an organelle.

Evolving a photosynthetic organelle.

Science.gov (United States)

Nakayama, Takuro; Archibald, John M

2012-04-24

The evolution of plastids from cyanobacteria is believed to represent a singularity in the history of life. The enigmatic amoeba Paulinella and its 'recently' acquired photosynthetic inclusions provide a fascinating system through which to gain fresh insight into how endosymbionts become organelles.The plastids, or chloroplasts, of algae and plants evolved from cyanobacteria by endosymbiosis. This landmark event conferred on eukaryotes the benefits of photosynthesis--the conversion of solar energy into chemical energy--and in so doing had a huge impact on the course of evolution and the climate of Earth 1. From the present state of plastids, however, it is difficult to trace the evolutionary steps involved in this momentous development, because all modern-day plastids have fully integrated into their hosts. Paulinella chromatophora is a unicellular eukaryote that bears photosynthetic entities called chromatophores that are derived from cyanobacteria and has thus received much attention as a possible example of an organism in the early stages of organellogenesis. Recent studies have unlocked the genomic secrets of its chromatophore 23 and provided concrete evidence that the Paulinella chromatophore is a bona fide photosynthetic organelle 4. The question is how Paulinella can help us to understand the process by which an endosymbiont is converted into an organelle.

Whole genome sequencing in clinical and public health microbiology.

Science.gov (United States)

Kwong, J C; McCallum, N; Sintchenko, V; Howden, B P

2015-04-01

Genomics and whole genome sequencing (WGS) have the capacity to greatly enhance knowledge and understanding of infectious diseases and clinical microbiology.The growth and availability of bench-top WGS analysers has facilitated the feasibility of genomics in clinical and public health microbiology.Given current resource and infrastructure limitations, WGS is most applicable to use in public health laboratories, reference laboratories, and hospital infection control-affiliated laboratories.As WGS represents the pinnacle for strain characterisation and epidemiological analyses, it is likely to replace traditional typing methods, resistance gene detection and other sequence-based investigations (e.g., 16S rDNA PCR) in the near future.Although genomic technologies are rapidly evolving, widespread implementation in clinical and public health microbiology laboratories is limited by the need for effective semi-automated pipelines, standardised quality control and data interpretation, bioinformatics expertise, and infrastructure.

The draft genome of a termite illuminates alternative social organization

Science.gov (United States)

Termites have substantial economic and ecological impact worldwide. They are also the oldest organisms living in complex societies, having evolved a caste system independent of that of eusocial Hymenoptera (ants, bees and wasps). Here we provide the first genome sequence for a termite, Zootermopsis ...

Learning to live together: mutualism between self-splicing introns and their hosts

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Chalamcharla Venkata R

2011-04-01

Full Text Available Abstract Group I and II introns can be considered as molecular parasites that interrupt protein-coding and structural RNA genes in all domains of life. They function as self-splicing ribozymes and thereby limit the phenotypic costs associated with disruption of a host gene while they act as mobile DNA elements to promote their spread within and between genomes. Once considered purely selfish DNA elements, they now seem, in the light of recent work on the molecular mechanisms regulating bacterial and phage group I and II intron dynamics, to show evidence of co-evolution with their hosts. These previously underappreciated relationships serve the co-evolving entities particularly well in times of environmental stress.

Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits

Science.gov (United States)

2011-01-01

Background Cyanobacteria belong to an ancient group of photosynthetic prokaryotes with pronounced variations in their cellular differentiation strategies, physiological capacities and choice of habitat. Sequencing efforts have shown that genomes within this phylum are equally diverse in terms of size and protein-coding capacity. To increase our understanding of genomic changes in the lineage, the genomes of 58 contemporary cyanobacteria were analysed for shared and unique orthologs. Results A total of 404 protein families, present in all cyanobacterial genomes, were identified. Two of these are unique to the phylum, corresponding to an AbrB family transcriptional regulator and a gene that escapes functional annotation although its genomic neighbourhood is conserved among the organisms examined. The evolution of cyanobacterial genome sizes involves a mix of gains and losses in the clade encompassing complex cyanobacteria, while a single event of reduction is evident in a clade dominated by unicellular cyanobacteria. Genome sizes and gene family copy numbers evolve at a higher rate in the former clade, and multi-copy genes were predominant in large genomes. Orthologs unique to cyanobacteria exhibiting specific characteristics, such as filament formation, heterocyst differentiation, diazotrophy and symbiotic competence, were also identified. An ancestral character reconstruction suggests that the most recent common ancestor of cyanobacteria had a genome size of approx. 4.5 Mbp and 1678 to 3291 protein-coding genes, 4%-6% of which are unique to cyanobacteria today. Conclusions The different rates of genome-size evolution and multi-copy gene abundance suggest two routes of genome development in the history of cyanobacteria. The expansion strategy is driven by gene-family enlargment and generates a broad adaptive potential; while the genome streamlining strategy imposes adaptations to highly specific niches, also reflected in their different functional capacities. A few

Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits

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Nylander Johan AA

2011-06-01

Full Text Available Abstract Background Cyanobacteria belong to an ancient group of photosynthetic prokaryotes with pronounced variations in their cellular differentiation strategies, physiological capacities and choice of habitat. Sequencing efforts have shown that genomes within this phylum are equally diverse in terms of size and protein-coding capacity. To increase our understanding of genomic changes in the lineage, the genomes of 58 contemporary cyanobacteria were analysed for shared and unique orthologs. Results A total of 404 protein families, present in all cyanobacterial genomes, were identified. Two of these are unique to the phylum, corresponding to an AbrB family transcriptional regulator and a gene that escapes functional annotation although its genomic neighbourhood is conserved among the organisms examined. The evolution of cyanobacterial genome sizes involves a mix of gains and losses in the clade encompassing complex cyanobacteria, while a single event of reduction is evident in a clade dominated by unicellular cyanobacteria. Genome sizes and gene family copy numbers evolve at a higher rate in the former clade, and multi-copy genes were predominant in large genomes. Orthologs unique to cyanobacteria exhibiting specific characteristics, such as filament formation, heterocyst differentiation, diazotrophy and symbiotic competence, were also identified. An ancestral character reconstruction suggests that the most recent common ancestor of cyanobacteria had a genome size of approx. 4.5 Mbp and 1678 to 3291 protein-coding genes, 4%-6% of which are unique to cyanobacteria today. Conclusions The different rates of genome-size evolution and multi-copy gene abundance suggest two routes of genome development in the history of cyanobacteria. The expansion strategy is driven by gene-family enlargment and generates a broad adaptive potential; while the genome streamlining strategy imposes adaptations to highly specific niches, also reflected in their different

Genomic taxonomy of vibrios

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Iida Tetsuya

2009-10-01

Full Text Available Abstract Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA, supertrees, Average Amino Acid Identity (AAI, genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.. A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in

Cephalopod genomics

DEFF Research Database (Denmark)

Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

2012-01-01

The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

Comparing Mycobacterium tuberculosis genomes using genome topology networks.

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Jiang, Jianping; Gu, Jianlei; Zhang, Liang; Zhang, Chenyi; Deng, Xiao; Dou, Tonghai; Zhao, Guoping; Zhou, Yan

2015-02-14

Over the last decade, emerging research methods, such as comparative genomic analysis and phylogenetic study, have yielded new insights into genotypes and phenotypes of closely related bacterial strains. Several findings have revealed that genomic structural variations (SVs), including gene gain/loss, gene duplication and genome rearrangement, can lead to different phenotypes among strains, and an investigation of genes affected by SVs may extend our knowledge of the relationships between SVs and phenotypes in microbes, especially in pathogenic bacteria. In this work, we introduce a 'Genome Topology Network' (GTN) method based on gene homology and gene locations to analyze genomic SVs and perform phylogenetic analysis. Furthermore, the concept of 'unfixed ortholog' has been proposed, whose members are affected by SVs in genome topology among close species. To improve the precision of 'unfixed ortholog' recognition, a strategy to detect annotation differences and complete gene annotation was applied. To assess the GTN method, a set of thirteen complete M. tuberculosis genomes was analyzed as a case study. GTNs with two different gene homology-assigning methods were built, the Clusters of Orthologous Groups (COG) method and the orthoMCL clustering method, and two phylogenetic trees were constructed accordingly, which may provide additional insights into whole genome-based phylogenetic analysis. We obtained 24 unfixable COG groups, of which most members were related to immunogenicity and drug resistance, such as PPE-repeat proteins (COG5651) and transcriptional regulator TetR gene family members (COG1309). The GTN method has been implemented in PERL and released on our website. The tool can be downloaded from http://homepage.fudan.edu.cn/zhouyan/gtn/ , and allows re-annotating the 'lost' genes among closely related genomes, analyzing genes affected by SVs, and performing phylogenetic analysis. With this tool, many immunogenic-related and drug resistance-related genes

Detection of Hepatitis B Virus (HBV) Genomes and HBV Drug Resistant Variants by Deep Sequencing Analysis of HBV Genomes in Immune Cell Subsets of HBV Mono-Infected and/or Human Immunodeficiency Virus Type-1 (HIV-1) and HBV Co-Infected Individuals

Science.gov (United States)

Lee, Z.; Nishikawa, S.; Gao, S.; Eksteen, J. B.; Czub, M.; Gill, M. J.; Osiowy, C.; van der Meer, F.; van Marle, G.; Coffin, C. S.

2015-01-01

The hepatitis B virus (HBV) and the human immunodeficiency virus type 1 (HIV-1) can infect cells of the lymphatic system. It is unknown whether HIV-1 co-infection impacts infection of peripheral blood mononuclear cell (PBMC) subsets by the HBV. Aims To compare the detection of HBV genomes and HBV sequences in unsorted PBMCs and subsets (i.e., CD4+ T, CD8+ T, CD14+ monocytes, CD19+ B, CD56+ NK cells) in HBV mono-infected vs. HBV/HIV-1 co-infected individuals. Methods Total PBMC and subsets isolated from 14 HBV mono-infected (4/14 before and after anti-HBV therapy) and 6 HBV/HIV-1 co-infected individuals (5/6 consistently on dual active anti-HBV/HIV therapy) were tested for HBV genomes, including replication indicative HBV covalently closed circular (ccc)-DNA, by nested PCR/nucleic hybridization and/or quantitative PCR. In CD4+, and/or CD56+ subsets from two HBV monoinfected cases, the HBV polymerase/overlapping surface region was analyzed by next generation sequencing. Results All analyzed whole PBMC from HBV monoinfected and HBV/HIV coinfected individuals were HBV genome positive. Similarly, HBV DNA was detected in all target PBMC subsets regardless of antiviral therapy, but was absent from the CD4+ T cell subset from all HBV/HIV-1 positive cases (PHBV monoinfected cases on tenofovir therapy, mutations at residues associated with drug resistance and/or immune escape (i.e., G145R) were detected in a minor percentage of the population. Summary HBV genomes and drug resistant variants were detectable in PBMC subsets from HBV mono-infected individuals. The HBV replicates in PBMC subsets of HBV/HIV-1 patients except the CD4+ T cell subpopulation. PMID:26390290

Extremely Low Genomic Diversity of Rickettsia japonica Distributed in Japan.

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Akter, Arzuba; Ooka, Tadasuke; Gotoh, Yasuhiro; Yamamoto, Seigo; Fujita, Hiromi; Terasoma, Fumio; Kida, Kouji; Taira, Masakatsu; Nakadouzono, Fumiko; Gokuden, Mutsuyo; Hirano, Manabu; Miyashiro, Mamoru; Inari, Kouichi; Shimazu, Yukie; Tabara, Kenji; Toyoda, Atsushi; Yoshimura, Dai; Itoh, Takehiko; Kitano, Tomokazu; Sato, Mitsuhiko P; Katsura, Keisuke; Mondal, Shakhinur Islam; Ogura, Yoshitoshi; Ando, Shuji; Hayashi, Tetsuya

2017-01-01

Rickettsiae are obligate intracellular bacteria that have small genomes as a result of reductive evolution. Many Rickettsia species of the spotted fever group (SFG) cause tick-borne diseases known as "spotted fevers". The life cycle of SFG rickettsiae is closely associated with that of the tick, which is generally thought to act as a bacterial vector and reservoir that maintains the bacterium through transstadial and transovarial transmission. Each SFG member is thought to have adapted to a specific tick species, thus restricting the bacterial distribution to a relatively limited geographic region. These unique features of SFG rickettsiae allow investigation of how the genomes of such biologically and ecologically specialized bacteria evolve after genome reduction and the types of population structures that are generated. Here, we performed a nationwide, high-resolution phylogenetic analysis of Rickettsia japonica, an etiological agent of Japanese spotted fever that is distributed in Japan and Korea. The comparison of complete or nearly complete sequences obtained from 31 R. japonica strains isolated from various sources in Japan over the past 30 years demonstrated an extremely low level of genomic diversity. In particular, only 34 single nucleotide polymorphisms were identified among the 27 strains of the major lineage containing all clinical isolates and tick isolates from the three tick species. Our data provide novel insights into the biology and genome evolution of R. japonica, including the possibilities of recent clonal expansion and a long generation time in nature due to the long dormant phase associated with tick life cycles. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Understanding Cancer Genome and Its Evolution by Next Generation Sequencing

DEFF Research Database (Denmark)

Hou, Yong

Cancer will cause 13 million deaths by the year of 2030, ranking the second leading cause of death worldwide. Previous studies indicate that most of the cancers originate from cells that acquired somatic mutations and evolved as Darwin Theory. Ten biological insights of cancer have been summarized...... recently. Cutting-age technologies like next generation sequencing (NGS) enable exploring cancer genome and evolution much more efficiently. However, integrated cancer genome sequencing studies showed great inter-/intra-tumoral heterogeneity (ITH) and complex evolution patterns beyond the cancer biological...... knowledge we previously know. There is very limited knowledge of East Asia lung cancer genome except enrichment of EGFR mutations and lack of KRAS mutations. We carried out integrated genomic, transcriptomic and methylomic analysis of 335 primary Chinese lung adenocarcinomas (LUAD) and 35 corresponding...

Comparative Genomics of Green Sulfur Bacteria

DEFF Research Database (Denmark)

Ussery, David; Davenport, C; Tümmler, B

2010-01-01

Eleven completely sequenced Chlorobi genomes were compared in oligonucleotide usage, gene contents, and synteny. The green sulfur bacteria (GSB) are equipped with a core genome that sustains their anoxygenic phototrophic lifestyle by photosynthesis, sulfur oxidation, and CO(2) fixation. Whole...... weight of 10(6), and are probably instrumental for the bacteria to generate their own intimate (micro)environment....

SOLiD™ sequencing of genomes of clinical isolates of Leishmania donovani from India confirm leptomonas co-infection and raise some key questions.

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Neeloo Singh

Full Text Available BACKGROUND: Known as 'neglected disease' because relatively little effort has been applied to finding cures, leishmaniasis kills more than 150,000 people every year and debilitates millions more. Visceral leishmaniasis (VL, also called Kala Azar (KA or black fever in India, claims around 20,000 lives every year. Whole genome analysis presents an excellent means to identify new targets for drugs, vaccine and diagnostics development, and also provide an avenue into the biological basis of parasite virulence in the L. donovani complex prevalent in India. METHODOLOGY/PRINCIPAL FINDINGS: In our presently described study, the next generation SOLiD™ platform was successfully utilized for the first time to carry out whole genome sequencing of L. donovani clinical isolates from India. We report the exceptional occurrence of insect trypanosomatids in clinical cases of visceral leishmaniasis (Kala Azar patients in India. We confirm with whole genome sequencing analysis data that isolates which were sequenced from Kala Azar (visceral leishmaniasis cases were genetically related to Leptomonas. The co-infection in splenic aspirate of these patients with a species of Leptomonas and how likely is it that the infection might be pathogenic, are key questions which need to be investigated. We discuss our results in the context of some important probable hypothesis in this article. CONCLUSIONS/SIGNIFICANCE: Our intriguing results of unusual cases of Kala Azar found to be most similar to Leptomonas species put forth important clinical implications for the treatment of Kala Azar in India. Leptomonas have been shown to be highly susceptible to several standard leishmaniacides in vitro. There is very little divergence among these two species viz. Leishmania sp. and L. seymouri, in terms of genomic sequence and organization. A more extensive perception of the phenomenon of co-infection needs to be addressed from molecular pathogenesis and eco

Primordial soup or vinaigrette: did the RNA world evolve at acidic pH?

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Bernhardt Harold S

2012-01-01

Full Text Available Abstract Background The RNA world concept has wide, though certainly not unanimous, support within the origin-of-life scientific community. One view is that life may have emerged as early as the Hadean Eon 4.3-3.8 billion years ago with an atmosphere of high CO2 producing an acidic ocean of the order of pH 3.5-6. Compatible with this scenario is the intriguing proposal that life arose within alkaline (pH 9-11 deep-sea hydrothermal vents like those of the 'Lost City', with the interface with the acidic ocean creating a proton gradient sufficient to drive the first metabolism. However, RNA is most stable at pH 4-5 and is unstable at alkaline pH, raising the possibility that RNA may have first arisen in the acidic ocean itself (possibly near an acidic hydrothermal vent, acidic volcanic lake or comet pond. As the Hadean Eon progressed, the ocean pH is inferred to have gradually risen to near neutral as atmospheric CO2 levels decreased. Presentation of the hypothesis We propose that RNA is well suited for a world evolving at acidic pH. This is supported by the enhanced stability at acidic pH of not only the RNA phosphodiester bond but also of the aminoacyl-(tRNA and peptide bonds. Examples of in vitro-selected ribozymes with activities at acid pH have recently been documented. The subsequent transition to a DNA genome could have been partly driven by the gradual rise in ocean pH, since DNA has greater stability than RNA at alkaline pH, but not at acidic pH. Testing the hypothesis We have proposed mechanisms for two key RNA world activities that are compatible with an acidic milieu: (i non-enzymatic RNA replication of a hemi-protonated cytosine-rich oligonucleotide, and (ii specific aminoacylation of tRNA/hairpins through triple helix interactions between the helical aminoacyl stem and a single-stranded aminoacylating ribozyme. Implications of the hypothesis Our hypothesis casts doubt on the hypothesis that RNA evolved in the vicinity of alkaline

Effects of racial and ethnic group and health literacy on responses to genomic risk information in a medically underserved population.

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Kaphingst, Kimberly A; Stafford, Jewel D; McGowan, Lucy D'Agostino; Seo, Joann; Lachance, Christina R; Goodman, Melody S

2015-02-01

Few studies have examined how individuals respond to genomic risk information for common, chronic diseases. This randomized study examined differences in responses by type of genomic information (genetic test/family history) and disease condition (diabetes/heart disease), and by race/ethnicity in a medically underserved population. 1,057 English-speaking adults completed a survey containing 1 of 4 vignettes (2-by-2 randomized design). Differences in dependent variables (i.e., interest in receiving genomic assessment, discussing with doctor or family, changing health habits) by experimental condition and race/ethnicity were examined using chi-squared tests and multivariable regression analysis. No significant differences were found in dependent variables by type of genomic information or disease condition. In multivariable models, Hispanics were more interested in receiving a genomic assessment than Whites (OR = 1.93; p literacy had greater interest than those with adequate health literacy. Blacks (OR = 1.78; p = .001) and Hispanics (OR = 1.85; p = .001) had greater interest in discussing information with family than Whites. Non-Hispanic Blacks (OR = 1.45; p = .04) had greater interest in discussing genomic information with a doctor than Whites. Blacks (β = -0.41; p literacy was negatively associated with number of health habits participants intended to change. Findings suggest that race/ethnicity may affect responses to genomic risk information. Additional research could examine how cognitive representations of this information differ across racial/ethnic groups. Health literacy is also critical to consider in developing approaches to communicating genomic information.

From hacking the human genome to editing organs.

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Tobita, Takamasa; Guzman-Lepe, Jorge; Collin de l'Hortet, Alexandra

2015-01-01

In the recent decades, human genome engineering has been one of the major interesting research subjects, essentially because it raises new possibilities for personalized medicine and biotechnologies. With the development of engineered nucleases such as the Zinc Finger Nucleases (ZFNs), the Transcription activator-like effector nucleases (TALENs) and more recently the Clustered Regularly Interspaced short Palindromic Repeats (CRISPR), the field of human genome edition has evolved very rapidly. Every new genetic tool is broadening the scope of applications on human tissues, even before we can completely master each of these tools. In this review, we will present the recent advances regarding human genome edition tools, we will discuss the numerous implications they have in research and medicine, and we will mention the limits and concerns about such technologies.

Genomic resources for multiple species in the Drosophila ananassae species group.

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Signor, Sarah; Seher, Thaddeus; Kopp, Artyom

2013-01-01

The development of genomic resources in non-model taxa is essential for understanding the genetic basis of biological diversity. Although the genomes of many Drosophila species have been sequenced, most of the phenotypic diversity in this genus remains to be explored. To facilitate the genetic analysis of interspecific and intraspecific variation, we have generated new genomic resources for seven species and subspecies in the D. ananassae species subgroup. We have generated large amounts of transcriptome sequence data for D. ercepeae, D. merina, D. bipectinata, D. malerkotliana malerkotliana, D. m. pallens, D. pseudoananassae pseudoananassae, and D. p. nigrens. de novo assembly resulted in contigs covering more than half of the predicted transcriptome and matching an average of 59% of annotated genes in the complete genome of D. ananassae. Most contigs, corresponding to an average of 49% of D. ananassae genes, contain sequence polymorphisms that can be used as genetic markers. Subsets of these markers were validated by genotyping the progeny of inter- and intraspecific crosses. The ananassae subgroup is an excellent model system for examining the molecular basis of speciation and phenotypic evolution. The new genomic resources will facilitate the genetic analysis of inter- and intraspecific differences in this lineage. Transcriptome sequencing provides a simple and cost-effective way to identify molecular markers at nearly single-gene density, and is equally applicable to any non-model taxa.

A genomic comparison of two termites with different social complexity

DEFF Research Database (Denmark)

Korb, Judith; Thomas-Poulsen, Michael; Hu, Haofu

2015-01-01

large and complex societies with morphologically distinct castes that are life-time sterile. Here we compare key characteristics of genomic architecture, focusing on genes involved in communication, immune defenses, mating biology and symbiosis that were likely important in termite social evolution. We......The termites evolved eusociality and complex societies before the ants, but have been studied much less. The recent publication of the first two termite genomes provides a unique comparative opportunity, particularly because the sequenced termites represent opposite ends of the social complexity...

Estimating phylogenetic trees from genome-scale data.

Science.gov (United States)

Liu, Liang; Xi, Zhenxiang; Wu, Shaoyuan; Davis, Charles C; Edwards, Scott V

2015-12-01

The heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. Phylogenetic methods known as "species tree" methods have been proposed to directly address one important source of gene tree heterogeneity, namely the incomplete lineage sorting that occurs when evolving lineages radiate rapidly, resulting in a diversity of gene trees from a single underlying species tree. Here we review theory and empirical examples that help clarify conflicts between species tree and concatenation methods, and misconceptions in the literature about the performance of species tree methods. Considering concatenation as a special case of the multispecies coalescent model helps explain differences in the behavior of the two methods on phylogenomic data sets. Recent work suggests that species tree methods are more robust than concatenation approaches to some of the classic challenges of phylogenetic analysis, including rapidly evolving sites in DNA sequences and long-branch attraction. We show that approaches, such as binning, designed to augment the signal in species tree analyses can distort the distribution of gene trees and are inconsistent. Computationally efficient species tree methods incorporating biological realism are a key to phylogenetic analysis of whole-genome data. © 2015 New York Academy of Sciences.

Robustness to Faults Promotes Evolvability: Insights from Evolving Digital Circuits.

Science.gov (United States)

Milano, Nicola; Nolfi, Stefano

2016-01-01

We demonstrate how the need to cope with operational faults enables evolving circuits to find more fit solutions. The analysis of the results obtained in different experimental conditions indicates that, in absence of faults, evolution tends to select circuits that are small and have low phenotypic variability and evolvability. The need to face operation faults, instead, drives evolution toward the selection of larger circuits that are truly robust with respect to genetic variations and that have a greater level of phenotypic variability and evolvability. Overall our results indicate that the need to cope with operation faults leads to the selection of circuits that have a greater probability to generate better circuits as a result of genetic variation with respect to a control condition in which circuits are not subjected to faults.

Genomic sovereignty and the African promise: mining the African genome for the benefit of Africa.

Science.gov (United States)

de Vries, Jantina; Pepper, Michael

2012-08-01

Scientific interest in genomics in Africa is on the rise with a number of funding initiatives aimed specifically at supporting research in this area. Genomics research on material of African origin raises a number of important ethical issues. A prominent concern relates to sample export, which is increasingly seen by researchers and ethics committees across the continent as being problematic. The concept of genomic sovereignty proposes that unique patterns of genomic variation can be found in human populations, and that these are commercially, scientifically or symbolically valuable and in need of protection against exploitation. Although it is appealing as a response to increasing concerns regarding sample export, there are a number of important conceptual problems relating to the term. It is not clear, for instance, whether it is appropriate that ownership over human genomic samples should rest with national governments. Furthermore, ethnic groups in Africa are frequently spread across multiple nation states, and protection offered in one state may not prevent researchers from accessing the same group elsewhere. Lastly, scientific evidence suggests that the assumption that genomic data is unique for population groups is false. Although the frequency with which particular variants are found can differ between groups, such genes or variants per se are not unique to any population group. In this paper, the authors describe these concerns in detail and argue that the concept of genomic sovereignty alone may not be adequate to protect the genetic resources of people of African descent.

Deep ancestry of programmed genome rearrangement in lampreys.

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Timoshevskiy, Vladimir A; Lampman, Ralph T; Hess, Jon E; Porter, Laurie L; Smith, Jeramiah J

2017-09-01

In most multicellular organisms, the structure and content of the genome is rigorously maintained over the course of development. However some species have evolved genome biologies that permit, or require, developmentally regulated changes in the physical structure and content of the genome (programmed genome rearrangement: PGR). Relatively few vertebrates are known to undergo PGR, although all agnathans surveyed to date (several hagfish and one lamprey: Petromyzon marinus) show evidence of large scale PGR. To further resolve the ancestry of PGR within vertebrates, we developed probes that allow simultaneous tracking of nearly all sequences eliminated by PGR in P. marinus and a second lamprey species (Entosphenus tridentatus). These comparative analyses reveal conserved subcellular structures (lagging chromatin and micronuclei) associated with PGR and provide the first comparative embryological evidence in support of the idea that PGR represents an ancient and evolutionarily stable strategy for regulating inherent developmental/genetic conflicts between germline and soma. Copyright © 2017 Elsevier Inc. All rights reserved.

Endogenous retroviruses of sheep: a model system for understanding physiological adaptation to an evolving ruminant genome.

Science.gov (United States)

Spencer, Thomas E; Palmarini, Massimo

2012-01-01

Endogenous retroviruses (ERVs) are present in the genome of all vertebrates and are remnants of ancient exogenous retroviral infections of the host germline transmitted vertically from generation to generation. Sheep betaretroviruses offer a unique model system to study the complex interaction between retroviruses and their host. The sheep genome contains 27 endogenous betaretroviruses (enJSRVs) related to the exogenous and pathogenic Jaagsiekte sheep retrovirus (JSRV), the causative agent of a transmissible lung cancer in sheep. The enJSRVs can protect their host against JSRV infection by blocking early and late steps of the JSRV replication cycle. In the female reproductive tract, enJSRVs are specifically expressed in the uterine luminal and glandular epithelia as well as in the conceptus (embryo and associated extraembryonic membranes) trophectoderm and in utero loss-of-function experiments found the enJSRVs envelope (env) to be essential for conceptus elongation and trophectoderm growth and development. Collectively, available evidence in sheep and other mammals indicate that ERVs coevolved with their hosts for millions of years and were positively selected for biological roles in genome plasticity and evolution, protection of the host against infection of related pathogenic and exogenous retroviruses, and placental development.

Heritage – A Conceptually Evolving and Dissonant Phenomenon ...

African Journals Online (AJOL)

I therefore, drawing from literature and experiences gained during field observations and focus group interviews, came up with the idea of working with three viewpoints of heritage. Drawing on real life cases I argue that current heritage management and education practices' failure to recognise and respect the evolving, ...

The Sequenced Angiosperm Genomes and Genome Databases.

Science.gov (United States)

Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

2018-01-01

Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

The evolutionary value of recombination is constrained by genome modularity.

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Darren P Martin

2005-10-01

Full Text Available Genetic recombination is a fundamental evolutionary mechanism promoting biological adaptation. Using engineered recombinants of the small single-stranded DNA plant virus, Maize streak virus (MSV, we experimentally demonstrate that fragments of genetic material only function optimally if they reside within genomes similar to those in which they evolved. The degree of similarity necessary for optimal functionality is correlated with the complexity of intragenomic interaction networks within which genome fragments must function. There is a striking correlation between our experimental results and the types of MSV recombinants that are detectable in nature, indicating that obligatory maintenance of intragenome interaction networks strongly constrains the evolutionary value of recombination for this virus and probably for genomes in general.

Predictions of Gene Family Distributions in Microbial Genomes: Evolution by Gene Duplication and Modification

International Nuclear Information System (INIS)

Yanai, Itai; Camacho, Carlos J.; DeLisi, Charles

2000-01-01

A universal property of microbial genomes is the considerable fraction of genes that are homologous to other genes within the same genome. The process by which these homologues are generated is not well understood, but sequence analysis of 20 microbial genomes unveils a recurrent distribution of gene family sizes. We show that a simple evolutionary model based on random gene duplication and point mutations fully accounts for these distributions and permits predictions for the number of gene families in genomes not yet complete. Our findings are consistent with the notion that a genome evolves from a set of precursor genes to a mature size by gene duplications and increasing modifications. (c) 2000 The American Physical Society

Predictions of Gene Family Distributions in Microbial Genomes: Evolution by Gene Duplication and Modification

Energy Technology Data Exchange (ETDEWEB)

Yanai, Itai; Camacho, Carlos J.; DeLisi, Charles

2000-09-18

A universal property of microbial genomes is the considerable fraction of genes that are homologous to other genes within the same genome. The process by which these homologues are generated is not well understood, but sequence analysis of 20 microbial genomes unveils a recurrent distribution of gene family sizes. We show that a simple evolutionary model based on random gene duplication and point mutations fully accounts for these distributions and permits predictions for the number of gene families in genomes not yet complete. Our findings are consistent with the notion that a genome evolves from a set of precursor genes to a mature size by gene duplications and increasing modifications. (c) 2000 The American Physical Society.

Preface: evolving rotifers, evolving science: Proceedings of the XIV International Rotifer Symposium

Czech Academy of Sciences Publication Activity Database

Devetter, Miloslav; Fontaneto, D.; Jersabek, Ch.D.; Welch, D.B.M.; May, L.; Walsh, E.J.

2017-01-01

Roč. 796, č. 1 (2017), s. 1-6 ISSN 0018-8158 Institutional support: RVO:60077344 Keywords : evolving rotifers * 14th International Rotifer Symposium * evolving science Subject RIV: EG - Zoology OBOR OECD: Zoology Impact factor: 2.056, year: 2016

Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation.

Science.gov (United States)

Simmons, Sheri L; Dibartolo, Genevieve; Denef, Vincent J; Goltsman, Daniela S Aliaga; Thelen, Michael P; Banfield, Jillian F

2008-07-22

Deeply sampled community genomic (metagenomic) datasets enable comprehensive analysis of heterogeneity in natural microbial populations. In this study, we used sequence data obtained from the dominant member of a low-diversity natural chemoautotrophic microbial community to determine how coexisting closely related individuals differ from each other in terms of gene sequence and gene content, and to uncover evidence of evolutionary processes that occur over short timescales. DNA sequence obtained from an acid mine drainage biofilm was reconstructed, taking into account the effects of strain variation, to generate a nearly complete genome tiling path for a Leptospirillum group II species closely related to L. ferriphilum (sampling depth approximately 20x). The population is dominated by one sequence type, yet we detected evidence for relatively abundant variants (>99.5% sequence identity to the dominant type) at multiple loci, and a few rare variants. Blocks of other Leptospirillum group II types ( approximately 94% sequence identity) have recombined into one or more variants. Variant blocks of both types are more numerous near the origin of replication. Heterogeneity in genetic potential within the population arises from localized variation in gene content, typically focused in integrated plasmid/phage-like regions. Some laterally transferred gene blocks encode physiologically important genes, including quorum-sensing genes of the LuxIR system. Overall, results suggest inter- and intrapopulation genetic exchange involving distinct parental genome types and implicate gain and loss of phage and plasmid genes in recent evolution of this Leptospirillum group II population. Population genetic analyses of single nucleotide polymorphisms indicate variation between closely related strains is not maintained by positive selection, suggesting that these regions do not represent adaptive differences between strains. Thus, the most likely explanation for the observed patterns of

Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation.

Directory of Open Access Journals (Sweden)

Sheri L Simmons

2008-07-01

Full Text Available Deeply sampled community genomic (metagenomic datasets enable comprehensive analysis of heterogeneity in natural microbial populations. In this study, we used sequence data obtained from the dominant member of a low-diversity natural chemoautotrophic microbial community to determine how coexisting closely related individuals differ from each other in terms of gene sequence and gene content, and to uncover evidence of evolutionary processes that occur over short timescales. DNA sequence obtained from an acid mine drainage biofilm was reconstructed, taking into account the effects of strain variation, to generate a nearly complete genome tiling path for a Leptospirillum group II species closely related to L. ferriphilum (sampling depth approximately 20x. The population is dominated by one sequence type, yet we detected evidence for relatively abundant variants (>99.5% sequence identity to the dominant type at multiple loci, and a few rare variants. Blocks of other Leptospirillum group II types ( approximately 94% sequence identity have recombined into one or more variants. Variant blocks of both types are more numerous near the origin of replication. Heterogeneity in genetic potential within the population arises from localized variation in gene content, typically focused in integrated plasmid/phage-like regions. Some laterally transferred gene blocks encode physiologically important genes, including quorum-sensing genes of the LuxIR system. Overall, results suggest inter- and intrapopulation genetic exchange involving distinct parental genome types and implicate gain and loss of phage and plasmid genes in recent evolution of this Leptospirillum group II population. Population genetic analyses of single nucleotide polymorphisms indicate variation between closely related strains is not maintained by positive selection, suggesting that these regions do not represent adaptive differences between strains. Thus, the most likely explanation for the

Genomic Analysis of the Emergence and Rapid Global Dissemination of the Clonal Group 258 Klebsiella pneumoniae Pandemic.

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Jolene R Bowers

Full Text Available Multidrug-resistant Klebsiella pneumoniae producing the KPC carbapenemase have rapidly spread throughout the world, causing severe healthcare-associated infections with limited antimicrobial treatment options. Dissemination of KPC-producing K. pneumoniae is largely attributed to expansion of a single dominant strain, ST258. In this study, we explore phylogenetic relationships and evolution within ST258 and its clonal group, CG258, using whole genome sequence analysis of 167 isolates from 20 countries collected over 17 years. Our results show a common ST258 ancestor emerged from its diverse parental clonal group around 1995 and likely acquired blaKPC prior to dissemination. Over the past two decades, ST258 has remained highly clonal despite diversity in accessory elements and divergence in the capsule polysaccharide synthesis locus. Apart from the large recombination event that gave rise to ST258, few mutations set it apart from its clonal group. However, one mutation occurs in a global transcription regulator. Characterization of outer membrane protein sequences revealed a profile in ST258 that includes a truncated OmpK35 and modified OmpK37. Our work illuminates potential genomic contributors to the pathogenic success of ST258, helps us better understand the global dissemination of this strain, and identifies genetic markers unique to ST258.

Accelerated proteomic visualization of individual predatory venoms of Conus purpurascens reveals separately evolved predation-evoked venom cabals.

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Himaya, S W A; Marí, Frank; Lewis, Richard J

2018-01-10

Cone snail venoms have separately evolved for predation and defense. Despite remarkable inter- and intra-species variability, defined sets of synergistic venom peptides (cabals) are considered essential for prey capture by cone snails. To better understand the role of predatory cabals in cone snails, we used a high-throughput proteomic data mining and visualisation approach. Using this approach, the relationship between the predatory venom peptides from nine C. purpurascens was systematically analysed. Surprisingly, potentially synergistic levels of κ-PVIIA and δ-PVIA were only identified in five of nine specimens. In contrast, the remaining four specimens lacked significant levels of these known excitotoxins and instead contained high levels of the muscle nAChR blockers ψ-PIIIE and αA-PIVA. Interestingly, one of nine specimens expressed both cabals, suggesting that these sub-groups might represent inter-breeding sub-species of C. purpurascens. High throughput cluster analysis also revealed these two cabals clustered with distinct groups of venom peptides that are presently uncharacterised. This is the first report showing that the cone snails of the same species can deploy two separate and distinct predatory cabals for prey capture and shows that the cabals deployed by this species can be more complex than presently realized. Our semi-automated proteomic analysis facilitates the deconvolution of complex venoms to identify co-evolved families of peptides and help unravel their evolutionary relationships in complex venoms.

Conservation, Divergence, and Genome-Wide Distribution of PAL and POX A Gene Families in Plants.

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Rawal, H C; Singh, N K; Sharma, T R

2013-01-01

Genome-wide identification and phylogenetic and syntenic comparison were performed for the genes responsible for phenylalanine ammonia lyase (PAL) and peroxidase A (POX A) enzymes in nine plant species representing very diverse groups like legumes (Glycine max and Medicago truncatula), fruits (Vitis vinifera), cereals (Sorghum bicolor, Zea mays, and Oryza sativa), trees (Populus trichocarpa), and model dicot (Arabidopsis thaliana) and monocot (Brachypodium distachyon) species. A total of 87 and 1045 genes in PAL and POX A gene families, respectively, have been identified in these species. The phylogenetic and syntenic comparison along with motif distributions shows a high degree of conservation of PAL genes, suggesting that these genes may predate monocot/eudicot divergence. The POX A family genes, present in clusters at the subtelomeric regions of chromosomes, might be evolving and expanding with higher rate than the PAL gene family. Our analysis showed that during the expansion of POX A gene family, many groups and subgroups have evolved, resulting in a high level of functional divergence among monocots and dicots. These results will act as a first step toward the understanding of monocot/eudicot evolution and functional characterization of these gene families in the future.

Conservation, Divergence, and Genome-Wide Distribution of PAL and POX A Gene Families in Plants

Directory of Open Access Journals (Sweden)

H. C. Rawal

2013-01-01

Full Text Available Genome-wide identification and phylogenetic and syntenic comparison were performed for the genes responsible for phenylalanine ammonia lyase (PAL and peroxidase A (POX A enzymes in nine plant species representing very diverse groups like legumes (Glycine max and Medicago truncatula, fruits (Vitis vinifera, cereals (Sorghum bicolor, Zea mays, and Oryza sativa, trees (Populus trichocarpa, and model dicot (Arabidopsis thaliana and monocot (Brachypodium distachyon species. A total of 87 and 1045 genes in PAL and POX A gene families, respectively, have been identified in these species. The phylogenetic and syntenic comparison along with motif distributions shows a high degree of conservation of PAL genes, suggesting that these genes may predate monocot/eudicot divergence. The POX A family genes, present in clusters at the subtelomeric regions of chromosomes, might be evolving and expanding with higher rate than the PAL gene family. Our analysis showed that during the expansion of POX A gene family, many groups and subgroups have evolved, resulting in a high level of functional divergence among monocots and dicots. These results will act as a first step toward the understanding of monocot/eudicot evolution and functional characterization of these gene families in the future.

Lack of evolvability in self-sustaining autocatalytic networks constraints metabolism-first scenarios for the origin of life.

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Vasas, Vera; Szathmáry, Eörs; Santos, Mauro

2010-01-26

A basic property of life is its capacity to experience Darwinian evolution. The replicator concept is at the core of genetics-first theories of the origin of life, which suggest that self-replicating oligonucleotides or their similar ancestors may have been the first "living" systems and may have led to the evolution of an RNA world. But problems with the nonenzymatic synthesis of biopolymers and the origin of template replication have spurred the alternative metabolism-first scenario, where self-reproducing and evolving proto-metabolic networks are assumed to have predated self-replicating genes. Recent theoretical work shows that "compositional genomes" (i.e., the counts of different molecular species in an assembly) are able to propagate compositional information and can provide a setup on which natural selection acts. Accordingly, if we stick to the notion of replicator as an entity that passes on its structure largely intact in successive replications, those macromolecular aggregates could be dubbed "ensemble replicators" (composomes) and quite different from the more familiar genes and memes. In sharp contrast with template-dependent replication dynamics, we demonstrate here that replication of compositional information is so inaccurate that fitter compositional genomes cannot be maintained by selection and, therefore, the system lacks evolvability (i.e., it cannot substantially depart from the asymptotic steady-state solution already built-in in the dynamical equations). We conclude that this fundamental limitation of ensemble replicators cautions against metabolism-first theories of the origin of life, although ancient metabolic systems could have provided a stable habitat within which polymer replicators later evolved.

A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group.

Science.gov (United States)

Singh, Reema; Schilde, Christina; Schaap, Pauline

2016-11-17

Dictyostelia are a well-studied group of organisms with colonial multicellularity, which are members of the mostly unicellular Amoebozoa. A phylogeny based on SSU rDNA data subdivided all Dictyostelia into four major groups, but left the position of the root and of six group-intermediate taxa unresolved. Recent phylogenies inferred from 30 or 213 proteins from sequenced genomes, positioned the root between two branches, each containing two major groups, but lacked data to position the group-intermediate taxa. Since the positions of these early diverging taxa are crucial for understanding the evolution of phenotypic complexity in Dictyostelia, we sequenced six representative genomes of early diverging taxa. We retrieved orthologs of 47 housekeeping proteins with an average size of 890 amino acids from six newly sequenced and eight published genomes of Dictyostelia and unicellular Amoebozoa and inferred phylogenies from single and concatenated protein sequence alignments. Concatenated alignments of all 47 proteins, and four out of five subsets of nine concatenated proteins all produced the same consensus phylogeny with 100% statistical support. Trees inferred from just two out of the 47 proteins, individually reproduced the consensus phylogeny, highlighting that single gene phylogenies will rarely reflect correct species relationships. However, sets of two or three concatenated proteins again reproduced the consensus phylogeny, indicating that a small selection of genes suffices for low cost classification of as yet unincorporated or newly discovered dictyostelid and amoebozoan taxa by gene amplification. The multi-locus consensus phylogeny shows that groups 1 and 2 are sister clades in branch I, with the group-intermediate taxon D. polycarpum positioned as outgroup to group 2. Branch II consists of groups 3 and 4, with the group-intermediate taxon Polysphondylium violaceum positioned as sister to group 4, and the group-intermediate taxon Dictyostelium polycephalum

Genomes of planktonic Acidimicrobiales: widening horizons for marine Actinobacteria by metagenomics.

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Mizuno, Carolina Megumi; Rodriguez-Valera, Francisco; Ghai, Rohit

2015-02-10

The genomes of four novel marine Actinobacteria have been assembled from large metagenomic data sets derived from the Mediterranean deep chlorophyll maximum (DCM). These are the first marine representatives belonging to the order Acidimicrobiales and only the second group of planktonic marine Actinobacteria to be described. Their streamlined genomes and photoheterotrophic lifestyle suggest that they are planktonic, free-living microbes. A novel rhodopsin clade, acidirhodopsins, related to freshwater actinorhodopsins, was found in these organisms. Their genomes suggest a capacity to assimilate C2 compounds, some using the glyoxylate bypass and others with the ethylmalonyl-coenzyme A (CoA) pathway. They are also able to derive energy from dimethylsulfopropionate (DMSP), sulfonate, and carbon monoxide oxidation, all commonly available in the marine habitat. These organisms appear to be prevalent in the deep photic zone at or around the DCM. The presence of sister clades to the marine Acidimicrobiales in freshwater aquatic habitats provides a new example of marine-freshwater transitions with potential evolutionary insights. Despite several studies showing the importance and abundance of planktonic Actinobacteria in the marine habitat, a representative genome was only recently described. In order to expand the genomic repertoire of marine Actinobacteria, we describe here the first Acidimicrobidae genomes of marine origin and provide insights about their ecology. They display metabolic versatility in the acquisition of carbon and appear capable of utilizing diverse sources of energy. One of the genomes harbors a new kind of rhodopsin related to the actinorhodopsin clade of freshwater origin that is widespread in the oceans. Our data also support their preference to inhabit the deep chlorophyll maximum and the deep photic zone. This work contributes to the perception of marine actinobacterial groups as important players in the marine environment with distinct and

Meiosis evolves: adaptation to external and internal environments.

Science.gov (United States)

Bomblies, Kirsten; Higgins, James D; Yant, Levi

2015-10-01

306 I. 306 II. 307 III. 312 IV. 317 V. 318 319 References 319 SUMMARY: Meiosis is essential for the fertility of most eukaryotes and its structures and progression are conserved across kingdoms. Yet many of its core proteins show evidence of rapid or adaptive evolution. What drives the evolution of meiosis proteins? How can constrained meiotic processes be modified in response to challenges without compromising their essential functions? In surveying the literature, we found evidence of two especially potent challenges to meiotic chromosome segregation that probably necessitate adaptive evolutionary responses: whole-genome duplication and abiotic environment, especially temperature. Evolutionary solutions to both kinds of challenge are likely to involve modification of homologous recombination and synapsis, probably via adjustments of core structural components important in meiosis I. Synthesizing these findings with broader patterns of meiosis gene evolution suggests that the structural components of meiosis coevolve as adaptive modules that may change in primary sequence and function while maintaining three-dimensional structures and protein interactions. The often sharp divergence of these genes among species probably reflects periodic modification of entire multiprotein complexes driven by genomic or environmental changes. We suggest that the pressures that cause meiosis to evolve to maintain fertility may cause pleiotropic alterations of global crossover rates. We highlight several important areas for future research. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Quantifying selection in evolving populations using time-resolved genetic data

Science.gov (United States)

Illingworth, Christopher J. R.; Mustonen, Ville

2013-01-01

Methods which uncover the molecular basis of the adaptive evolution of a population address some important biological questions. For example, the problem of identifying genetic variants which underlie drug resistance, a question of importance for the treatment of pathogens, and of cancer, can be understood as a matter of inferring selection. One difficulty in the inference of variants under positive selection is the potential complexity of the underlying evolutionary dynamics, which may involve an interplay between several contributing processes, including mutation, recombination and genetic drift. A source of progress may be found in modern sequencing technologies, which confer an increasing ability to gather information about evolving populations, granting a window into these complex processes. One particularly interesting development is the ability to follow evolution as it happens, by whole-genome sequencing of an evolving population at multiple time points. We here discuss how to use time-resolved sequence data to draw inferences about the evolutionary dynamics of a population under study. We begin by reviewing our earlier analysis of a yeast selection experiment, in which we used a deterministic evolutionary framework to identify alleles under selection for heat tolerance, and to quantify the selection acting upon them. Considering further the use of advanced intercross lines to measure selection, we here extend this framework to cover scenarios of simultaneous recombination and selection, and of two driver alleles with multiple linked neutral, or passenger, alleles, where the driver pair evolves under an epistatic fitness landscape. We conclude by discussing the limitations of the approach presented and outlining future challenges for such methodologies.

Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture.

Science.gov (United States)

Macqueen, Daniel J; Primmer, Craig R; Houston, Ross D; Nowak, Barbara F; Bernatchez, Louis; Bergseth, Steinar; Davidson, William S; Gallardo-Escárate, Cristian; Goldammer, Tom; Guiguen, Yann; Iturra, Patricia; Kijas, James W; Koop, Ben F; Lien, Sigbjørn; Maass, Alejandro; Martin, Samuel A M; McGinnity, Philip; Montecino, Martin; Naish, Kerry A; Nichols, Krista M; Ólafsson, Kristinn; Omholt, Stig W; Palti, Yniv; Plastow, Graham S; Rexroad, Caird E; Rise, Matthew L; Ritchie, Rachael J; Sandve, Simen R; Schulte, Patricia M; Tello, Alfredo; Vidal, Rodrigo; Vik, Jon Olav; Wargelius, Anna; Yáñez, José Manuel

2017-06-27

We describe an emerging initiative - the 'Functional Annotation of All Salmonid Genomes' (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance.

Compactness of viral genomes: effect of disperse and localized random mutations

Science.gov (United States)

Lošdorfer Božič, Anže; Micheletti, Cristian; Podgornik, Rudolf; Tubiana, Luca

2018-02-01

Genomes of single-stranded RNA viruses have evolved to optimize several concurrent properties. One of them is the architecture of their genomic folds, which must not only feature precise structural elements at specific positions, but also allow for overall spatial compactness. The latter was shown to be disrupted by random synonymous mutations, a disruption which can consequently negatively affect genome encapsidation. In this study, we use three mutation schemes with different degrees of locality to mutate the genomes of phage MS2 and Brome Mosaic virus in order to understand the observed sensitivity of the global compactness of their folds. We find that mutating local stretches of their genomes’ sequence or structure is less disruptive to their compactness compared to inducing randomly-distributed mutations. Our findings are indicative of a mechanism for the conservation of compactness acting on a global scale of the genomes, and have several implications for understanding the interplay between local and global architecture of viral RNA genomes.

A mixture of "cheats" and "co-operators" can enable maximal group benefit.

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R Craig MaClean

Full Text Available Is a group best off if everyone co-operates? Theory often considers this to be so (e.g. the "conspiracy of doves", this understanding underpinning social and economic policy. We observe, however, that after competition between "cheat" and "co-operator" strains of yeast, population fitness is maximized under co-existence. To address whether this might just be a peculiarity of our experimental system or a result with broader applicability, we assemble, benchmark, dissect, and test a systems model. This reveals the conditions necessary to recover the unexpected result. These are 3-fold: (a that resources are used inefficiently when they are abundant, (b that the amount of co-operation needed cannot be accurately assessed, and (c the population is structured, such that co-operators receive more of the resource than the cheats. Relaxing any of the assumptions can lead to population fitness being maximized when cheats are absent, which we experimentally demonstrate. These three conditions will often be relevant, and hence in order to understand the trajectory of social interactions, understanding the dynamics of the efficiency of resource utilization and accuracy of information will be necessary.

ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis-Regulatory Evolution in Lepidoptera

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James J. Lewis

2016-09-01

Full Text Available Uncovering phylogenetic patterns of cis-regulatory evolution remains a fundamental goal for evolutionary and developmental biology. Here, we characterize the evolution of regulatory loci in butterflies and moths using chromatin immunoprecipitation sequencing (ChIP-seq annotation of regulatory elements across three stages of head development. In the process we provide a high-quality, functionally annotated genome assembly for the butterfly, Heliconius erato. Comparing cis-regulatory element conservation across six lepidopteran genomes, we find that regulatory sequences evolve at a pace similar to that of protein-coding regions. We also observe that elements active at multiple developmental stages are markedly more conserved than elements with stage-specific activity. Surprisingly, we also find that stage-specific proximal and distal regulatory elements evolve at nearly identical rates. Our study provides a benchmark for genome-wide patterns of regulatory element evolution in insects, and it shows that developmental timing of activity strongly predicts patterns of regulatory sequence evolution.

New CO and HCN sources associated with IRAS carbon stars

Science.gov (United States)

NGUYEN-Q-RIEU; Epchtein, N.; TRUONG-BACH; Cohen, M.

1987-01-01

Emission of CO and HCN was detected in 22 out of a sample of 53 IRAS sources classified as unidentified carbon-rich objects. The sample was selected according to the presence of the silicon carbide feature as revealed by low-resolution spectra. The molecular line widths indicate that the CO and HCN emission arises from the circumstellar envelopes of very highly evolved stars undergoing mass loss. The visible stars tend to be deficient in CO as compared with unidentified sources. Most the detected CO and HCN IRAS stars are distinct and thick-shelled objects, but their infrared and CO luminosities are similar to those of IRC + 102156 AFGL and IRC-CO evolved stars. The 12 micron flux seems to be a good indicator of the distance, hence a guide for molecular searches.

Genome-wide comparative analysis reveals similar types of NBS genes in hybrid Citrus sinensis genome and original Citrus clementine genome and provides new insights into non-TIR NBS genes.

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Yunsheng Wang

Full Text Available In this study, we identified and compared nucleotide-binding site (NBS domain-containing genes from three Citrus genomes (C. clementina, C. sinensis from USA and C. sinensis from China. Phylogenetic analysis of all Citrus NBS genes across these three genomes revealed that there are three approximately evenly numbered groups: one group contains the Toll-Interleukin receptor (TIR domain and two different Non-TIR groups in which most of proteins contain the Coiled Coil (CC domain. Motif analysis confirmed that the two groups of CC-containing NBS genes are from different evolutionary origins. We partitioned NBS genes into clades using NBS domain sequence distances and found most clades include NBS genes from all three Citrus genomes. This suggests that three Citrus genomes have similar numbers and types of NBS genes. We also mapped the re-sequenced reads of three pomelo and three mandarin genomes onto the C. sinensis genome. We found that most NBS genes of the hybrid C. sinensis genome have corresponding homologous genes in both pomelo and mandarin genomes. The homologous NBS genes in pomelo and mandarin suggest that the parental species of C. sinensis may contain similar types of NBS genes. This explains why the hybrid C. sinensis and original C. clementina have similar types of NBS genes in this study. Furthermore, we found that sequence variation amongst Citrus NBS genes were shaped by multiple independent and shared accelerated mutation accumulation events among different groups of NBS genes and in different Citrus genomes. Our comparative analyses yield valuable insight into the structure, organization and evolution of NBS genes in Citrus genomes. Furthermore, our comprehensive analysis showed that the non-TIR NBS genes can be divided into two groups that come from different evolutionary origins. This provides new insights into non-TIR genes, which have not received much attention.

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.

Science.gov (United States)

Braasch, Ingo; Gehrke, Andrew R; Smith, Jeramiah J; Kawasaki, Kazuhiko; Manousaki, Tereza; Pasquier, Jeremy; Amores, Angel; Desvignes, Thomas; Batzel, Peter; Catchen, Julian; Berlin, Aaron M; Campbell, Michael S; Barrell, Daniel; Martin, Kyle J; Mulley, John F; Ravi, Vydianathan; Lee, Alison P; Nakamura, Tetsuya; Chalopin, Domitille; Fan, Shaohua; Wcisel, Dustin; Cañestro, Cristian; Sydes, Jason; Beaudry, Felix E G; Sun, Yi; Hertel, Jana; Beam, Michael J; Fasold, Mario; Ishiyama, Mikio; Johnson, Jeremy; Kehr, Steffi; Lara, Marcia; Letaw, John H; Litman, Gary W; Litman, Ronda T; Mikami, Masato; Ota, Tatsuya; Saha, Nil Ratan; Williams, Louise; Stadler, Peter F; Wang, Han; Taylor, John S; Fontenot, Quenton; Ferrara, Allyse; Searle, Stephen M J; Aken, Bronwen; Yandell, Mark; Schneider, Igor; Yoder, Jeffrey A; Volff, Jean-Nicolas; Meyer, Axel; Amemiya, Chris T; Venkatesh, Byrappa; Holland, Peter W H; Guiguen, Yann; Bobe, Julien; Shubin, Neil H; Di Palma, Federica; Alföldi, Jessica; Lindblad-Toh, Kerstin; Postlethwait, John H

2016-04-01

To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.

Genomic analysis of NAC transcription factors in banana (Musa acuminata) and definition of NAC orthologous groups for monocots and dicots.

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Cenci, Albero; Guignon, Valentin; Roux, Nicolas; Rouard, Mathieu

2014-05-01

Identifying the molecular mechanisms underlying tolerance to abiotic stresses is important in crop breeding. A comprehensive understanding of the gene families associated with drought tolerance is therefore highly relevant. NAC transcription factors form a large plant-specific gene family involved in the regulation of tissue development and responses to biotic and abiotic stresses. The main goal of this study was to set up a framework of orthologous groups determined by an expert sequence comparison of NAC genes from both monocots and dicots. In order to clarify the orthologous relationships among NAC genes of different species, we performed an in-depth comparative study of four divergent taxa, in dicots and monocots, whose genomes have already been completely sequenced: Arabidopsis thaliana, Vitis vinifera, Musa acuminata and Oryza sativa. Due to independent evolution, NAC copy number is highly variable in these plant genomes. Based on an expert NAC sequence comparison, we propose forty orthologous groups of NAC sequences that were probably derived from an ancestor gene present in the most recent common ancestor of dicots and monocots. These orthologous groups provide a curated resource for large-scale protein sequence annotation of NAC transcription factors. The established orthology relationships also provide a useful reference for NAC function studies in newly sequenced genomes such as M. acuminata and other plant species.

Complete genome sequence of the bacteriochlorophyll a-containing Roseibacterium elongatum type strain (DSM 19469(T)), a representative of the Roseobacter group isolated from Australian coast sand.

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Riedel, Thomas; Fiebig, Anne; Göker, Markus; Klenk, Hans-Peter

2014-06-15

Roseibacterium elongatum Suzuki et al. 2006 is a pink-pigmented and bacteriochlorophyll a-producing representative of the Roseobacter group within the alphaproteobacterial family Rhodobacteraceae. Representatives of the marine 'Roseobacter group' were found to be abundant in the ocean and play an important role in global and biogeochemical processes. In the present study we describe the features of R. elongatum strain OCh 323(T) together with its genome sequence and annotation. The 3,555,102 bp long genome consists of one circular chromosome with no extrachromosomal elements and is one of the smallest known Roseobacter genomes. It contains 3,540 protein-coding genes and 59 RNA genes. Genome analysis revealed the presence of a photosynthetic gene cluster, which putatively enables a photoheterotrophic lifestyle. Gene sequences associated with quorum sensing, motility, surface attachment, and thiosulfate and carbon monoxide oxidation could be detected. The genome was sequenced as part of the activities of the Transregional Collaborative Research Centre 51 (TRR51) funded by the German Research Foundation (DFG).

Genomic evolution of Staphylococcus aureus isolates colonizing the nares and progressing to bacteremia.

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Jeanne B Benoit

Full Text Available Nasal colonization by Staphylococcus aureus is a key risk factor for bacteremia. The objective of this study is to identify genomic modifications occurring in nasal carriage strains of S. aureus as they progress to bacteremia in a cohort of hospitalized patients.Eight patients with S. aureus bacteremia were identified. Genomic sequences of the bloodstream isolates were compared with 57 nasal isolates collected longitudinally prior to the occurrence of bacteremia, which covered a timespan of up to 326 days before bacteremia.Within each subject, nasal colonizing strains were closely related to bacteremia strains. Within a subject, the number of single nucleotide polymorphisms (SNPs observed between time points was greater than within a single time point. Co-colonization and strain replacement were observed in one case. In all cases colonization progressed to bacteremia without addition of new virulence genes. In one case, a mutation in the accessory gene regulator gene caused abrogation of agr function.S. aureus evolves in the human nares at a variable rate. Progression of S. aureus nasal colonization to nosocomial infection is seldom associated with acquisition of new virulence determinants. Mutation in the agr gene with abrogation of function was associated with progression to bacteremia in one case.

The complete genome sequence of Clostridium indolis DSM 755(T.).

Science.gov (United States)

Biddle, Amy S; Leschine, Susan; Huntemann, Marcel; Han, James; Chen, Amy; Kyrpides, Nikos; Markowitz, Victor; Palaniappan, Krishna; Ivanova, Natalia; Mikhailova, Natalia; Ovchinnikova, Galina; Schaumberg, Andrew; Pati, Amrita; Stamatis, Dimitrios; Reddy, Tatiparthi; Lobos, Elizabeth; Goodwin, Lynne; Nordberg, Henrik P; Cantor, Michael N; Hua, Susan X; Woyke, Tanja; Blanchard, Jeffrey L

2014-06-15

Clostridium indolis DSM 755(T) is a bacterium commonly found in soils and the feces of birds and mammals. Despite its prevalence, little is known about the ecology or physiology of this species. However, close relatives, C. saccharolyticum and C. hathewayi, have demonstrated interesting metabolic potentials related to plant degradation and human health. The genome of C. indolis DSM 755(T) reveals an abundance of genes in functional groups associated with the transport and utilization of carbohydrates, as well as citrate, lactate, and aromatics. Ecologically relevant gene clusters related to nitrogen fixation and a unique type of bacterial microcompartment, the CoAT BMC, are also detected. Our genome analysis suggests hypotheses to be tested in future culture based work to better understand the physiology of this poorly described species.

New Measurement for Correlation of Co-evolution Relationship of Subsequences in Protein.

Science.gov (United States)

Gao, Hongyun; Yu, Xiaoqing; Dou, Yongchao; Wang, Jun

2015-12-01

Many computational tools have been developed to measure the protein residues co-evolution. Most of them only focus on co-evolution for pairwise residues in a protein sequence. However, number of residues participate in co-evolution might be multiple. And some co-evolved residues are clustered in several distinct regions in primary structure. Therefore, the co-evolution among the adjacent residues and the correlation between the distinct regions offer insights into function and evolution of the protein and residues. Subsequence is used to represent the adjacent multiple residues in one distinct region. In the paper, co-evolution relationship in each subsequence is represented by mutual information matrix (MIM). Then, Pearson's correlation coefficient: R value is developed to measure the similarity correlation of two MIMs. MSAs from Catalytic Data Base (Catalytic Site Atlas, CSA) are used for testing. R value characterizes a specific class of residues. In contrast to individual pairwise co-evolved residues, adjacent residues without high individual MI values are found since the co-evolved relationship among them is similar to that among another set of adjacent residues. These subsequences possess some flexibility in the composition of side chains, such as the catalyzed environment.

Tollip or not Tollip: what are the evolving questions behind it?

Directory of Open Access Journals (Sweden)

Denis Prudencio Luiz

Full Text Available Tollip plays an important role in the interleukin-1 receptor IL-1R and Toll pathways. As a modulator of the immune pathway, it indirectly controls the amount of antimicrobial peptides. This could indicate a vital step in maintaining animal immune systems and preventing infection. Evolutionary questions are crucial to understanding the conservation and functioning of the biochemical pathways like the Tollip-mediated one. Through an analysis of 36 sequences of the Tollip protein from different animal taxa, downloaded from Kyoto Encyclopedia of Genes and Genomes (KEGG databank, we inferred diverse evolutionary parameters, such as molecular selection and structure conservation, by analyzing residue by residue, beyond the canonical parameters to this type of study, as maximum likelihood trees. We found that Tollip presented different trends in its evolving history. In primates, the protein is becoming more unstable, just the opposite is observed in the arthropod group. The most interesting finding was the concentration of positively selected residues at amino terminal ends. Some observed topological incongruences in maximum likelihood trees of complete and curated Tollip data sets could be explained through horizontal transfers, evidenced by recombination detection. These results suggest that there is more to be researched and understood about this protein.

Abundances of elements of the palladium group in the atmospheres of evolved stars. I. Molybdenum

International Nuclear Information System (INIS)

Orlov, M.Ya.; Shavrina, A.V.

1988-01-01

The abundance of molybdenum in the atmospheres of the K giants υ Ser, 9 Boo, and ρ Boo has been determined using spectra with reciprocal dispersion 6 angstrom/mm and the method of model atmospheres. Data on the abundance of this element in the atmospheres of other evolved stars are also given

Detection of selection signatures of population-specific genomic regions selected during domestication process in Jinhua pigs.

Science.gov (United States)

Li, Zhengcao; Chen, Jiucheng; Wang, Zhen; Pan, Yuchun; Wang, Qishan; Xu, Ningying; Wang, Zhengguang

2016-12-01

Chinese pigs have been undergoing both natural and artificial selection for thousands of years. Jinhua pigs are of great importance, as they can be a valuable model for exploring the genetic mechanisms linked to meat quality and other traits such as disease resistance, reproduction and production. The purpose of this study was to identify distinctive footprints of selection between Jinhua pigs and other breeds utilizing genome-wide SNP data. Genotyping by genome reducing and sequencing was implemented in order to perform cross-population extended haplotype homozygosity to reveal strong signatures of selection for those economically important traits. This work was performed at a 2% genome level, which comprised 152 006 SNPs genotyped in a total of 517 individuals. Population-specific footprints of selective sweeps were searched for in the genome of Jinhua pigs using six native breeds and three European breeds as reference groups. Several candidate genes associated with meat quality, health and reproduction, such as GH1, CRHR2, TRAF4 and CCK, were found to be overlapping with the significantly positive outliers. Additionally, the results revealed that some genomic regions associated with meat quality, immune response and reproduction in Jinhua pigs have evolved directionally under domestication and subsequent selections. The identified genes and biological pathways in Jinhua pigs showed different selection patterns in comparison with the Chinese and European breeds. © 2016 Stichting International Foundation for Animal Genetics.

Dynamical community structure of populations evolving on genotype networks

International Nuclear Information System (INIS)

Capitán, José A.; Aguirre, Jacobo; Manrubia, Susanna

2015-01-01

Neutral evolutionary dynamics of replicators occurs on large and heterogeneous networks of genotypes. These networks, formed by all genotypes that yield the same phenotype, have a complex architecture that conditions the molecular composition of populations and their movements on genome spaces. Here we consider as an example the case of populations evolving on RNA secondary structure neutral networks and study the community structure of the network revealed through dynamical properties of the population at equilibrium and during adaptive transients. We unveil a rich hierarchical community structure that, eventually, can be traced back to the non-trivial relationship between RNA secondary structure and sequence composition. We demonstrate that usual measures of modularity that only take into account the static, topological structure of networks, cannot identify the community structure disclosed by population dynamics

Final report of the group research. Genome analysis on the biological effects of radiation. Second research group of NIRS

International Nuclear Information System (INIS)

2001-10-01

This report concerns investigations on the title conducted by 5 subgroups of National Institute of Radiological Sciences (NIRS) during the period of 1993-2001. The report involves the organization of research teams and summary reports from the subgroups for Genome sequencing and informatics, Genome analysis on model organisms, The genome analysis on the specific chromosomal region related to radiation-sensitivity, Molecular analysis on the structure and function of particular regions of human genome, and Generation and characterization of DNA repair-deficient model mice. Significant results are as follows: Sequencing of the radiation sensitivity gene ATM, finding of a novel cell cycle regulator gene NPAT and regulation of gene expression of ATM/NPAT; Findings that the cause of the variability related to instability of human genome is derived from particular repeat structures of 5 and 35 bases and of the instability mutation, from the mutation of EPILS (mRNA synthase gene); Program development for novel human genome finding in the DNA sequences and making novel human gene as a resource by polymerase chain reaction (PCR) technique; and generation of the highly UV-sensitive mouse model for human xeroderma pigmentosum G. Conclusion is that findings will contribute for better understanding of the genes functioning radiation sensitivity and also biodefense mechanism against radiation and other environmental stress. (N.I.)

Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence-Function Space and Genome Context to Discover Novel Functions.

Science.gov (United States)

Gerlt, John A

2017-08-22

The exponentially increasing number of protein and nucleic acid sequences provides opportunities to discover novel enzymes, metabolic pathways, and metabolites/natural products, thereby adding to our knowledge of biochemistry and biology. The challenge has evolved from generating sequence information to mining the databases to integrating and leveraging the available information, i.e., the availability of "genomic enzymology" web tools. Web tools that allow identification of biosynthetic gene clusters are widely used by the natural products/synthetic biology community, thereby facilitating the discovery of novel natural products and the enzymes responsible for their biosynthesis. However, many novel enzymes with interesting mechanisms participate in uncharacterized small-molecule metabolic pathways; their discovery and functional characterization also can be accomplished by leveraging information in protein and nucleic acid databases. This Perspective focuses on two genomic enzymology web tools that assist the discovery novel metabolic pathways: (1) Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST) for generating sequence similarity networks to visualize and analyze sequence-function space in protein families and (2) Enzyme Function Initiative-Genome Neighborhood Tool (EFI-GNT) for generating genome neighborhood networks to visualize and analyze the genome context in microbial and fungal genomes. Both tools have been adapted to other applications to facilitate target selection for enzyme discovery and functional characterization. As the natural products community has demonstrated, the enzymology community needs to embrace the essential role of web tools that allow the protein and genome sequence databases to be leveraged for novel insights into enzymological problems.

Complete genome sequence of Lactobacillus plantarum LZ95, a potential probiotic strain producing bacteriocins and B-group vitamin riboflavin.

Science.gov (United States)

Li, Ping; Gu, Qing

2016-07-10

Lactobacillus plantarum LZ95 is a potential probiotic isolated from newborn infant fecal and it is identified to produce riboflavin with great antimicrobial activity. The complete genome sequence of this strain was reported in the present study. The genome contains a 3,261,418-bp chromosome and two plasmids. Genes, related to the biosynthesis of bacteriocins and riboflavin, were identified. This work will facilitate to reveal the biosynthetic mechanism of bacteriocins and B-group vitamins in lactic acid bacteria and provide evidence for its potential application in food industry. Copyright © 2016 Elsevier B.V. All rights reserved.

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

Energy Technology Data Exchange (ETDEWEB)

Novichkov, Pavel S.; Rodionov, Dmitry A.; Stavrovskaya, Elena D.; Novichkova, Elena S.; Kazakov, Alexey E.; Gelfand, Mikhail S.; Arkin, Adam P.; Mironov, Andrey A.; Dubchak, Inna

2010-05-26

RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics approach. The server allows the user to rapidly generate reference sets of regulons and regulatory motif profiles in a group of prokaryotic genomes. The new concept of a cluster of co-regulated orthologous operons allows the user to distribute the analysis of large regulons and to perform the comparative analysis of multiple clusters independently. Two major workflows currently implemented in RegPredict are: (i) regulon reconstruction for a known regulatory motif and (ii) ab initio inference of a novel regulon using several scenarios for the generation of starting gene sets. RegPredict provides a comprehensive collection of manually curated positional weight matrices of regulatory motifs. It is based on genomic sequences, ortholog and operon predictions from the MicrobesOnline. An interactive web interface of RegPredict integrates and presents diverse genomic and functional information about the candidate regulon members from several web resources. RegPredict is freely accessible at http://regpredict.lbl.gov.

Weighted Evolving Networks with Self-organized Communities

International Nuclear Information System (INIS)

Xie Zhou; Wang Xiaofan; Li Xiang

2008-01-01

In order to describe the self-organization of communities in the evolution of weighted networks, we propose a new evolving model for weighted community-structured networks with the preferential mechanisms functioned in different levels according to community sizes and node strengths, respectively. Theoretical analyses and numerical simulations show that our model captures power-law distributions of community sizes, node strengths, and link weights, with tunable exponents of ν ≥ 1, γ > 2, and α > 2, respectively, sharing large clustering coefficients and scaling clustering spectra, and covering the range from disassortative networks to assortative networks. Finally, we apply our new model to the scientific co-authorship networks with both their weighted and unweighted datasets to verify its effectiveness

Genome-Wide Comparative Functional Analyses Reveal Adaptations of Salmonella sv. Newport to a Plant Colonization Lifestyle

Directory of Open Access Journals (Sweden)

Marcos H. de Moraes

2018-05-01

Full Text Available Outbreaks of salmonellosis linked to the consumption of vegetables have been disproportionately associated with strains of serovar Newport. We tested the hypothesis that strains of sv. Newport have evolved unique adaptations to persistence in plants that are not shared by strains of other Salmonella serovars. We used a genome-wide mutant screen to compare growth in tomato fruit of a sv. Newport strain from an outbreak traced to tomatoes, and a sv. Typhimurium strain from animals. Most genes in the sv. Newport strain that were selected during persistence in tomatoes were shared with, and similarly selected in, the sv. Typhimurium strain. Many of their functions are linked to central metabolism, including amino acid biosynthetic pathways, iron acquisition, and maintenance of cell structure. One exception was a greater need for the core genes involved in purine metabolism in sv. Typhimurium than in sv. Newport. We discovered a gene, papA, that was unique to sv. Newport and contributed to the strain’s fitness in tomatoes. The papA gene was present in about 25% of sv. Newport Group III genomes and generally absent from other Salmonella genomes. Homologs of papA were detected in the genomes of Pantoea, Dickeya, and Pectobacterium, members of the Enterobacteriacea family that can colonize both plants and animals.

A discovery of novel microRNAs in the silkworm (Bombyx mori) genome.

Science.gov (United States)

Yu, Xiaomin; Zhou, Qing; Cai, Yimei; Luo, Qibin; Lin, Hongbin; Hu, Songnian; Yu, Jun

2009-12-01

MicroRNAs (miRNAs) are pivotal regulators involved in various physiological and pathological processes via their post-transcriptional regulation of gene expressions. We sequenced 14 libraries of small RNAs constructed from samples spanning the life cycle of silkworms, and discovered 50 novel miRNAs previously not known in animals and verified 43 of them using stem-loop RT-PCR. Our genome-wide analyses of 27 species-specific miRNAs suggest they arise from transposable elements, protein-coding genes duplication/transposition and random foldback sequences; which is consistent with the idea that novel animal miRNAs may evolve from incomplete self-complementary transcripts and become fixed in the process of co-adaptation with their targets. Computational prediction suggests that the silkworm-specific miRNAs may have a preference of regulating genes that are related to life-cycle-associated traits, and these genes can serve as potential targets for subsequent studies of the modulating networks in the development of Bombyx mori.

Complete Genome Sequence of Treponema paraluiscuniculi, Strain Cuniculi A: The Loss of Infectivity to Humans Is Associated with Genome Decay

Science.gov (United States)

Šmajs, David; Zobaníková, Marie; Strouhal, Michal; Čejková, Darina; Dugan-Rocha, Shannon; Pospíšilová, Petra; Norris, Steven J.; Albert, Tom; Qin, Xiang; Hallsworth-Pepin, Kym; Buhay, Christian; Muzny, Donna M.; Chen, Lei; Gibbs, Richard A.; Weinstock, George M.

2011-01-01

Treponema paraluiscuniculi is the causative agent of rabbit venereal spirochetosis. It is not infectious to humans, although its genome structure is very closely related to other pathogenic Treponema species including Treponema pallidum subspecies pallidum, the etiological agent of syphilis. In this study, the genome sequence of Treponema paraluiscuniculi, strain Cuniculi A, was determined by a combination of several high-throughput sequencing strategies. Whereas the overall size (1,133,390 bp), arrangement, and gene content of the Cuniculi A genome closely resembled those of the T. pallidum genome, the T. paraluiscuniculi genome contained a markedly higher number of pseudogenes and gene fragments (51). In addition to pseudogenes, 33 divergent genes were also found in the T. paraluiscuniculi genome. A set of 32 (out of 84) affected genes encoded proteins of known or predicted function in the Nichols genome. These proteins included virulence factors, gene regulators and components of DNA repair and recombination. The majority (52 or 61.9%) of the Cuniculi A pseudogenes and divergent genes were of unknown function. Our results indicate that T. paraluiscuniculi has evolved from a T. pallidum-like ancestor and adapted to a specialized host-associated niche (rabbits) during loss of infectivity to humans. The genes that are inactivated or altered in T. paraluiscuniculi are candidates for virulence factors important in the infectivity and pathogenesis of T. pallidum subspecies. PMID:21655244

Complete genome sequence of Treponema paraluiscuniculi, strain Cuniculi A: the loss of infectivity to humans is associated with genome decay.

Directory of Open Access Journals (Sweden)

David Šmajs

Full Text Available Treponema paraluiscuniculi is the causative agent of rabbit venereal spirochetosis. It is not infectious to humans, although its genome structure is very closely related to other pathogenic Treponema species including Treponema pallidum subspecies pallidum, the etiological agent of syphilis. In this study, the genome sequence of Treponema paraluiscuniculi, strain Cuniculi A, was determined by a combination of several high-throughput sequencing strategies. Whereas the overall size (1,133,390 bp, arrangement, and gene content of the Cuniculi A genome closely resembled those of the T. pallidum genome, the T. paraluiscuniculi genome contained a markedly higher number of pseudogenes and gene fragments (51. In addition to pseudogenes, 33 divergent genes were also found in the T. paraluiscuniculi genome. A set of 32 (out of 84 affected genes encoded proteins of known or predicted function in the Nichols genome. These proteins included virulence factors, gene regulators and components of DNA repair and recombination. The majority (52 or 61.9% of the Cuniculi A pseudogenes and divergent genes were of unknown function. Our results indicate that T. paraluiscuniculi has evolved from a T. pallidum-like ancestor and adapted to a specialized host-associated niche (rabbits during loss of infectivity to humans. The genes that are inactivated or altered in T. paraluiscuniculi are candidates for virulence factors important in the infectivity and pathogenesis of T. pallidum subspecies.

The genome of the fire ant Solenopsis invicta

DEFF Research Database (Denmark)

Wurm, Yannick; Wang, John; Riba-Grognuz, Oksana

2011-01-01

Ants have evolved very complex societies and are key ecosystem members. Some ants, such as the fire ant Solenopsis invicta, are also major pests. Here, we present a draft genome of S. invicta, assembled from Roche 454 and Illumina sequencing reads obtained from a focal haploid male and his brothe...

The lipoxygenase gene family: a genomic fossil of shared polyploidy between Glycine max and Medicago truncatula

Directory of Open Access Journals (Sweden)

Choi Beom-Soon

2008-12-01

Full Text Available Abstract Background Soybean lipoxygenases (Lxs play important roles in plant resistance and in conferring the distinct bean flavor. Lxs comprise a multi-gene family that includes GmLx1, GmLx2 and GmLx3, and many of these genes have been characterized. We were interested in investigating the relationship between the soybean lipoxygenase isozymes from an evolutionary perspective, since soybean has undergone two rounds of polyploidy. Here we report the tetrad genome structure of soybean Lx regions produced by ancient and recent polyploidy. Also, comparative genomics with Medicago truncatula was performed to estimate Lxs in the common ancestor of soybean and Medicago. Results Two Lx regions in Medicago truncatula showing synteny with soybean were analyzed. Differential evolutionary rates between soybean and Medicago were observed and the median Ks values of Mt-Mt, Gm-Mt, and Gm-Gm paralogs were determined to be 0.75, 0.62, and 0.46, respectively. Thus the comparison of Gm-Mt paralogs (Ks = 0.62 and Gm-Mt orthologs (Ks = 0.45 supports the ancient duplication of Lx regions in the common ancestor prior to the Medicago-Glycine split. After speciation, no Lx regions generated by another polyploidy were identified in Medicago. Instead tandem duplication of Lx genes was observed. On the other hand, a lineage-specific duplication occurred in soybean resulting in two pairs of Lx regions. Each pair of soybean regions was co-orthologous to one Lx region in Medicago. A total of 34 Lx genes (15 MtLxs and 19 GmLxs were divided into two groups by phylogenetic analysis. Our study shows that the Lx gene family evolved from two distinct Lx genes in the most recent common ancestor. Conclusion This study analyzed two pairs of Lx regions generated by two rounds of polyploidy in soybean. Each pair of soybean homeologous regions is co-orthologous to one region of Medicago, demonstrating the quartet structure of the soybean genome. Differential evolutionary rates between

One Year Genome Evolution of Lausannevirus in Allopatric versus Sympatric Conditions.

Science.gov (United States)

Mueller, Linda; Bertelli, Claire; Pillonel, Trestan; Salamin, Nicolas; Greub, Gilbert

2017-06-01

Amoeba-resisting microorganisms raised a great interest during the last decade. Among them, some large DNA viruses present huge genomes up to 2.5 Mb long, exceeding the size of small bacterial genomes. The rate of genome evolution in terms of mutation, deletion, and gene acquisition in these genomes is yet unknown. Given the suspected high plasticity of viral genomes, the microevolution of the 346 kb genome of Lausannevirus, a member of Megavirales, was studied. Hence, Lausannevirus was co-cultured within the amoeba Acanthamoeba castellanii over one year. Despite a low number of mutations, the virus showed a genome reduction of 3.7% after 12 months. Lausannevirus genome evolution in sympatric conditions was investigated by its co-culture with Estrella lausannensis, an obligate intracellular bacterium, in the amoeba A. castellanii during one year. Cultures were split every 3 months. Genome sequencing revealed that in these conditions both, Lausannevirus and E. lausannensis, show stable genome, presenting no major rearrangement. In fact, after one year they acquired from 2 to 7 and from 4 to 10 mutations per culture for Lausannevirus and E. lausannensis, respectively. Interestingly, different mutations in the endonuclease encoding genes of Lausannevirus were observed in different subcultures, highlighting the importance of this gene product in the replication of Lausannevirus. Conversely, mutations in E. lausannensis were mainly located in a gene encoding for a phosphoenolpyruvate-protein phosphotransferase (PtsI), implicated in sugar metabolism. Moreover, in our conditions and with our analyses we detected no horizontal gene transfer during one year of co-culture. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Comparative Genomic Analysis of Clinical and Environmental Vibrio Vulnificus Isolates Revealed Biotype 3 Evolutionary Relationships

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Yael eKotton

2015-01-01

Full Text Available In 1996 a common-source outbreak of severe soft tissue and bloodstream infections erupted among Israeli fish farmers and fish consumers due to changes in fish marketing policies. The causative pathogen was a new strain of Vibrio vulnificus, named biotype 3, which displayed a unique biochemical and genotypic profile. Initial observations suggested that the pathogen erupted as a result of genetic recombination between two distinct populations. We applied a whole genome shotgun sequencing approach using several V. vulnificus strains from Israel in order to study the pan genome of V. vulnificus and determine the phylogenetic relationship of biotype 3 with existing populations. The core genome of V. vulnificus based on 16 draft and complete genomes consisted of 3068 genes, representing between 59% and 78% of the whole genome of 16 strains. The accessory genome varied in size from 781 kbp to 2044 kbp. Phylogenetic analysis based on whole, core, and accessory genomes displayed similar clustering patterns with two main clusters, clinical (C and environmental (E, all biotype 3 strains formed a distinct group within the E cluster. Annotation of accessory genomic regions found in biotype 3 strains and absent from the core genome yielded 1732 genes, of which the vast majority encoded hypothetical proteins, phage-related proteins, and mobile element proteins. A total of 1916 proteins (including 713 hypothetical proteins were present in all human pathogenic strains (both biotype 3 and non-biotype 3 and absent from the environmental strains. Clustering analysis of the non-hypothetical proteins revealed 148 protein clusters shared by all human pathogenic strains; these included transcriptional regulators, arylsulfatases, methyl-accepting chemotaxis proteins, acetyltransferases, GGDEF family proteins, transposases, type IV secretory system (T4SS proteins, and integrases. Our study showed that V. vulnificus biotype 3 evolved from environmental populations and

Randomized controlled trial of group cognitive behavioral therapy compared to a discussion group for co-morbid anxiety and depression in older adults.

Science.gov (United States)

Wuthrich, V M; Rapee, R M; Kangas, M; Perini, S

2016-03-01

Co-morbid anxiety and depression in older adults is associated with worse physical and mental health outcomes and poorer response to psychological and pharmacological treatments in older adults. However, there is a paucity of research focused on testing the efficacy of the co-morbid treatment of anxiety and depression in older adults using psychological interventions. Accordingly, the primary objective of the current study was to test the effects of a group cognitive behavior therapy (CBT) program in treating co-morbid anxiety and depression in a sample of older age adults. A total of 133 community-dwelling participants aged ⩾60 years (mean age = 67.35, s.d. = 5.44, male = 59) with both an anxiety disorder and unipolar mood disorder, as assessed on the Anxiety Disorder Interview Schedule (ADIS), were randomly allocated to an 11-week CBT group or discussion group. Participants with Mini-Mental State Examination scores <26 were excluded. Participants were assessed pre-treatment, post-treatment and at 6 months follow-up on the ADIS, a brief measure of well-being, Geriatric Anxiety Inventory and Geriatric Depression Scale. Both conditions resulted in significant improvements over time on all diagnostic, symptom and wellbeing measures. Significant group × time interaction effects emerged at post-treatment only for diagnostic severity of the primary disorder, mean severity of all anxiety disorders, mood disorders, and all disorders, and recovery rates on primary disorder. Group CBT produced faster and sustained improvements in anxiety and depression on diagnostic severity and recovery rates compared to an active control in older adults.

A simple method for the parallel deep sequencing of full influenza A genomes

DEFF Research Database (Denmark)

Kampmann, Marie-Louise; Fordyce, Sarah Louise; Avila Arcos, Maria del Carmen

2011-01-01

Given the major threat of influenza A to human and animal health, and its ability to evolve rapidly through mutation and reassortment, tools that enable its timely characterization are necessary to help monitor its evolution and spread. For this purpose, deep sequencing can be a very valuable tool....... This study reports a comprehensive method that enables deep sequencing of the complete genomes of influenza A subtypes using the Illumina Genome Analyzer IIx (GAIIx). By using this method, the complete genomes of nine viruses were sequenced in parallel, representing the 2009 pandemic H1N1 virus, H5N1 virus...

Multiplexed genome engineering and genotyping methods applications for synthetic biology and metabolic engineering.

Science.gov (United States)

Wang, Harris H; Church, George M

2011-01-01

Engineering at the scale of whole genomes requires fundamentally new molecular biology tools. Recent advances in recombineering using synthetic oligonucleotides enable the rapid generation of mutants at high efficiency and specificity and can be implemented at the genome scale. With these techniques, libraries of mutants can be generated, from which individuals with functionally useful phenotypes can be isolated. Furthermore, populations of cells can be evolved in situ by directed evolution using complex pools of oligonucleotides. Here, we discuss ways to utilize these multiplexed genome engineering methods, with special emphasis on experimental design and implementation. Copyright © 2011 Elsevier Inc. All rights reserved.

An evolvable oestrogen receptor activity sensor: development of a modular system for integrating multiple genes into the yeast genome

NARCIS (Netherlands)

Fox, J.E.; Bridgham, J.T.; Bovee, T.F.H.; Thornton, J.W.

2007-01-01

To study a gene interaction network, we developed a gene-targeting strategy that allows efficient and stable genomic integration of multiple genetic constructs at distinct target loci in the yeast genome. This gene-targeting strategy uses a modular plasmid with a recyclable selectable marker and a

A note on the environmental Kuznets curve for CO2: A pooled mean group approach

International Nuclear Information System (INIS)

Iwata, Hiroki; Okada, Keisuke; Samreth, Sovannroeun

2011-01-01

This paper investigates whether the environmental Kuznets curve (EKC) hypothesis for CO 2 emissions is satisfied using the panel data of 28 countries by taking nuclear energy into account. Using the pooled mean group (PMG) estimation method, our main results indicate that (1) the impacts of nuclear energy on CO 2 emissions are significantly negative, (2) CO 2 emissions actually increase monotonically within the sample period in all cases: the full sample, OECD countries, and non-OECD countries, and (3) the growth rate in CO 2 emissions with income is decreasing in OECD countries and increasing in non-OECD countries.

The pineapple genome and the evolution of CAM photosynthesis.

Science.gov (United States)

Ming, Ray; VanBuren, Robert; Wai, Ching Man; Tang, Haibao; Schatz, Michael C; Bowers, John E; Lyons, Eric; Wang, Ming-Li; Chen, Jung; Biggers, Eric; Zhang, Jisen; Huang, Lixian; Zhang, Lingmao; Miao, Wenjing; Zhang, Jian; Ye, Zhangyao; Miao, Chenyong; Lin, Zhicong; Wang, Hao; Zhou, Hongye; Yim, Won C; Priest, Henry D; Zheng, Chunfang; Woodhouse, Margaret; Edger, Patrick P; Guyot, Romain; Guo, Hao-Bo; Guo, Hong; Zheng, Guangyong; Singh, Ratnesh; Sharma, Anupma; Min, Xiangjia; Zheng, Yun; Lee, Hayan; Gurtowski, James; Sedlazeck, Fritz J; Harkess, Alex; McKain, Michael R; Liao, Zhenyang; Fang, Jingping; Liu, Juan; Zhang, Xiaodan; Zhang, Qing; Hu, Weichang; Qin, Yuan; Wang, Kai; Chen, Li-Yu; Shirley, Neil; Lin, Yann-Rong; Liu, Li-Yu; Hernandez, Alvaro G; Wright, Chris L; Bulone, Vincent; Tuskan, Gerald A; Heath, Katy; Zee, Francis; Moore, Paul H; Sunkar, Ramanjulu; Leebens-Mack, James H; Mockler, Todd; Bennetzen, Jeffrey L; Freeling, Michael; Sankoff, David; Paterson, Andrew H; Zhu, Xinguang; Yang, Xiaohan; Smith, J Andrew C; Cushman, John C; Paull, Robert E; Yu, Qingyi

2015-12-01

Pineapple (Ananas comosus (L.) Merr.) is the most economically valuable crop possessing crassulacean acid metabolism (CAM), a photosynthetic carbon assimilation pathway with high water-use efficiency, and the second most important tropical fruit. We sequenced the genomes of pineapple varieties F153 and MD2 and a wild pineapple relative, Ananas bracteatus accession CB5. The pineapple genome has one fewer ancient whole-genome duplication event than sequenced grass genomes and a conserved karyotype with seven chromosomes from before the ρ duplication event. The pineapple lineage has transitioned from C3 photosynthesis to CAM, with CAM-related genes exhibiting a diel expression pattern in photosynthetic tissues. CAM pathway genes were enriched with cis-regulatory elements associated with the regulation of circadian clock genes, providing the first cis-regulatory link between CAM and circadian clock regulation. Pineapple CAM photosynthesis evolved by the reconfiguration of pathways in C3 plants, through the regulatory neofunctionalization of preexisting genes and not through the acquisition of neofunctionalized genes via whole-genome or tandem gene duplication.

Gelfand-Dikii Hamiltonian operator and co-ad joint representation of the Volterra group

International Nuclear Information System (INIS)

Lebedev, D.R.; Manin, Yu.I.

1978-01-01

It is shown that the Gelfand-Dikii Hamiltonian structure is an analogue of a very special class of finite-dimensional symplectic structures, namely, the Kirillow structures on the orbits of the co-adjoint representation of the Lie groups. The Lie group is represented by the Volterra operators. The main interest lies in the possibility of application of the ideology of ''geometric quantization'' to the Lax equations

CoVaCS: a consensus variant calling system.

Science.gov (United States)

Chiara, Matteo; Gioiosa, Silvia; Chillemi, Giovanni; D'Antonio, Mattia; Flati, Tiziano; Picardi, Ernesto; Zambelli, Federico; Horner, David Stephen; Pesole, Graziano; Castrignanò, Tiziana

2018-02-05

The advent and ongoing development of next generation sequencing technologies (NGS) has led to a rapid increase in the rate of human genome re-sequencing data, paving the way for personalized genomics and precision medicine. The body of genome resequencing data is progressively increasing underlining the need for accurate and time-effective bioinformatics systems for genotyping - a crucial prerequisite for identification of candidate causal mutations in diagnostic screens. Here we present CoVaCS, a fully automated, highly accurate system with a web based graphical interface for genotyping and variant annotation. Extensive tests on a gold standard benchmark data-set -the NA12878 Illumina platinum genome- confirm that call-sets based on our consensus strategy are completely in line with those attained by similar command line based approaches, and far more accurate than call-sets from any individual tool. Importantly our system exhibits better sensitivity and higher specificity than equivalent commercial software. CoVaCS offers optimized pipelines integrating state of the art tools for variant calling and annotation for whole genome sequencing (WGS), whole-exome sequencing (WES) and target-gene sequencing (TGS) data. The system is currently hosted at Cineca, and offers the speed of a HPC computing facility, a crucial consideration when large numbers of samples must be analysed. Importantly, all the analyses are performed automatically allowing high reproducibility of the results. As such, we believe that CoVaCS can be a valuable tool for the analysis of human genome resequencing studies. CoVaCS is available at: https://bioinformatics.cineca.it/covacs .

A study of volatile organic compounds evolved from the decaying human body.

Science.gov (United States)

Statheropoulos, M; Spiliopoulou, C; Agapiou, A

2005-10-29

Two men were found dead near the island of Samos, Greece, in the Mediterranean sea. The estimated time of death for both victims was 3-4 weeks. Autopsy revealed no remarkable external injuries or acute poisoning. The exact cause of death remained unclear because the bodies had advanced decomposition. Volatile organic compounds (VOCs) evolved from these two corpses were determined by thermal desorption/gas chromatography/mass spectrometry analysis (TD/GC/MS). Over 80 substances have been identified and quantified. The most prominent among them were dimethyl disulfide (13.39 nmol/L), toluene (10.11 nmol/L), hexane (5.58 nmol/L), benzene 1,2,4-trimethyl (4.04 nmol/L), 2-propanone (3.84 nmol/L), 3-pentanone (3.59 nmol/L). Qualitative and quantitative differences among the evolved VOCs and CO2 mean concentration values might indicate different rates of decomposition between the two bodies. The study of the evolved VOCs appears to be a promising adjunct to the forensic pathologist as they may offer important information which can be used in his final evaluation.

The Ever-Evolving Concept of the Gene: The Use of RNA/Protein Experimental Techniques to Understand Genome Functions

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Andrea Cipriano

2018-03-01

Full Text Available The completion of the human genome sequence together with advances in sequencing technologies have shifted the paradigm of the genome, as composed of discrete and hereditable coding entities, and have shown the abundance of functional noncoding DNA. This part of the genome, previously dismissed as “junk” DNA, increases proportionally with organismal complexity and contributes to gene regulation beyond the boundaries of known protein-coding genes. Different classes of functionally relevant nonprotein-coding RNAs are transcribed from noncoding DNA sequences. Among them are the long noncoding RNAs (lncRNAs, which are thought to participate in the basal regulation of protein-coding genes at both transcriptional and post-transcriptional levels. Although knowledge of this field is still limited, the ability of lncRNAs to localize in different cellular compartments, to fold into specific secondary structures and to interact with different molecules (RNA or proteins endows them with multiple regulatory mechanisms. It is becoming evident that lncRNAs may play a crucial role in most biological processes such as the control of development, differentiation and cell growth. This review places the evolution of the concept of the gene in its historical context, from Darwin's hypothetical mechanism of heredity to the post-genomic era. We discuss how the original idea of protein-coding genes as unique determinants of phenotypic traits has been reconsidered in light of the existence of noncoding RNAs. We summarize the technological developments which have been made in the genome-wide identification and study of lncRNAs and emphasize the methodologies that have aided our understanding of the complexity of lncRNA-protein interactions in recent years.

Current approaches on non-invasive prenatal diagnosis: Prenatal genomics, transcriptomics, personalized fetal diagnosis

Directory of Open Access Journals (Sweden)

Tuba Günel

2014-12-01

Full Text Available Recent developments in molecular genetics improved our knowledge on fetal genome and physiology. Novel scientific innovations in prenatal diagnosis have accelerated in the last decade changing our vision immensely. Data obtained from fetal genomic studies brought new insights to fetal medicine and by the advances in fetal DNA and RNA sequencing technology novel treatment strategies has evolved. Non-invasive prenatal diagnosis found ground in genetics and the results are widely studied in scientific arena. When Lo and colleges proved fetal genetic material can be extracted from maternal plasma and fetal DNA can be isolated from maternal serum, the gate to many exciting discoveries was open. Microarray technology and advances in sequencing helped fetal diagnosis as well as other areas of medicine. Today it is a very crucial prerequisite for physicians practicing prenatal diagnosis to have a profound knowledge in genetics. Prevailing practical use and application of fetal genomic tests in maternal and fetal medicine mandates obstetricians to update their knowledge in genetics. The purpose of this review is to assist physicians to understand and update their knowledge in fetal genetic testing from maternal blood, individualized prenatal counseling and advancements on the subject by sharing our experiences as İstanbul University Fetal Nucleic Acid Research Group.

Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture.

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Driscoll, Connor B; Otten, Timothy G; Brown, Nathan M; Dreher, Theo W

2017-01-01

Here we report three complete bacterial genome assemblies from a PacBio shotgun metagenome of a co-culture from Upper Klamath Lake, OR. Genome annotations and culture conditions indicate these bacteria are dependent on carbon and nitrogen fixation from the cyanobacterium Aphanizomenon flos-aquae, whose genome was assembled to draft-quality . Due to their taxonomic novelty relative to previously sequenced bacteria, we have temporarily designated these bacteria as incertae sedis Hyphomonadaceae strain UKL13-1 (3,501,508 bp and 56.12% GC), incertae sedis Betaproteobacterium strain UKL13-2 (3,387,087 bp and 54.98% GC), and incertae sedis Bacteroidetes strain UKL13-3 (3,236,529 bp and 37.33% GC). Each genome consists of a single circular chromosome with no identified plasmids. When compared with binned Illumina assemblies of the same three genomes, there was ~7% discrepancy in total genome length. Gaps where Illumina assemblies broke were often due to repetitive elements. Within these missing sequences were essential genes and genes associated with a variety of functional categories. Annotated gene content reveals that both Proteobacteria are aerobic anoxygenic phototrophs, with Betaproteobacterium UKL13-2 potentially capable of phototrophic oxidation of sulfur compounds. Both proteobacterial genomes contain transporters suggesting they are scavenging fixed nitrogen from A. flos-aquae in the form of ammonium. Bacteroidetes UKL13-3 has few completely annotated biosynthetic pathways, and has a comparatively higher proportion of unannotated genes. The genomes were detected in only a few other freshwater metagenomes, suggesting that these bacteria are not ubiquitous in freshwater systems. Our results indicate that long-read sequencing is a viable method for sequencing dominant members from low-diversity microbial communities, and should be considered for environmental metagenomics when conditions meet these requirements.