WorldWideScience

Sample records for helianthus petiolaris genome

  1. Reconstructing the origin of Helianthus deserticola: Survival and selection on the desert floor

    Gross, B.L.; Kane, D.L.; Lexer, C.; Ludwig, F.; Rosenthal, D.R.; Donovan, L.A.; Rieseberg, L.H.

    2004-01-01

    The diploid hybrid species Helianthus deserticola inhabits the desert floor, an extreme environment relative to its parental species Helianthus annuus and Helianthus petiolaris. Adaptation to the desert floor may have occurred via selection acting on transgressive, or extreme, traits in early

  2. Analysis of transposons and repeat composition of the sunflower (Helianthus annuus L.) genome.

    Cavallini, Andrea; Natali, Lucia; Zuccolo, Andrea; Giordani, Tommaso; Jurman, Irena; Ferrillo, Veronica; Vitacolonna, Nicola; Sarri, Vania; Cattonaro, Federica; Ceccarelli, Marilena; Cionini, Pier Giorgio; Morgante, Michele

    2010-02-01

    A sample-sequencing strategy combined with slot-blot hybridization and FISH was used to study the composition of the repetitive component of the sunflower genome. One thousand six hundred thirty-eight sequences for a total of 954,517 bp were analyzed. The fraction of sequences that can be classified as repetitive using computational and hybridization approaches amounts to 62% in total. Almost two thirds remain as yet uncharacterized in nature. Of those characterized, most belong to the gypsy superfamily of LTR-retrotransposons. Unlike in other species, where single families can account for large fractions of the genome, it appears that no transposon family has been amplified to very high levels in sunflower. All other known classes of transposable elements were also found. One family of unknown nature (contig 61) was the most repeated in the sunflower genome. The evolution of the repetitive component in the Helianthus genus and in other Asteraceae was studied by comparative analysis of the hybridization of total genomic DNAs from these species to the sunflower small-insert library and compared to gene-based phylogeny. Very little similarity is observed between Helianthus species and two related Asteraceae species outside of the genus. Most repetitive elements are similar in annual and perennial Helianthus species indicating that sequence amplification largely predates such divergence. Gypsy-like elements are more represented in the annuals than in the perennials, while copia-like elements are similarly represented, attesting a different amplification history of the two superfamilies of LTR-retrotransposons in the Helianthus genus.

  3. Effect of wild Helianthus cytoplasms on agronomic and oil characteristics of cultivated sunflower (H. annuus L.)

    Sunflower (Helianthus annuus L.) productions reliance on a single source of cytoplasmic male-sterility, PET1, derived from H. petiolaris Nutt., makes the crop genetically vulnerable. Twenty diverse cytoplasmic substitution lines from annual and perennial wild species were compared with the inbred li...

  4. The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements.

    Staton, S Evan; Bakken, Bradley H; Blackman, Benjamin K; Chapman, Mark A; Kane, Nolan C; Tang, Shunxue; Ungerer, Mark C; Knapp, Steven J; Rieseberg, Loren H; Burke, John M

    2012-10-01

    Aside from polyploidy, transposable elements are the major drivers of genome size increases in plants. Thus, understanding the diversity and evolutionary dynamics of transposable elements in sunflower (Helianthus annuus L.), especially given its large genome size (∼3.5 Gb) and the well-documented cases of amplification of certain transposons within the genus, is of considerable importance for understanding the evolutionary history of this emerging model species. By analyzing approximately 25% of the sunflower genome from random sequence reads and assembled bacterial artificial chromosome (BAC) clones, we show that it is composed of over 81% transposable elements, 77% of which are long terminal repeat (LTR) retrotransposons. Moreover, the LTR retrotransposon fraction in BAC clones harboring genes is disproportionately composed of chromodomain-containing Gypsy LTR retrotransposons ('chromoviruses'), and the majority of the intact chromoviruses contain tandem chromodomain duplications. We show that there is a bias in the efficacy of homologous recombination in removing LTR retrotransposon DNA, thereby providing insight into the mechanisms associated with transposable element (TE) composition in the sunflower genome. We also show that the vast majority of observed LTR retrotransposon insertions have likely occurred since the origin of this species, providing further evidence that biased LTR retrotransposon activity has played a major role in shaping the chromatin and DNA landscape of the sunflower genome. Although our findings on LTR retrotransposon age and structure could be influenced by the selection of the BAC clones analyzed, a global analysis of random sequence reads indicates that the evolutionary patterns described herein apply to the sunflower genome as a whole. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.

  5. Genome-wide analysis of LTR-retrotransposon diversity and its impact on the evolution of the genus Helianthus (L.).

    Mascagni, Flavia; Giordani, Tommaso; Ceccarelli, Marilena; Cavallini, Andrea; Natali, Lucia

    2017-08-18

    Genome divergence by mobile elements activity and recombination is a continuous process that plays a key role in the evolution of species. Nevertheless, knowledge on retrotransposon-related variability among species belonging to the same genus is still limited. Considering the importance of the genus Helianthus, a model system for studying the ecological genetics of speciation and adaptation, we performed a comparative analysis of the repetitive genome fraction across ten species and one subspecies of sunflower, focusing on long terminal repeat retrotransposons at superfamily, lineage and sublineage levels. After determining the relative genome size of each species, genomic DNA was isolated and subjected to Illumina sequencing. Then, different assembling and clustering approaches allowed exploring the repetitive component of all genomes. On average, repetitive DNA in Helianthus species represented more than 75% of the genome, being composed mostly by long terminal repeat retrotransposons. Also, the prevalence of Gypsy over Copia superfamily was observed and, among lineages, Chromovirus was by far the most represented. Although nearly all the same sublineages are present in all species, we found considerable variability in the abundance of diverse retrotransposon lineages and sublineages, especially between annual and perennial species. This large variability should indicate that different events of amplification or loss related to these elements occurred following species separation and should have been involved in species differentiation. Our data allowed us inferring on the extent of interspecific repetitive DNA variation related to LTR-RE abundance, investigating the relationship between changes of LTR-RE abundance and the evolution of the genus, and determining the degree of coevolution of different LTR-RE lineages or sublineages between and within species. Moreover, the data suggested that LTR-RE abundance in a species was affected by the annual or perennial

  6. The Population Genomics of Sunflowers and Genomic Determinants of Protein Evolution Revealed by RNAseq

    Loren H. Rieseberg

    2012-10-01

    Full Text Available Few studies have investigated the causes of evolutionary rate variation among plant nuclear genes, especially in recently diverged species still capable of hybridizing in the wild. The recent advent of Next Generation Sequencing (NGS permits investigation of genome wide rates of protein evolution and the role of selection in generating and maintaining divergence. Here, we use individual whole-transcriptome sequencing (RNAseq to refine our understanding of the population genomics of wild species of sunflowers (Helianthus spp. and the factors that affect rates of protein evolution. We aligned 35 GB of transcriptome sequencing data and identified 433,257 polymorphic sites (SNPs in a reference transcriptome comprising 16,312 genes. Using SNP markers, we identified strong population clustering largely corresponding to the three species analyzed here (Helianthus annuus, H. petiolaris, H. debilis, with one distinct early generation hybrid. Then, we calculated the proportions of adaptive substitution fixed by selection (alpha and identified gene ontology categories with elevated values of alpha. The “response to biotic stimulus” category had the highest mean alpha across the three interspecific comparisons, implying that natural selection imposed by other organisms plays an important role in driving protein evolution in wild sunflowers. Finally, we examined the relationship between protein evolution (dN/dS ratio and several genomic factors predicted to co-vary with protein evolution (gene expression level, divergence and specificity, genetic divergence [FST], and nucleotide diversity pi. We find that variation in rates of protein divergence was correlated with gene expression level and specificity, consistent with results from a broad range of taxa and timescales. This would in turn imply that these factors govern protein evolution both at a microevolutionary and macroevolutionary timescale. Our results contribute to a general understanding of the

  7. Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L. Genome

    Navdeep Gill

    2014-04-01

    Full Text Available Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is >78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are “novel” to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence.

  8. Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome

    Gill, Navdeep; Buti, Matteo; Kane, Nolan; Bellec, Arnaud; Helmstetter, Nicolas; Berges, Hélène; Rieseberg, Loren H.

    2014-01-01

    Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is >78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are “novel” to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence. PMID:24833511

  9. Rapid screening and distribution of bioactive compounds in different parts of Berberis petiolaris using direct analysis in real time mass spectrometry

    Awantika Singh

    2015-10-01

    Full Text Available Berberis petiolaris Wall. ex G. Don, an unexplored medicinal plant belonging to the family Berberidaceae, is a large deciduous shrub found in Western Himalaya between 1800–3000 m. Chemical profiling of fruit, leaf, root and stem was done by direct analysis in real time mass spectrometry followed by multivariate analysis for discrimination among the plant parts. The bioactive compounds, including magnoflorine, berberine, jatrorrhizine, thalifendine/berberrubine, demethyleneberberine, reticuline, 8-oxoberberine, N-methyltetrahydroberberine, tetrahydropalmatine, tetrahydroberberine and palmatine, were identified by their exact mass measurement and the corresponding molecular formula of each compound. A comparative study of distribution pattern for all these bioactive alkaloids showed qualitative and quantitative variations in different parts of B. petiolaris. Principal component analysis clearly discriminated each part of B. petiolaris plant. Keywords: Berberis petiolaris, Alkaloids, Profiling, DART–TOF–MS, Statistical analysis

  10. Helianthus tuberosus L.

    Jane

    2011-08-17

    Aug 17, 2011 ... The first frost kills the stems and leaves, but tubers withstand freezing for months. Average tuber yields of 16 to 20 ton/ha may be expected from crops grown under ordinary farm conditions. Yields of tops for forage average are 18 to 28 ton/ha green weight (Duke,. 1983). The effect of cutting of Helianthus ...

  11. Sunflower (Helianthus annuus L.).

    Radonic, Laura M; Lewi, Dalia M; López, Nilda E; Hopp, H Esteban; Escandón, Alejandro S; Bilbao, Marisa López

    2015-01-01

    Sunflower (Helianthus annuus L.) is still considered as a recalcitrant species to in vitro culture and transformation in spite of the publication of different protocols. Here we describe a routine transformation system of this crop which requires mature HA89 genotype seeds and Agrobacterium tumefaciens EHA105 strain for gene delivery, being both easily available. Selection of transformed shoots depends on root development in kanamycin-selective media, instead of shoot color, avoiding selection of escapes. The establishment of this protocol proved successful for the incorporation of both reporter and agronomic important genes and also for the evaluation of the specific expression patterns of different promoters in transgenic sunflower plants. Stable expression of the incorporated transgenes was confirmed by RT-PCR and GUS reporter gene visualization. Stable inheritance of transgenes was successfully followed until T2 generation in several independent lines.

  12. Genotyping-by-sequencing uncovers the introgression alien segments associated with Sclerotinia basal stalk rot resistance from wild species—I. Helianthus argophyllus and H. petiolaris

    Basal stalk rot (BSR), caused by Sclerotinia Sclerotiorum, is a devastating disease in sunflower worldwide. The progress of breeding for Sclerotinia BSR resistance has been hampered due to the lack of effective sources of resistance for cultivated sunflower. Our objective was to transfer BSR resista...

  13. Characterisation and expression of the mitochondrial genome of a new type of cytoplasmic male-sterile sunflower

    Spassova, Mariana; Moneger, Françoise; Leaver, Christopher J.; Petrov, Peter; Atanassov, Atanas; Nijkamp, H. John J.; Hille, Jacques

    1994-01-01

    A new cytoplasmic male sterile sunflower, CMS3, was characterised in relation to the Petiolaris (PET1) cytoplasmic male-sterile sunflower, CMS89. Southern blot analysis showed that the mitochondrial genome of CMS3 contains unique rearrangements in at least five loci (atp6, atp9, atpA, nad1 + 5 and

  14. MEDICAL IMPORTANCE OF HELIANTHUS TUBEROSUS- A REVIEW

    Ali Esmail Al-Snafi

    2018-01-01

    Phytochemical analysis of Helianthus tuberosus showed that it contained coumarins, unsaturated fatty acids, polyacetylenic derivatives, phenols, flavonoids, sesquiterpenes, protein, amino acid, reducing sugars, organic acids, lactones and cardiac glycoside. The pharmacological investigations revealed that Helianthus tuberosus exerted antioxidant, anticancer, antidiabetic, antifungal and α-Glucosidase inhibitory activity, as well as it produced inulin which used as functional food and possesse...

  15. Gene transfer from wild Helianthus to sunflower: topicalities and limits

    Breton Catherine

    2010-03-01

    Full Text Available Sunflower (2n=17 belongs to the Helianthus genus (Asteraceae. Wild Helianthus species display morphological variation for branching and stem number, for architecture and seed size, and for resistance to abiotic and biotic stresses due to which they thrive in different environments in North America. The genus is divided into botanical sections, two for annual as sunflower, and two for perennial species as Jerusalem artichoke that produces rhizomes (tubers. We explain the difficulties and successes obtained by crossing sunflower with these species to improve the agronomic traits of the sunflower crop. It is easier to cross the annual species than the perennials’ with sunflower. Several traits such as Cytoplasmic male sterility and restorer Rf-PET1 genes, Downy mildew resistance, Phomopsis resistance, Sclerotinia resistance, Rust resistance, and Orobanche resistance have already been introduced from annual species into sunflower crop, but the complex genomic organization of these species compared to sunflower limits their important potential. Perennial species are much more diverse, and their genomes display 2n, 4n, or 6n chromosomes for n 17. The realities of inter-specific hybridization are relatively disappointing due to the introgression lines that have low oil and low seed yield. We report here several attempts to introgress agronomic traits from these species to sunflower, and we present as a case study, an introgressed progenies from H. mollis, a diploid species with sessile small leaves. We constructed a preliminary genetic map with AFLP markers in 21 BC1 plants, and we then showed that some progenies display 6 to 44% of introgression from H. mollis. Although this study is promising due to the novel compact architecture of the progenies, we cannot estimate the transferability from H. mollis to other perennial Helianthus to improve sunflower.

  16. Triploid Production from Interspecific Crosses of Two Diploid Perennial Helianthus with Diploid Cultivated Sunflower (Helianthus annuus L.).

    Liu, Zhao; Seiler, Gerald J; Gulya, Thomas J; Feng, Jiuhuan; Rashid, Khalid Y; Cai, Xiwen; Jan, Chao-Chien

    2017-04-03

    Wild Helianthus species are a valuable genetic resource for the improvement of cultivated sunflower. We report the discovery and characterization of a unique high frequency production of triploids when cultivated sunflower was pollinated by specific accessions of diploid Helianthus nuttallii T. & G. and H. maximiliani Schr. Genomic in situ hybridization (GISH) analyses indicated that the triploid F 1 s had two genomes from the wild pollen sources and one from the cultivated line. Mitotic chromosome analyses indicated that the frequency of triploid progenies from the crosses of cultivated lines × H. nuttallii accession 102 (N102) was significantly higher than those of unexpected polyploid progenies from the crosses of wild perennial species × N102, and no unexpected polyploids were obtained from the reverse crosses. Pollen stainability analysis suggested the existence of a low percentage of unreduced (2 n ) male gametes in some accessions, especially N102 and H. maximiliani accession 1113 (M1113), which were generated at the telophase II and tetrad stages of meiosis. The triploid F 1 s could be the results of preferred fertilization of the low frequency of 2 n male gametes with the female gametes of the cultivated sunflower, due to the dosage factors related to recognition and rejection of foreign pollen during fertilization. The triploids have been used to produce amphiploids and aneuploids. Future studies of the male gametes' fate from pollination through fertilization will further uncover the mechanism of this whole genome transmission. Studies of the genetic control of this trait will facilitate research on sunflower polyploidy speciation and evolution, and the utilization of this trait in sunflower breeding. Copyright © 2017 Liu et al.

  17. [Study of Chloroplast DNA Polymorphism in the Sunflower (Helianthus L.)].

    Markina, N V; Usatov, A V; Logacheva, M D; Azarin, K V; Gorbachenko, C F; Kornienko, I V; Gavrilova, V A; Tihobaeva, V E

    2015-08-01

    The polymorphism of microsatellite loci of chloroplast genome in six Helianthus species and 46 lines of cultivated sunflower H. annuus (17 CMS lines and 29 Rf-lines) were studied. The differences between species are confined to four SSR loci. Within cultivated forms of the sunflower H. annuus, the polymorphism is absent. A comparative analysis was performed on sequences of the cpDNA inbred line 3629, line 398941 of the wild sunflower, and the American line HA383 H. annuus. As a result, 52 polymorphic loci represented by 27 SSR and 25 SNP were found; they can be used for genotyping of H. annuus samples, including cultural varieties: twelve polymorphic positions, of which eight are SSR and four are SNP.

  18. Copia and Gypsy retrotransposons activity in sunflower (Helianthus annuus L.)

    2009-01-01

    Background Retrotransposons are heterogeneous sequences, widespread in eukaryotic genomes, which refer to the so-called mobile DNA. They resemble retroviruses, both in their structure and for their ability to transpose within the host genome, of which they make up a considerable portion. Copia- and Gypsy-like retrotransposons are the two main classes of retroelements shown to be ubiquitous in plant genomes. Ideally, the retrotransposons life cycle results in the synthesis of a messenger RNA and then self-encoded proteins to process retrotransposon mRNA in double stranded extra-chromosomal cDNA copies which may integrate in new chromosomal locations. Results The RT-PCR and IRAP protocol were applied to detect the presence of Copia and Gypsy retrotransposon transcripts and of new events of integration in unstressed plants of a sunflower (Helianthus annuus L.) selfed line. Results show that in sunflower retrotransposons transcription occurs in all analyzed organs (embryos, leaves, roots, and flowers). In one out of sixty-four individuals analyzed, retrotransposons transcription resulted in the integration of a new element into the genome. Conclusion These results indicate that the retrotransposon life cycle is firmly controlled at a post transcriptional level. A possible silencing mechanism is discussed. PMID:20030800

  19. Genotyping-by-sequencing targeting of a novel downy mildew resistance gene Pl 20 from wild Helianthus argophyllus for sunflower (Helianthus annuus L.).

    Ma, G J; Markell, S G; Song, Q J; Qi, L L

    2017-07-01

    Genotyping-by-sequencing revealed a new downy mildew resistance gene, Pl 20 , from wild Helianthus argophyllus located on linkage group 8 of the sunflower genome and closely linked to SNP markers that facilitate the marker-assisted selection of resistance genes. Downy mildew (DM), caused by Plasmopara halstedii, is one of the most devastating and yield-limiting diseases of sunflower. Downy mildew resistance identified in wild Helianthus argophyllus accession PI 494578 was determined to be effective against the predominant and virulent races of P. halstedii occurring in the United States. The evaluation of 114 BC 1 F 2:3 families derived from the cross between HA 89 and PI 494578 against P. halstedii race 734 revealed that single dominant gene controls downy mildew resistance in the population. Genotyping-by-sequencing analysis conducted in the BC 1 F 2 population indicated that the DM resistance gene derived from wild H. argophyllus PI 494578 is located on the upper end of the linkage group (LG) 8 of the sunflower genome, as was determined single nucleotide polymorphism (SNP) markers associated with DM resistance. Analysis of 11 additional SNP markers previously mapped to this region revealed that the resistance gene, named Pl 20 , co-segregated with four markers, SFW02745, SFW09076, S8_11272025, and S8_11272046, and is flanked by SFW04358 and S8_100385559 at an interval of 1.8 cM. The newly discovered P. halstedii resistance gene has been introgressed from wild species into cultivated sunflower to provide a novel gene with DM resistance. The homozygous resistant individuals were selected from BC 2 F 2 progenies with the use of markers linked to the Pl 20 gene, and these lines should benefit the sunflower community for Helianthus improvement.

  20. Genetics and mapping of a novel downy mildew resistance gene, Pl(18), introgressed from wild Helianthus argophyllus into cultivated sunflower (Helianthus annuus L.).

    Qi, L L; Foley, M E; Cai, X W; Gulya, T J

    2016-04-01

    A novel downy mildew resistance gene, Pl(18), was introgressed from wild Helianthus argophyllus into cultivated sunflower and genetically mapped to linkage group 2 of the sunflower genome. The new germplasm, HA-DM1, carrying Pl(18) has been released to the public. Sunflower downy mildew (DM) is considered to be the most destructive foliar disease that has spread to every major sunflower-growing country of the world, except Australia. A new dominant downy mildew resistance gene (Pl 18) transferred from wild Helianthus argophyllus (PI 494573) into cultivated sunflower was mapped to linkage group (LG) 2 of the sunflower genome using bulked segregant analysis with 869 simple sequence repeat (SSR) markers. Phenotyping 142 BC1F2:3 families derived from the cross of HA 89 and H. argophyllus confirmed the single gene inheritance of resistance. Since no other Pl gene has been mapped to LG2, this gene was novel and designated as Pl (18). SSR markers CRT214 and ORS203 flanked Pl(18) at a genetic distance of 1.1 and 0.4 cM, respectively. Forty-six single nucleotide polymorphism (SNP) markers that cover the Pl(18) region were surveyed for saturation mapping of the region. Six co-segregating SNP markers were 1.2 cM distal to Pl(18), and another four co-segregating SNP markers were 0.9 cM proximal to Pl(18). The new BC2F4-derived germplasm, HA-DM1, carrying Pl(18) has been released to the public. This new line is highly resistant to all Plasmopara halstedii races identified in the USA providing breeders with an effective new source of resistance against downy mildew in sunflower. The molecular markers that were developed will be especially useful in marker-assisted selection and pyramiding of Pl resistance genes because of their close proximity to the gene and the availability of high-throughput SNP detection assays.

  1. Allelopathic potential of sunflower (Helianthus annus L.) on soil ...

    STORAGESEVER

    2008-09-17

    Sep 17, 2008 ... The effect of a sunflower (Helianthus annuus L.) variety, namely Hysun 38, on metals and of aqueous extracts of its leaves on germination in two varieties of wheat, namely Margalla 99 and Chakwall 97, were studied under laboratory conditions. In particular, the effect of leaf extract on hormones produced ...

  2. Broomrape (Orobanche cumana Wallr.) resistance breeding utilizing wild Helianthus species

    Wild Helianthus species possess valuable resistance genes for sunflower broomrape (Orobanche cumana Wallr.), especially the 39 largely under-utilized perennial species. Resistance to race F has been transferred into cultivated background via bridging of interspecific amphiploids. More recently, a si...

  3. Association mapping in sunflower (Helianthus annuus L.) reveals independent control of apical vs. basal branching.

    Nambeesan, Savithri U; Mandel, Jennifer R; Bowers, John E; Marek, Laura F; Ebert, Daniel; Corbi, Jonathan; Rieseberg, Loren H; Knapp, Steven J; Burke, John M

    2015-03-11

    Shoot branching is an important determinant of plant architecture and influences various aspects of growth and development. Selection on branching has also played an important role in the domestication of crop plants, including sunflower (Helianthus annuus L.). Here, we describe an investigation of the genetic basis of variation in branching in sunflower via association mapping in a diverse collection of cultivated sunflower lines. Detailed phenotypic analyses revealed extensive variation in the extent and type of branching within the focal population. After correcting for population structure and kinship, association analyses were performed using a genome-wide collection of SNPs to identify genomic regions that influence a variety of branching-related traits. This work resulted in the identification of multiple previously unidentified genomic regions that contribute to variation in branching. Genomic regions that were associated with apical and mid-apical branching were generally distinct from those associated with basal and mid-basal branching. Homologs of known branching genes from other study systems (i.e., Arabidopsis, rice, pea, and petunia) were also identified from the draft assembly of the sunflower genome and their map positions were compared to those of associations identified herein. Numerous candidate branching genes were found to map in close proximity to significant branching associations. In sunflower, variation in branching is genetically complex and overall branching patterns (i.e., apical vs. basal) were found to be influenced by distinct genomic regions. Moreover, numerous candidate branching genes mapped in close proximity to significant branching associations. Although the sunflower genome exhibits localized islands of elevated linkage disequilibrium (LD), these non-random associations are known to decay rapidly elsewhere. The subset of candidate genes that co-localized with significant associations in regions of low LD represents the most

  4. Sunflower (Helianthus annuus) fatty acid synthase complex: enoyl-[acyl carrier protein]-reductase genes.

    González-Thuillier, Irene; Venegas-Calerón, Mónica; Garcés, Rafael; von Wettstein-Knowles, Penny; Martínez-Force, Enrique

    2015-01-01

    Enoyl-[acyl carrier protein]-reductases from sunflower. A major factor contributing to the amount of fatty acids in plant oils are the first steps of their synthesis. The intraplastidic fatty acid biosynthetic pathway in plants is catalysed by type II fatty acid synthase (FAS). The last step in each elongation cycle is carried out by the enoyl-[ACP]-reductase, which reduces the dehydrated product of β-hydroxyacyl-[ACP] dehydrase using NADPH or NADH. To determine the mechanisms involved in the biosynthesis of fatty acids in sunflower (Helianthus annuus) seeds, two enoyl-[ACP]-reductase genes have been identified and cloned from developing seeds with 75 % identity: HaENR1 (GenBank HM021137) and HaENR2 (HM021138). The two genes belong to the ENRA and ENRB families in dicotyledons, respectively. The genetic duplication most likely originated after the separation of di- and monocotyledons. RT-qPCR revealed distinct tissue-specific expression patterns. Highest expression of HaENR1 was in roots, stems and developing cotyledons whereas that of H a ENR2 was in leaves and early stages of seed development. Genomic DNA gel blot analyses suggest that both are single-copy genes. In vivo activity of the ENR enzymes was tested by complementation experiments with the JP1111 fabI(ts) E. coli strain. Both enzymes were functional demonstrating that they interacted with the bacterial FAS components. That different fatty acid profiles resulted infers that the two Helianthus proteins have different structures, substrate specificities and/or reaction rates. The latter possibility was confirmed by in vitro analysis with affinity-purified heterologous-expressed enzymes that reduced the crotonyl-CoA substrate using NADH with different V max.

  5. Transcriptome resources for the perennial sunflower Helianthus maximiliani obtained from ecologically divergent populations.

    Kawakami, Takeshi; Darby, Brian J; Ungerer, Mark C

    2014-07-01

    Next-generation sequencing (NGS) technologies provide a rapid means to generate genomic resources for species exhibiting interesting ecological and evolutionary variation but for which such resources are scant or nonexistent. In the current report, we utilize 454 pyrosequencing to obtain transcriptome information for multiple individuals and tissue types from geographically disparate and ecologically differentiated populations of the perennial sunflower species Helianthus maximiliani. A total of 850 275 raw reads were obtained averaging 355 bp in length. Reads were assembled, postprocessing, into 16 681 unique contigs with an N50 of 898 bp and a total length of 13.6 Mb. A majority (67%) of these contigs were annotated based on comparison with the Arabidopsis thaliana genome (TAIR10). Contigs were identified that exhibit high similarity to genes associated with natural variation in flowering time and freezing tolerance in other plant species and will facilitate future studies aimed at elucidating the molecular basis of clinal life history variation and adaptive differentiation in H. maximiliani. Large numbers of gene-associated simple sequence repeats (SSRs) and single-nucleotide polymorphisms (SNPs) also were identified that can be deployed in mapping and population genomic analyses. © 2014 John Wiley & Sons Ltd.

  6. Triploid production from interspecific crosses of two diploid perennial Helianthus with cultivated sunflower

    Wild Helianthus species are a valuable genetic source for the improvement of cultivated sunflower. We report the discovery and characterization of a unique high frequency production of triploids when cultivated sunflower was pollinated by specific accessions of diploid Helianthus nuttallii T. &. G. ...

  7. Genomes

    Brown, T. A. (Terence A.)

    2002-01-01

    ... of genome expression and replication processes, and transcriptomics and proteomics. This text is richly illustrated with clear, easy-to-follow, full color diagrams, which are downloadable from the book's website...

  8. RNA-seq analysis and de novo transcriptome assembly of Jerusalem artichoke (Helianthus tuberosus Linne).

    Jung, Won Yong; Lee, Sang Sook; Kim, Chul Wook; Kim, Hyun-Soon; Min, Sung Ran; Moon, Jae Sun; Kwon, Suk-Yoon; Jeon, Jae-Heung; Cho, Hye Sun

    2014-01-01

    Jerusalem artichoke (Helianthus tuberosus L.) has long been cultivated as a vegetable and as a source of fructans (inulin) for pharmaceutical applications in diabetes and obesity prevention. However, transcriptomic and genomic data for Jerusalem artichoke remain scarce. In this study, Illumina RNA sequencing (RNA-Seq) was performed on samples from Jerusalem artichoke leaves, roots, stems and two different tuber tissues (early and late tuber development). Data were used for de novo assembly and characterization of the transcriptome. In total 206,215,632 paired-end reads were generated. These were assembled into 66,322 loci with 272,548 transcripts. Loci were annotated by querying against the NCBI non-redundant, Phytozome and UniProt databases, and 40,215 loci were homologous to existing database sequences. Gene Ontology terms were assigned to 19,848 loci, 15,434 loci were matched to 25 Clusters of Eukaryotic Orthologous Groups classifications, and 11,844 loci were classified into 142 Kyoto Encyclopedia of Genes and Genomes pathways. The assembled loci also contained 10,778 potential simple sequence repeats. The newly assembled transcriptome was used to identify loci with tissue-specific differential expression patterns. In total, 670 loci exhibited tissue-specific expression, and a subset of these were confirmed using RT-PCR and qRT-PCR. Gene expression related to inulin biosynthesis in tuber tissue was also investigated. Exsiting genetic and genomic data for H. tuberosus are scarce. The sequence resources developed in this study will enable the analysis of thousands of transcripts and will thus accelerate marker-assisted breeding studies and studies of inulin biosynthesis in Jerusalem artichoke.

  9. Transcriptome changes induced by arbuscular mycorrhizal fungi in sunflower (Helianthus annuus L.) roots.

    Vangelisti, Alberto; Natali, Lucia; Bernardi, Rodolfo; Sbrana, Cristiana; Turrini, Alessandra; Hassani-Pak, Keywan; Hughes, David; Cavallini, Andrea; Giovannetti, Manuela; Giordani, Tommaso

    2018-01-08

    Arbuscular mycorrhizal (AM) fungi are essential elements of soil fertility, plant nutrition and productivity, facilitating soil mineral nutrient uptake. Helianthus annuus is a non-model, widely cultivated species. Here we used an RNA-seq approach for evaluating gene expression variation at early and late stages of mycorrhizal establishment in sunflower roots colonized by the arbuscular fungus Rhizoglomus irregulare. mRNA was isolated from roots of plantlets at 4 and 16 days after inoculation with the fungus. cDNA libraries were built and sequenced with Illumina technology. Differential expression analysis was performed between control and inoculated plants. Overall 726 differentially expressed genes (DEGs) between inoculated and control plants were retrieved. The number of up-regulated DEGs greatly exceeded the number of down-regulated DEGs and this difference increased in later stages of colonization. Several DEGs were specifically involved in known mycorrhizal processes, such as membrane transport, cell wall shaping, and other. We also found previously unidentified mycorrhizal-induced transcripts. The most important DEGs were carefully described in order to hypothesize their roles in AM symbiosis. Our data add a valuable contribution for deciphering biological processes related to beneficial fungi and plant symbiosis, adding an Asteraceae, non-model species for future comparative functional genomics studies.

  10. Translocation of 11C from leaves of Helianthus: preliminary results

    Fensom, D.S.; Aikman, D.; Scobie, J.; Drinkwater, A.; Ledingham, K.W.O.

    1977-01-01

    11 C fed to leaves as 11 CO 2 was used to study the dynamics of short-term translocation of photosynthate in Helianthus. As in 14 C studies small amounts of tracer were often detected in the stem close to the fed leaf in th first 5 min, followed by a larger mass flow after 15 min. The speed of mass flow of tracer movement was calculated to be 60 to 400 cm.h -1 depending on the method of calculation. There was no evidence in the premass flow for discrete spots along the stem or petiole where tracer accumulated. Neither was there firm evidence for pulses of tracer moving steadily forward, but there were point fluctuations of greater variability than would be expected by chance alone, which suggest the possibility of aberrations of movement superimposed on the mass flow. Details of these aberrations could not be assessed with certainty from these preliminary experiments owing to the rather low tracer activity. The translocation profiles were sensitive to the prior light conditioning of the plant and above all to chilling. In Helianthus the latter produced temporary restrictions in translocation which lasted for some 10-12 min. (author)

  11. Ecogeography and utility to plant breeding of the crop wild relatives of sunflower (Helianthus annuus L.

    Michael Benjamin Kantar

    2015-10-01

    Full Text Available Crop wild relatives (CWR are a rich source of genetic diversity for crop improvement. Combining ecogeographic and phylogenetic techniques can inform both conservation and breeding. Geographic occurrence, bioclimatic, and biophysical data were used to predict species distributions, range overlap and niche occupancy in 36 taxa closely related to sunflower (Helianthus annuus L.. Taxa lacking comprehensive ex situ conservation were identified. The predicted distributions for 36 Helianthus taxa identified substantial range overlap and asymmetry and niche conservatism. Specific taxa (e.g., Helianthus deblis Nutt., Helianthus anomalus Blake, and Helianthus divaricatus L. were identified as targets for traits of interest, particularly for abiotic stress tolerance and adaptation to extreme soil properties. The combination of techniques demonstrates the potential for publicly available ecogeographic and phylogenetic data to facilitate the identification of possible sources of abiotic stress traits for plant breeding programs. Much of the primary genepool (wild H. annuus occurs in extreme environments indicating that introgression of targeted traits may be relatively straightforward. Sister taxa in Helianthus have greater range overlap than more distantly related taxa within the genus. This adds to a growing body of literature suggesting that in plants (unlike some animal groups, geographic isolation may not be necessary for speciation.

  12. Ecogeography and utility to plant breeding of the crop wild relatives of sunflower (Helianthus annuus L.)

    Kantar, Michael B.; Sosa, Chrystian C.; Khoury, Colin K.; Castañeda-Álvarez, Nora P.; Achicanoy, Harold A.; Bernau, Vivian; Kane, Nolan C.; Marek, Laura; Seiler, Gerald; Rieseberg, Loren H.

    2015-01-01

    Crop wild relatives (CWR) are a rich source of genetic diversity for crop improvement. Combining ecogeographic and phylogenetic techniques can inform both conservation and breeding. Geographic occurrence, bioclimatic, and biophysical data were used to predict species distributions, range overlap and niche occupancy in 36 taxa closely related to sunflower (Helianthus annuus L.). Taxa lacking comprehensive ex situ conservation were identified. The predicted distributions for 36 Helianthus taxa identified substantial range overlap, range asymmetry and niche conservatism. Specific taxa (e.g., Helianthus deblis Nutt., Helianthus anomalus Blake, and Helianthus divaricatus L.) were identified as targets for traits of interest, particularly for abiotic stress tolerance, and adaptation to extreme soil properties. The combination of techniques demonstrates the potential for publicly available ecogeographic and phylogenetic data to facilitate the identification of possible sources of abiotic stress traits for plant breeding programs. Much of the primary genepool (wild H. annuus) occurs in extreme environments indicating that introgression of targeted traits may be relatively straightforward. Sister taxa in Helianthus have greater range overlap than more distantly related taxa within the genus. This adds to a growing body of literature suggesting that in plants (unlike some animal groups), geographic isolation may not be necessary for speciation. PMID:26500675

  13. Solid phase fermentation of Helianthus tuberosus for ethanol

    Baerwald, G.; Hamad, S.H.

    1989-01-01

    The direct fermentation of pure inulin and hammer mill crushed Helianthus tuberosus tubers (topinambur, Jerusalem artichoke) was studied using two heat-tolerant yeasts, namely Kluyveromyces marxianus and Candida kefyr. A Saccharomyces cerevisiae was included in the study so as to compare the yields of these two yeasts with that of a commercial distiller's yeast. The inulin fermentation was carried out in an 18-L bioreactor using the fed-batch and the batch-fermentation methods. The final ethanol concentration was 6.1% (L/L) which represents 82% of the theoretical yield. Commercial scale experiments with hammer mill crushed tubers gave yields lower than those found in the laboratory: 69% of the theoretical yield for direct fermentation without enzyme addition, and about 91% when cellolytic enzymes were added.

  14. Bioaccumulation of 137Cs and 60Co by Helianthus annuus

    Hornik, M.; Pipiska, M.; Vrtoch, L.; Augustin, J.; Lesny, J.

    2005-01-01

    The 60 Co and 137 Cs bioaccumulation by Helianthus annuus L. was measured during 9 day cultivation at 20 ± 2 o C in hydroponic Hoagland medium. Previous starvation for K + and for NH 4 + 2.2 and 2.7 times, respectively, enhanced 137 Cs uptake rate. Previous cultivation in surplus of K + ions 50 mmol·l -1 has no effect on 137 Cs bioaccumulation rate. Both 137 Cs and 60 Co bioaccumulation significantly increase with dilution of basic Hoagland medium up to 1:7 for caesium and up to 1:3 for cobalt followed by mild decrease at higher dilutions. Root to shoot specific 137 Cs radioactivity ratio (Bq.g -1 /Bq·g -1 , fresh wt.) increased with dilution from 1.46 to 9.6-9.8. The values root to shoot specific radioactivity ratio for 60 Co were less dependent on the nutrient concentrations and were within the range 5.7 to 8.5. 137 Cs was localized mainly in young leaves (30%) and roots (39%) and 60 Co mainly in roots (67%) and leaves (20%). Obtained data showed less sensitivity of 60 Co uptake by sunflower on nutrient concentration in hydroponic media. (author)

  15. Helianthus annuus L. production using organic fertilization with manipueira

    Thiago Costa Ferreira

    2015-12-01

    Full Text Available Sunflower (Helianthus annuus L. is an annual plant native to the Americas. Is a grain-producing species with a high oil content, which can be used as a source of biodiesel as well as fodder. The cassava is a liquid derived from the cassava flour production. This organic waste can be used in agriculture due to its high content of nutrients such as, K, N, P, Ca, Mg and S and also avoiding harm the environment. The objective of this study was to evaluate the productivity of sunflower using organic fertilization with cassava. The experiment was conducted under field conditions at Lagoa Seca, PB State, and were analyzed the total production (PS, dry mass of the inflorescence (FCA, dry mass of seeds and inflorescence (FSC and total dry biomass (FT. The highest yield (934.52 kg ha-1 was obtained with no applied cassava. The dosage of 250 mL of cassava yielded maximum values for dry mass of the inflorescence (2,380 kg ha-1 and dry matter of the seeds and inflorescence (3,432 kg ha-1, promoting a increase of 32.03% and 132.55% respectively when compared to the control treatment. The higher value of total biomass was 28,017 kg ha-1 when applied 375 mL of manipueria. The cassava as a source of organic fertilizer favors the dry matter accumulation of sunflower without raising the grain yield.

  16. Growth and phenology of jerusalem artichoke (helianthus tuberosus L.)

    Paungbut, D.; Vorasoot, N.; Patanothai, A.; Jogloy, S.

    2015-01-01

    A standardized, accurate, and easy system is needed to describe Jerusalem artichoke (Helianthus tuberosus L.) plant development. Therefore, this study was designed to define stages of development descriptions for Jerusalem artichoke. Field experiments were conducted during early rainy season and the post rainy season of 2011 and 2012. Data were collected and uniform growth stage descriptions, based on visually observable events, were developed for the vegetative (V), reproductive (R) and tuberization (T) stages. The V stage was determined by counting the number of developed nodes on the main axis of the Jerusalem artichoke, beginning with emergence of the sprout seedling and ending with the initial visual appearance of the inflorescence. The proposed R stages include R1 (Floral bud formation), R2 (beginning bloom), R3 (flowering), R4 (beginning of anthesis), R5 (seed set) and R6 (seed maturity). The T stage include T1 (stolonization), T2 (tuber initiation), T3 (tuber formation), T4 (tuber bulking), T5 (skin set) and T6 (tuber maturity). The V, R and T stages can be measured separately and concurrently and apply to populations or single plants. The present study revealed that reproductive and tuberization development occurred more rapidly in the post-rainy season than in the early-rainy season. The proposed standard descriptions of Jerusalem artichoke development will help research and extension personnel better communicate results and recommendations related to this crop. (author)

  17. Helianthus debilis Nuttall subsp. cucumerifolius (Torrey & A. Gray Heiser (Asteraceae, a Newly Naturalized Plant in Taiwan

    Yen-Hsueh Tseng

    2008-09-01

    Full Text Available We document the naturalization of the New World Helianthus debilis Nuttall subsp. cucumerifolius (Torrey & A. Gray Heiser in central Taiwan. A taxonomic treatment, line drawings, and color photographs of this species from the wild are provided to aid in identification. This represents the first report of Helianthus species in Taiwan. The colony of H. debilis subsp. cucumerifolius was first observed in Taiwan in 1999. During our field survey in 2007 we witnessed the significant range expansion though the coast of Changhua County. The potential of H. debilis subsp. cucumerifolius to become an invasive species in Taiwan is worthy of attention.

  18. Discovery and introgression of the wild sunflower-derived novel downy mildew resistance gene Pl 19 in confection sunflower (Helianthus annuus L.).

    Zhang, Z W; Ma, G J; Zhao, J; Markell, S G; Qi, L L

    2017-01-01

    A new downy mildew resistance gene, Pl 19 , was identified from wild Helianthus annuus accession PI 435414, introduced to confection sunflower, and genetically mapped to linkage group 4 of the sunflower genome. Wild Helianthus annuus accession PI 435414 exhibited resistance to downy mildew, which is one of the most destructive diseases to sunflower production globally. Evaluation of the 140 BC 1 F 2:3 families derived from the cross of CMS CONFSCLB1 and PI 435414 against Plasmopara halstedii race 734 revealed that a single dominant gene controls downy mildew resistance in the population. Bulked segregant analysis conducted in the BC 1 F 2 population with 860 simple sequence repeat (SSR) markers indicated that the resistance derived from wild H. annuus was associated with SSR markers located on linkage group (LG) 4 of the sunflower genome. To map and tag this resistance locus, designated Pl 19 , 140 BC 1 F 2 individuals were used to construct a linkage map of the gene region. Two SSR markers, ORS963 and HT298, were linked to Pl 19 within a distance of 4.7 cM. After screening 27 additional single nucleotide polymorphism (SNP) markers previously mapped to this region, two flanking SNP markers, NSA_003564 and NSA_006089, were identified as surrounding the Pl 19 gene at a distance of 0.6 cM from each side. Genetic analysis indicated that Pl 19 is different from Pl 17 , which had previously been mapped to LG4, but is closely linked to Pl 17 . This new gene is highly effective against the most predominant and virulent races of P. halstedii currently identified in North America and is the first downy mildew resistance gene that has been transferred to confection sunflower. The selected resistant germplasm derived from homozygous BC 2 F 3 progeny provides a novel gene for use in confection sunflower breeding programs.

  19. Sugar yield and composition of tubers from Jerusalem Artichoke (Helianthus tuberosus) irrigated with saline waters

    Currently, major biofuel crops are also food crops that demand fertile soils and good-quality water. Jerusalem artichoke (Helianthus tuberosus, Asteraceae) produces high tonnage of tubers that are rich in sugars, mainly in the form of inulin. In this study, plants of the cultivar “White Fuseau” grow...

  20. The importance of competition in the isolation and establishment of Helianthus paradoxus (Asteraceae)

    Oscar W. Van Auken; Janis. K. Bush

    2007-01-01

    Helianthus paradoxus (the Pecos or puzzle sunflower) is a threatened, federally listed annual species that is found in a few locations in west Texas and New Mexico. Two greenhouse experiments were conducted to evaluate the ability of H. paradoxus to compete with its progenitors and a with potential ecosystem competitor, ...

  1. Stem cankers on sunflower (Helianthus annuus) in Australia reveal a complex of pathogenic Diaporthe (Phomopsis) species

    Thompson, S.M.; Tan, Y.P.; Young, A.J.; Neate, S.M.; Aitken, E.A.B.; Shivas, R.G.

    2012-01-01

    The identification of Diaporthe (anamorph Phomopsis) species associated with stem canker of sunflower (Helianthus annuus) in Australia was studied using morphology, DNA sequence analysis and pathology. Phylogenetic analysis revealed three clades that did not correspond with known taxa, and these are

  2. Sunflower (Helianthus annuus) fatty acid synthase complex: β-hydroxyacyl-[acyl carrier protein] dehydratase genes.

    González-Thuillier, Irene; Venegas-Calerón, Mónica; Sánchez, Rosario; Garcés, Rafael; von Wettstein-Knowles, Penny; Martínez-Force, Enrique

    2016-02-01

    Two sunflower hydroxyacyl-[acyl carrier protein] dehydratases evolved into two different isoenzymes showing distinctive expression levels and kinetics' efficiencies. β-Hydroxyacyl-[acyl carrier protein (ACP)]-dehydratase (HAD) is a component of the type II fatty acid synthase complex involved in 'de novo' fatty acid biosynthesis in plants. This complex, formed by four intraplastidial proteins, is responsible for the sequential condensation of two-carbon units, leading to 16- and 18-C acyl-ACP. HAD dehydrates 3-hydroxyacyl-ACP generating trans-2-enoyl-ACP. With the aim of a further understanding of fatty acid biosynthesis in sunflower (Helianthus annuus) seeds, two β-hydroxyacyl-[ACP] dehydratase genes have been cloned from developing seeds, HaHAD1 (GenBank HM044767) and HaHAD2 (GenBank GU595454). Genomic DNA gel blot analyses suggest that both are single copy genes. Differences in their expression patterns across plant tissues were detected. Higher levels of HaHAD2 in the initial stages of seed development inferred its key role in seed storage fatty acid synthesis. That HaHAD1 expression levels remained constant across most tissues suggest a housekeeping function. Heterologous expression of these genes in E. coli confirmed both proteins were functional and able to interact with the bacterial complex 'in vivo'. The large increase of saturated fatty acids in cells expressing HaHAD1 and HaHAD2 supports the idea that these HAD genes are closely related to the E. coli FabZ gene. The proposed three-dimensional models of HaHAD1 and HaHAD2 revealed differences at the entrance to the catalytic tunnel attributable to Phe166/Val1159, respectively. HaHAD1 F166V was generated to study the function of this residue. The 'in vitro' enzymatic characterization of the three HAD proteins demonstrated all were active, with the mutant having intermediate K m and V max values to the wild-type proteins.

  3. Toward a molecular cytogenetic map for cultivated sunflower (Helianthus annuus L.) by landed BAC/BIBAC clones.

    Feng, Jiuhuan; Liu, Zhao; Cai, Xiwen; Jan, Chao-Chien

    2013-01-01

    Conventional karyotypes and various genetic linkage maps have been established in sunflower (Helianthus annuus L., 2n = 34). However, the relationship between linkage groups and individual chromosomes of sunflower remains unknown and has considerable relevance for the sunflower research community. Recently, a set of linkage group-specific bacterial /binary bacterial artificial chromosome (BAC/BIBAC) clones was identified from two complementary BAC and BIBAC libraries constructed for cultivated sunflower cv. HA89. In the present study, we used these linkage group-specific clones (~100 kb in size) as probes to in situ hybridize to HA89 mitotic chromosomes at metaphase using the BAC-fluorescence in situ hybridization (FISH) technique. Because a characteristic of the sunflower genome is the abundance of repetitive DNA sequences, a high ratio of blocking DNA to probe DNA was applied to hybridization reactions to minimize the background noise. As a result, all sunflower chromosomes were anchored by one or two BAC/BIBAC clones with specific FISH signals. FISH analysis based on tandem repetitive sequences, such as rRNA genes, has been previously reported; however, the BAC-FISH technique developed here using restriction fragment length polymorphism (RFLP)-derived BAC/BIBAC clones as probes to apply genome-wide analysis is new for sunflower. As chromosome-specific cytogenetic markers, the selected BAC/BIBAC clones that encompass the 17 linkage groups provide a valuable tool for identifying sunflower cytogenetic stocks (such as trisomics) and tracking alien chromosomes in interspecific crosses. This work also demonstrates the potential of using a large-insert DNA library for the development of molecular cytogenetic resources.

  4. Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons among Wild and Cultivated Sunflower (Helianthus annuus) Genotypes.

    Mascagni, Flavia; Barghini, Elena; Giordani, Tommaso; Rieseberg, Loren H; Cavallini, Andrea; Natali, Lucia

    2015-11-24

    The sunflower (Helianthus annuus) genome contains a very large proportion of transposable elements, especially long terminal repeat retrotransposons. However, knowledge on the retrotransposon-related variability within this species is still limited. We used next-generation sequencing (NGS) technologies to perform a quantitative and qualitative survey of intraspecific variation of the retrotransposon fraction of the genome across 15 genotypes--7 wild accessions and 8 cultivars--of H. annuus. By mapping the Illumina reads of the 15 genotypes onto a library of sunflower long terminal repeat retrotransposons, we observed considerable variability in redundancy among genotypes, at both superfamily and family levels. In another analysis, we mapped Illumina paired reads to two sets of sequences, that is, long terminal repeat retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the sunflower genome by counting the number of paired reads in which one read mapped to a retrotransposon and the other to a gene. Large variability among genotypes was also ascertained for retrotransposon proximity to genes. Both long terminal repeat retrotransposon redundancy and proximity to genes varied among retrotransposon families and also between cultivated and wild genotypes. Such differences are discussed in relation to the possible role of long terminal repeat retrotransposons in the domestication of sunflower. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  5. Fytochemický výzkum Helianthus annuus L. II

    Niedobová, Soňa

    2007-01-01

    OF THE DIPLOMA THESIS My diploma thesis was intended on phytochemical study of polar extract of Helianthus annuus L. leaves and simultaneously biological tests were done (so-called bioassay - guided separation) - acute toxicity, antioxidant activity (DPPH test, FRAP metod) and antifungal activity. The Fraction 29 showed the highest antioxidant activity. The Fraction 22-24/3, obtained by preparative chromatography, was analyzed by gas chromatography. This analysis shows present of the oil-acid...

  6. Potential of Sunflower (Helianthus annuus L.) for Phytoremediation of Soils Contaminated with Heavy Metals

    Violina R. Angelova; Mariana N. Perifanova-Nemska; Galina P. Uzunova; Krasimir I. Ivanov; Huu Q. Lee

    2016-01-01

    A field study was conducted to evaluate the efficacy of the sunflower (Helianthus annuus L.) for phytoremediation of contaminated soils. The experiment was performed on an agricultural field contaminated by the Non-Ferrous-Metal Works near Plovdiv, Bulgaria. Field experiments with a randomized, complete block design with five treatments (control, compost amendments added at 20 and 40 t/daa, and vemicompost amendments added at 20 and 40 t/daa) were carried out. The accumulation of heavy metals...

  7. Accumulation of radioiodine from aqueous solution by hydroponically cultivated sunflower (Helianthus annuus L.)

    Soudek, Petr; Tykva, Richard; Vaňková, Radomíra; Vaněk, Tomáš

    2006-01-01

    Roč. 57, č. 3 (2006), s. 220-225 ISSN 0098-8472 R&D Projects: GA MŠk(CZ) 1P05OC042 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z50380511 Keywords : radiophytoremediation * Helianthus annuus * radioiodine Subject RIV: DK - Soil Contamination ; De-contamination incl. Pesticides Impact factor: 1.820, year: 2006

  8. IN VITRO PHYTOREMEDIATION OF PERSISTENT ORGANIC POLLUTANTS BY Helianthus annuus L. PLANTS

    Almeida, Marcos V. de; Rissato, Sandra R.; Galhiane, Mário S.; Fernandes, João R.; Lodi, Paulo C.; Campos, Marcelo C. de

    2018-01-01

    Plant model systems are needed to properly conduct basic laboratory studies prior to field applications of phytoremediation. In vitro plant cultures are a useful tool for such research. This study focuses on the removal and/or degradation of 24 persistent organic pollutants under in vitro conditions by Helianthus annuus L (sunflower). The main purpose of exploiting this plant for phytoremediation process is due to its strong adaptability to adverse environments conditions such as resistance t...

  9. PERENNIAL HELIANTHUS TAXA IN TÂRGU-MURES CITY AND ITS SURROUNDINGS

    FILEP RITA

    2010-12-01

    Full Text Available Although in the neighbouring countries several perennial Helianthus taxa have been recorded in the last decade, in Romania only three have been identified so far. The literature and herbaria data of Târgu-Mures date back to the end of the XIXth century, and only refer to H. × multiflorus and H. tuberosus. The aim of this study was to identify the perennial Helianthus taxa in this region and to prepare their current distribution map. The survey was conducted in Târgu Mures city and the neighbouring villages: Livezeni, Sântana de Mures, Sâncraiu de Mures, Sângeorgiu de Mures, and Corunca. Four taxa were identified: H. pauciflorus Nutt., H. × laetiflorus Pers., H. tuberosus L. s.str., and Helianthus tuberosus L. s.l. The first two taxa are cultivated as ornamental plants, H. tuberosus s. str. is cultivated in a few farms, whereas H. tuberosus s. l. is an invasive species that spreads along the rivers.

  10. [Protective effect of Helianthus annuus (sunflower) on myocardial infarction in New Zealand rabbit].

    Guardia-Espinoza, Edith; Herrera-Hurtado, Gianina Liseth del Carmen; Garrido-Jacobi, Saúl; Cárdenas-Peralta, Danitza; Martínez-Romero, Christian; Hernández-Figueroa, Pedro; Condori-Calizaya, Mary; La Barrera-Llacchua, Juan; Flores-Ángeles, Miguel

    2015-01-01

    Determine the protective effect of oil Helianthus annuus (Sunflower) on myocardial infarction induced by epinephrine in New Zealand rabbits. The rabbits were randomized into five groups (8 per group): blank, negative control, experimental 1 (10 mg / kg), experimental 2 (20 mg / kg) and three experimental (40 mg/ kg). Experimental groups 1, 2 and 3 received Helianthus annuus oil for two weeks. Epinephrine (2 mg/Kg) to the negative, Experimental Control 1, 2 and 3 groups was given over two consecutive days with an interval of 24 h after pretreatment with oil. Twenty four hours after the last administration, the rabbits were anesthetized and sacrificed. Serum troponin I and polymorphonuclear evaluated by .mu.m.sup.2. Significant difference between the negative control group and the experimental groups 1, 2 and 3 was found in the serum variables troponin I and polymorphonuclear by .mu.m.sup.2. Helianthus annuus oil at doses of 20 mg/kg has protective effect on myocardial infarction induced by epinephrine in New Zealand rabbits.

  11. Possibilities of the management of Helianthus tuberosus species in Poodri PLA (Czech Republic)

    Svehlakova, H.; Janikova, A.; Kupka, J.; Sotkova, N.; Rajdus, T.

    2017-10-01

    This article deals with the possibilities of population management of invasive and in Czech Republic no - native species Helianthus tuberosus. We have chosen study areas in Poodri PLA, it is located near the industrial city Ostrava (Moravian-Silesian region). Invasive Helianthus tuberosus forms monodominant vegetation, excludes the original and often rare plant species and reduces biodiversity. It is a risk for the further development of the landscape of Poodri PLA. There is no known effective way to dispose of invasive Helianthus tuberosus so far. We have applied the proposed management works on 15 monitoring areas and then evaluated their effectiveness. We have used chemical (herbicides) and mechanical (mowing, digging up) methods and their combinations. The most effective was the combination of 3 interventions: manual mowing - spraying - mowing by mechanization, just mowing itself rather promotes the spread of the population. We can say this is a pilot study from a long-term project dealing with the effectiveness of different ways of invasive plants management.

  12. Sorting through the chaff, nDNA gene trees for phylogenetic inference and hybrid identification of annual sunflowers (Helianthus sect. Helianthus).

    Moody, Michael L; Rieseberg, Loren H

    2012-07-01

    The annual sunflowers (Helianthus sect. Helianthus) present a formidable challenge for phylogenetic inference because of ancient hybrid speciation, recent introgression, and suspected issues with deep coalescence. Here we analyze sequence data from 11 nuclear DNA (nDNA) genes for multiple genotypes of species within the section to (1) reconstruct the phylogeny of this group, (2) explore the utility of nDNA gene trees for detecting hybrid speciation and introgression; and (3) test an empirical method of hybrid identification based on the phylogenetic congruence of nDNA gene trees from tightly linked genes. We uncovered considerable topological heterogeneity among gene trees with or without three previously identified hybrid species included in the analyses, as well as a general lack of reciprocal monophyly of species. Nonetheless, partitioned Bayesian analyses provided strong support for the reciprocal monophyly of all species except H. annuus (0.89 PP), the most widespread and abundant annual sunflower. Previous hypotheses of relationships among taxa were generally strongly supported (1.0 PP), except among taxa typically associated with H. annuus, apparently due to the paraphyly of the latter in all gene trees. While the individual nDNA gene trees provided a useful means for detecting recent hybridization, identification of ancient hybridization was problematic for all ancient hybrid species, even when linkage was considered. We discuss biological factors that affect the efficacy of phylogenetic methods for hybrid identification.

  13. The tolerance efficiency of Panicum maximum and Helianthus annuus in TNT-contaminated soil and nZVI-contaminated soil.

    Jiamjitrpanich, Waraporn; Parkpian, Preeda; Polprasert, Chongrak; Laurent, François; Kosanlavit, Rachain

    2012-01-01

    This study was designed to compare the initial method for phytoremediation involving germination and transplantation. The study was also to determine the tolerance efficiency of Panicum maximum (Purple guinea grass) and Helianthus annuus (Sunflower) in TNT-contaminated soil and nZVI-contaminated soil. It was found that the transplantation of Panicum maximum and Helianthus annuus was more suitable than germination as the initiate method of nano-phytoremediation potting test. The study also showed that Panicum maximum was more tolerance than Helianthus annuus in TNT and nZVI-contaminated soil. Therefore, Panicum maximum in the transplantation method should be selected as a hyperaccumulated plant for nano-phytoremediation potting tests. Maximum tolerance dosage of Panicum maximum to TNT-concentration soil was 320 mg/kg and nZVI-contaminated soil was 1000 mg/kg in the transplantation method.

  14. Economically Viable Components from Jerusalem Artichoke (Helianthus tuberosus L.) in a Biorefinery Concept

    Johansson, Eva; Prade, Thomas; Angelidaki, Irini

    2015-01-01

    Biorefinery applications are receiving growing interest due to climatic and waste disposal issues and lack of petroleum resources. Jerusalem artichoke (Helianthus tuberosus L.) is suitable for biorefinery applications due to high biomass production and limited cultivation requirements. This paper...... focuses on the potential of Jerusalem artichoke as a biorefinery crop and the most viable products in such a case. The carbohydrates in the tubers were found to have potential for production of platform chemicals, e.g., succinic acid. However, economic analysis showed that production of platform chemicals...

  15. Role of proline to induce salinity tolerance in Sunflower (helianthus annusl.)

    Iqbal, A.; Iftikhar, I.I.; Nawaz, H.; Nawaz, M.

    2014-01-01

    The potted experiment was conducted to determine the exogenous role of proline to induce salinity tolerance in sunflower (Helianthus annus L.). Salinity levels (0, 60 and 120 mmol) were created according to the saturation percentage of soil. Different levels (0, 30, 60 mmol) of proline were applied as a foliar spray on sunflower under saline and non saline conditions. Application of proline as a foliar spray ameliorated the toxic effects of salinity on growth, physiological and biochemical attributes of sunflower. Among different levels of proline, 60 mmol was found to be the most effective in ameliorating the toxic effects of salinity on sunflower. (author)

  16. Somatic embryogenesis from corolla tubes of interspecific amphiploids between cultivated sunflower (Helianthus annuus L.) and its wild species

    Somatic embryogenesis in vitro provides an efficient means of plant multiplication, facilitating sunflower improvement and germplasm innovation. In the present study, using interspecific amphiploids (2n=4x=68) between cultivated sunflower and wild perennial Helianthus species as explant donors, soma...

  17. Genetic diversity and population structure of the endangered whorled sunflower, Helianthus verticillatus, at two sites in Georgia

    Helianthus verticillatus, the whorled sunflower, is an endangered species endemic to only a few locations in Tennessee, Alabama, and Georgia. This sunflower is an aggressive grower and attractive to both plant enthusiasts and pollinators with its multiple, small yellow flowers in late fall. There is...

  18. Toward a molecular cytogenetic map for cultivated sunflower (Helianthus annuus L.) by landed BAC/BIBAC clones

    Conventional karyotypes and various genetic linkage maps have been established in sunflower (Helianthus annuus L., 2n=34). However, the relationship between linkage groups and individual chromosomes of sunflower remains unknown and has considerable relevance for the sunflower research community. Rec...

  19. High genetic diversity and low population structure in Porter's sunflower (Helianthus porteri).

    Gevaert, Scott D; Mandel, Jennifer R; Burke, John M; Donovan, Lisa A

    2013-01-01

    Granite outcrops in the southeastern United States are rare and isolated habitats that support edaphically controlled communities dominated by herbaceous plants. They harbor rare and endemic species that are expected to have low genetic variability and high population structure due to small population sizes and their disjunct habitat. We test this expectation for an annual outcrop endemic, Helianthus porteri (Porter's sunflower). Contrary to expectation, H. porteri has relatively high genetic diversity (H e = 0.681) and relatively low genetic structure among the native populations (F ST = 0.077) when compared to 5 other Helianthus species (N = 288; 18 expressed sequence tag-SSR markers). These findings suggest greater gene flow than expected. The potential for gene flow is supported by the analysis of transplant populations established with propagules from a common source in 1959. One population established close to a native population (1.5 km) at the edge of the natural range is genetically similar to and shares rare alleles with the adjacent native population and is distinct from the central source population. In contrast, a transplant population established north of the native range has remained similar to the source population. The relatively high genetic diversity and low population structure of this species, combined with the long-term success of transplanted populations, bode well for its persistence as long as the habitat persists.

  20. Enhanced phytoextraction: II. Effect of EDTA and citric acid on heavy metal uptake by Helianthus annuus from a calcareous soil.

    Lesage, E; Meers, E; Vervaeke, P; Lamsal, S; Hopgood, M; Tack, F M G; Verloo, M G

    2005-01-01

    High biomass producing plant species, such as Helianthus annuus, have potential for removing large amounts of trace metals by harvesting the aboveground biomass if sufficient metal concentrations in their biomass can be achieved However, the low bioavailability of heavy metals in soils and the limited translocation of heavy metals to the shoots by most high biomass producing plant species limit the efficiency of the phytoextraction process. Amendment of a contaminated soil with ethylene diamine tetraacetic acid (EDTA) or citric acid increases soluble heavy metal concentrations, potentially rendering them more available for plant uptake. This article discusses the effects of EDTA and citric acid on the uptake of heavy metals and translocation to aboveground harvestable plant parts in Helianthus annuus. EDTA was included in the research for comparison purposes in our quest for less persistent alternatives, suitable for enhanced phytoextraction. Plants were grown in a calcareous soil moderately contaminated with Cu, Pb, Zn, and Cd and treated with increasing concentrations of EDTA (0.1, 1, 3, 5, 7, and 10 mmol kg(-1) soil) or citric acid (0.01, 0.05, 0.25, 0.442, and 0.5 mol kg(-1) soil). Heavy metal concentrations in harvested shoots increased with EDTA concentration but the actual amount of phytoextracted heavy metals decreased at high EDTA concentrations, due to severe growth depression. Helianthus annuus suffered heavy metal stress due to the significantly increased bioavailable metal fraction in the soil. The rapid mineralization of citric acid and the high buffering capacity of the soil made citric acid inefficient in increasing the phytoextracted amounts of heavy metals. Treatments that did not exceed the buffering capacity of the soil (heavy metal concentrations. Treatments with high concentrations resulted in a dissolution of the carbonates and compaction of the soil. These physicochemical changes caused growth depression of Helianthus annuus. EDTA and citric

  1. Visitantes florales diurnos del girasol (Helianthus annuus, Asterales: Asteraceae en la Argentina Diurnal floral visitors of sunflower (Helianthus annuus, Asterales: Asteraceae in Argentina

    Juan P. Torretta

    2010-06-01

    Full Text Available El girasol (Helianthus annuus L. es un importante cultivo oleaginoso en la Argentina. Durante tres campañas agrícolas, se determinaron la diversidad y la abundancia del elenco de los visitantes florales diurnos de capítulos de girasol, en ocho sitios que cubren gran parte del área cultivada en Argentina. Setenta y seis morfo-especies de visitantes florales, pertenecientes a ocho órdenes, fueron capturados sobre capítulos de este cultivo. El principal orden fue Hymenoptera, con 37 especies o morfoespecies, de las cuales 32 fueron abejas (Apoidea. Las familias de abejas más representadas fueron Apidae (13, Megachilidae (11 y Halictidae (7. La abeja doméstica (Apis mellifera L. realizó el 93% de las visitas. La composición del elenco de visitantes no mostró un patrón de variación identificable a lo largo del día, ni con respecto a la distancia al borde del cultivo, pero varió entre sitios de muestreo. Se concluye que la abeja doméstica es el principal polinizador del girasol en la Argentina, aunque varias especies nativas de abejas (Melissodes tintinnans (Holmberg, M. rufithorax Brèthes, Melissoptila tandilensis Holmberg, y Megachile spp. podrían ser consideradas como potenciales polinizadores del cultivo.Sunflower (Helianthus annuus L. is an important oilseed crop in Argentina. During three agricultural years, the diversity and abundance of diurnal floral visitors of sunflower heads were determined in eight sites spanning much of this crop's cultivation area in Argentina. Seventysix morpho-species of floral visitors, belonging to eight orders, were captured on sunflower. The principal order was Hymenoptera, with 37 species or morpho-species, of which 32 were bees (Apoidea. The most represented bee families were Apidae (13, Megachilidae (11 and Halictidae (7. The domestic bee (Apis mellifera L. accounted for 93% of the visits. Floral visitor composition did not show an identifiable variation pattern either throughout the day or

  2. Characterization of F1 interspecific hybrids between wild Helianthus annuus L. populations and cultivated sunflower

    Terzić Sreten

    2006-01-01

    Full Text Available Phenotype, chromosomes pairing and pollen vitality were compared between parental populations and F1 hybrids of interspecific cross between Helianthus annuus L. and cultivated sunflower. The investigation of the simple sequence repeats (SSR polymorphism was also used to test the hybrid nature of F1 populations. The phenotypic traits of F1 hybrid plants were either closer to the wild species or intermediate. Irregular chromosome pairing was found in only 0 to 10% of meiocytes in the meiosis of F1 hybrid plants. Interspecific crosses were confirmed with SSR markers in all hybrid combinations. Alleles that were not present in parental DNA were frequently observed in F1 hybrids. That is additional evidence that those hybrid combinations were not produced by self-fertilization. The results suggest that SSR markers can be efficiently used for the F1 hybrid characterization in crosses between closely related species, in which, the changes of phenotype, meiosis and pollen vitality are not always significant.

  3. Enzymatic browning and after-cooking darkening of Jerusalem artichoke tubers (Helianthus tuberosus L.)

    Bach, Vibe; Bennedbæk-Jensen, Sidsel; Clausen, Morten Rahr

    2013-01-01

    Jerusalem artichoke tubers (Helianthus tuberosus L.) undergo enzymatic browning when peeled or cut, and turn grey after boiling, due to after-cooking darkening reactions between iron and phenolic acids. In an attempt to reveal the components responsible for these discolouration reactions, sensory...... evaluation and instrumental colour measurements were related to contents of total phenolics, phenolic acids, organic acids and iron in three varieties of raw and boiled Jerusalem artichoke tubers harvested in the autumn and the spring. No differences were found between varieties in sensory evaluated...... enzymatic browning, but Rema and Draga had higher scores than Mari in after-cooking darkening. Jerusalem artichoke tubers had higher contents of total phenolics, phenolic acids and citric acid in the autumn and low contents in the spring, while it was the opposite for malic acid. None of the chemical...

  4. Enzymatic browning and after-cooking darkening of Jerusalem artichoke tubers (Helianthus tuberosus L.).

    Bach, Vibe; Jensen, Sidsel; Clausen, Morten R; Bertram, Hanne C; Edelenbos, Merete

    2013-11-15

    Jerusalem artichoke tubers (Helianthus tuberosus L.) undergo enzymatic browning when peeled or cut, and turn grey after boiling, due to after-cooking darkening reactions between iron and phenolic acids. In an attempt to reveal the components responsible for these discolouration reactions, sensory evaluation and instrumental colour measurements were related to contents of total phenolics, phenolic acids, organic acids and iron in three varieties of raw and boiled Jerusalem artichoke tubers harvested in the autumn and the spring. No differences were found between varieties in sensory evaluated enzymatic browning, but Rema and Draga had higher scores than Mari in after-cooking darkening. Jerusalem artichoke tubers had higher contents of total phenolics, phenolic acids and citric acid in the autumn and low contents in the spring, while it was the opposite for malic acid. None of the chemical parameters investigated could explain the discolouration of the Jerusalem artichoke tubers. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. Genetic diversity of worldwide Jerusalem artichoke (Helianthus tuberosus) germplasm as revealed by RAPD markers.

    Wangsomnuk, P P; Khampa, S; Wangsomnuk, P; Jogloy, S; Mornkham, T; Ruttawat, B; Patanothai, A; Fu, Y B

    2011-12-12

    Jerusalem artichoke (Helianthus tuberosus) is a wild relative of the cultivated sunflower (H. annuus); it is an old tuber crop that has recently received renewed interest. We used RAPD markers to characterize 147 Jerusalem artichoke accessions from nine countries. Thirty RAPD primers were screened; 13 of them detected 357 reproducible RAPD bands, of which 337 were polymorphic. Various diversity analyses revealed several different patterns of RAPD variation. More than 93% of the RAPD variation was found within accessions of a country. Weak genetic differentiation was observed between wild and cultivated accessions. Six groups were detected in this germplasm set. Four ancestral groups were found for the Canadian germplasm. The most genetically distinct accessions were identified. These findings provide useful diversity information for understanding the Jerusalem artichoke gene pool, for conserving Jerusalem artichoke germplasm, and for choosing germplasm for genetic improvement.

  6. Effects of gamma radiation on stem diameter growth, carbon gain and biomass partitioning in Helianthus annuus

    Thiede, M.E.; Link, S.O.; Fellows, R.J.; Beedlow, P.A.

    1995-01-01

    To determine the effects of gamma radiation on stem diameter growth, carbon gain, and biomass partitioning, 19-day-old dwarf sunflower plants (Helianthus annuus, variety NK894) were given variable doses (0–40 Gy) from a 60Co gamma source. Exposure of plants to gamma radiation caused a significant reduction in stem growth and root biomass. Doses as low as 5 Gy resulted in a significant increase in leaf density, suggesting that very low doses of radiation could induce morphological growth changes. Carbohydrate analysis of plants exposed to 40 Gy demonstrated significantly more starch content in leaves and significantly less in stems 18 days after exposure compared with control plants. In contrast, the carbohydrate content of the roots of plants exposed to 40 Gy was not significantly different from non-irradiated plants 18 days after exposure. (author)

  7. Elimination of natural uranium and 226Ra from contaminated waters by rhizofiltration using Helianthus annuus L

    Vera Tome, F.; Blanco Rodriguez, P.; Lozano, J.C.

    2008-01-01

    The elimination of natural uranium and 226 Ra from contaminated waters by rhizofiltration was tested using Helianthus annuus L. (sunflower) seedlings growing in a hydroponic medium. Different experiments were designed to determine the optimum age of the seedlings for the remediation process, and also to study the principal way in which the radionuclides are removed from the solution by the sunflower roots. In every trial a precipitate appeared which contained a major fraction of the natural uranium and 226 Ra. The results indicated that the seedlings themselves induced the formation of this precipitate. When four-week-old seedlings were exposed to contaminated water, a period of only 2 days was sufficient to remove the natural uranium and 226 Ra from the solution: about 50% of the natural uranium and 70% of the 226 Ra were fixed in the roots, and essentially the rest was found in the precipitate, with only very small percentages fixed in the shoots and left in solution

  8. Isolation of Bioactive Compounds from Sunflower Leaves (Helianthus annuus L.) Extracted with Supercritical Carbon Dioxide.

    El Marsni, Zouhir; Torres, Ascension; Varela, Rosa M; Molinillo, José M G; Casas, Lourdes; Mantell, Casimiro; Martinez de la Ossa, Enrique J; Macias, Francisco A

    2015-07-22

    The work described herein is a continuation of our initial studies on the supercritical fluid extraction (SFE) with CO2 of bioactive substances from Helianthus annuus L. var. Arianna. The selected SFE extract showed high activity in the wheat coleoptile bioassay, in Petri dish phytotoxicity bioassays, and in the hydroponic culture of tomato seeds. Chromatographic fractionations of the extracts and a spectroscopic analysis of the isolated compounds showed 52 substances belonging to 10 different chemical classes, which were mainly sesquiterpene lactones, diterpenes, and flavonoids. Heliannuol M (31), helivypolides K and L (36, 37), and helieudesmanolide B (38) are described for the first time in the literature. Metabolites have been tested in the etiolated wheat coleoptile bioassay with good results in a noteworthy effect on germination. The most active compounds were also tested on tomato seeds, heliannuol A (30) and leptocarpin (45) being the most active, with values similar to those of the commercial herbicide.

  9. The effect of culinary preparation on carbohydrate composition, texture and sensory quality of Jerusalem artichoke tubers (Helianthus tuberosus L.)

    Bach, Vibe; Bennedbæk-Jensen, Sidsel; Kidmose, Ulla

    2013-01-01

    The Jerusalem artichoke (Helianthus tuberosus L.) tuber is a root vegetable with excellent gastronomic qualities, however the culinary properties are underexploited. Carbohydrate content, instrumental texture analysis and sensory profiling were used to study the effects of culinary preparation...... in three different varieties of Jerusalem artichoke tubers at two different harvest times. Texture attributes and sweetness were the best sensory attributes to discriminate between varieties, although differences in texture and taste were somewhat evened out during boiling and baking. Instrumentally...

  10. Genomic islands of divergence are not affected by geography of speciation in sunflowers.

    Renaut, S; Grassa, C J; Yeaman, S; Moyers, B T; Lai, Z; Kane, N C; Bowers, J E; Burke, J M; Rieseberg, L H

    2013-01-01

    Genomic studies of speciation often report the presence of highly differentiated genomic regions interspersed within a milieu of weakly diverged loci. The formation of these speciation islands is generally attributed to reduced inter-population gene flow near loci under divergent selection, but few studies have critically evaluated this hypothesis. Here, we report on transcriptome scans among four recently diverged pairs of sunflower (Helianthus) species that vary in the geographical context of speciation. We find that genetic divergence is lower in sympatric and parapatric comparisons, consistent with a role for gene flow in eroding neutral differences. However, genomic islands of divergence are numerous and small in all comparisons, and contrary to expectations, island number and size are not significantly affected by levels of interspecific gene flow. Rather, island formation is strongly associated with reduced recombination rates. Overall, our results indicate that the functional architecture of genomes plays a larger role in shaping genomic divergence than does the geography of speciation.

  11. Visitantes florales nocturnos del girasol (Helianthus annuus, Asterales: Asteraceae en la Argentina Nocturnal floral visitors of sunflower (Helianthus annuus, Asterales: Asteraceae in Argentina

    Juan P Torretta

    2009-12-01

    Full Text Available El girasol (Helianthus annuus es un cultivo oleaginoso, polinizado por Apis mellifera L. y otras abejas en distintas regiones del mundo. Sin embargo, sus flores también son visitadas por insectos de actividad nocturna. Durante tres campañas agrícolas, se determinó la diversidad de los visitantes nocturnos de capítulos de girasol, en cinco sitios de Argentina. También se estudió el comportamiento de forrajeo de los principales visitantes y la variación de la receptividad estigmática a lo largo del día, con el fin de establecer si estos visitantes contribuyen a la polinización. Al menos 67 especies o morfoespecies pertenecientes a cuatro órdenes de visitantes nocturnos fueron colectadas. El orden más rico y abundante fue Lepidoptera (44 especies o morfoespecies, cinco familias, seguido por Coleoptera (18 especies o morfoespecies, nueve familias, Orthoptera (tres morfoespecies, una familia y Blattaria (dos especies, una familia. Los lepidópteros forrajearon exclusivamente por néctar, mientras que los individuos de los demás órdenes consumieron polen y/o partes florales. El estigma se encontró receptivo durante las horas de luz, con una receptividad máxima al mediodía (12:00 - 14:00. Llamativamente, las flores del girasol son visitadas por mayor número de polillas que de abejas. Debido a que las polillas consumen néctar y potencialmente transportan polen entre flores, en un momento del día en que los estigmas se encuentran menos receptivos, es improbable que polinicen efectivamente el cultivo.Sunflower (Helianthus annuus is an oilseed crop pollinated by Apis mellifera L. and other diurnal bees in different regions of the world. However, their flowers are also visited by insects active at night. During three agricultural years, the diversity of nocturnal visitors to sunflower heads was assessed in five different sites in Argentina. The foraging behavior of the main visitors as well as the stigmatic receptivity variations along

  12. [Agrobacterium-mediated sunflower transformation (Helianthus annuus L.) in vitro and in Planta using strain of LBA4404 harboring binary vector pBi2E with dsRNA-suppressor proline dehydrogenase gene].

    Tishchenko, E N; Komisarenko, A G; Mikhal'skaia, S I; Sergeeva, L E; Adamenko, N I; Morgun, B V; Kochetov, A V

    2014-01-01

    To estimate the efficiency of proline dehydrogenase gene suppression towards increasing of sunflower (Helianthus annuus L.) tolerance level to water deficit and salinity, we employed strain LBA4404 harboring pBi2E with double-stranded RNA-suppressor, which were prepared on basis arabidopsis ProDH1 gene. The techniques of Agrobacterium-mediated transformation in vitro and in planta during fertilization sunflower have been proposed. There was shown the genotype-depended integration of T-DNA in sunflower genome. PCR-analysis showed that ProDH1 presents in genome of inbred lines transformed in planta, as well as in T1- and T2-generations. In trans-genic regenerants the essential accumulation of free L-proline during early stages of in vitro cultivation under normal conditions was shown. There was established the essential accumulation of free proline in transgenic regenerants during cultivation under lethal stress pressure (0.4 M mannitol and 2.0% sea water salts) and its decline upon the recovery period. These data are declared about effectiveness of suppression of sunflower ProDH and gene participation in processes connected with osmotolerance.

  13. Genotype by environment interaction in sunflower (Helianthus annus L.) to optimize trial network efficiency

    Gonzalez-Barrios, P.; Castro, M.; Pérez, O.; Vilaró, D.; Gutiérrez, L.

    2017-07-01

    Modeling genotype by environment interaction (GEI) is one of the most challenging aspects of plant breeding programs. The use of efficient trial networks is an effective way to evaluate GEI to define selection strategies. Furthermore, the experimental design and the number of locations, replications, and years are crucial aspects of multi-environment trial (MET) network optimization. The objective of this study was to evaluate the efficiency and performance of a MET network of sunflower (Helianthus annuus L.). Specifically, we evaluated GEI in the network by delineating mega-environments, estimating genotypic stability and identifying relevant environmental covariates. Additionally, we optimized the network by comparing experimental design efficiencies. We used the National Evaluation Network of Sunflower Cultivars of Uruguay (NENSU) in a period of 20 years. MET plot yield and flowering time information was used to evaluate GEI. Additionally, meteorological information was studied for each sunflower physiological stage. An optimal network under these conditions should have three replications, two years of evaluation and at least three locations. The use of incomplete randomized block experimental design showed reasonable performance. Three mega-environments were defined, explained mainly by different management of sowing dates. Late sowings dates had the worst performance in grain yield and oil production, associated with higher temperatures before anthesis and fewer days allocated to grain filling. The optimization of MET networks through the analysis of the experimental design efficiency, the presence of GEI, and appropriate management strategies have a positive impact on the expression of yield potential and selection of superior cultivars.

  14. Phytoremediation of heavy metal copper (Cu2+) by sunflower (Helianthus annuus l.)

    Mahardika, G.; Rinanti, A.; Fachrul, M. F.

    2018-01-01

    A study in microcosmic condition has been carried out to determine the effectiveness of Helianthus annuus as a hyperaccumulator plant for heavy metal, Copper (Cu2+), that exposed in the soil. Artificial pollutants containing Copper (Cu2+) 0, 60, 120, 180 ppm are exposed to uncontaminated soil. The 12-weeks old H. annuus seedling were grown in Cu2+ contaminated soil, with variations of absorption time 3, 6, and 9 weeks. Analysis of Cu2+ concentration on soil and H. annuus (root, stem, leaf) was analised by Atomic Absorbtion Spectrometry (AAS). H. annuus are capable for Cu2+ removal, and the highest removal of Cu2+ is 85.56%, the highest metal accumulation/bioconcentration factor (BCF) is 0.99 occurred at roots with 9 weeks of exposure time and the highest translocation factor (TF) is 0.71. This highest removal is five times better than absorption by stems and leaves. The results concluded, the use of H. annuus for phytoextraction of heavy metals Cu2+ in contaminated soil can be an alternative to the absorption of heavy metal Cu2+ with low concentration metals which is generally very difficult to do in physical-chemical removal.

  15. Seed Germination and Physiological Response of Sunflower (Helianthus annuus L. Cultivars under Saline Conditions

    Carmen BEINSAN

    2018-05-01

    Full Text Available The purpose of the experiment was to highlight the germination of sunflower seeds affected by the presence of saline stress and the identification of tolerant genotypes. The biological material was represented by sunflower cvs. (Helianthus annuus L.: Coril, Select, Santiago and Fundulea-206. To simulate the saline conditions, germination solutions of sodium chloride (NaCl were used with concentrations corresponding to the osmotic pressures -6 and -10 atm and the control seed hydration was performed with distilled water. Determination of seed germination, growth of seedling, percentage of plumules dry matter, chlorophyll content and free proline were performed. The experimental data obtained suppose the existence in the assimilation apparatus of sunflowers seedling subjected to stress a competitive chlorophyll/free proline biosynthesis processes. The experimental results regarding the effect of salinity on seed germination and seedling growth revealed important differences between genotypes. The radicle growth in the germination process were strongly affected by saline excess, with significant differences between cultivars. Saline stress results in significant reductions in the amount of chlorophyll, and high levels of free proline. It can be observed that with the increase of the stress level the percentage of the dry matter increases, indicating an accentuated water deficit.

  16. Economically Viable Components from Jerusalem Artichoke (Helianthus tuberosus L.) in a Biorefinery Concept

    Johansson, Eva; Prade, Thomas; Angelidaki, Irini; Svensson, Sven-Erik; Newson, William R.; Gunnarsson, Ingólfur Bragi; Persson Hovmalm, Helena

    2015-01-01

    Biorefinery applications are receiving growing interest due to climatic and waste disposal issues and lack of petroleum resources. Jerusalem artichoke (Helianthus tuberosus L.) is suitable for biorefinery applications due to high biomass production and limited cultivation requirements. This paper focuses on the potential of Jerusalem artichoke as a biorefinery crop and the most viable products in such a case. The carbohydrates in the tubers were found to have potential for production of platform chemicals, e.g., succinic acid. However, economic analysis showed that production of platform chemicals as a single product was too expensive to be competitive with petrochemically produced sugars. Therefore, production of several products from the same crop is a must. Additional products are protein based ones from tubers and leaves and biogas from residues, although both are of low value and amount. High bioactive activity was found in the young leaves of the crop, and the sesquiterpene lactones are of specific interest, as other compounds from this group have shown inhibitory effects on several human diseases. Thus, future focus should be on understanding the usefulness of small molecules, to develop methods for their extraction and purification and to further develop sustainable and viable methods for the production of platform chemicals. PMID:25913379

  17. Sorption characteristics of pectin isolated from Jerusalem Artichoke tubers (Helianthus tuberosus L.

    N. Toshkov

    2015-05-01

    Full Text Available Introduction. The aim of the present study is the isolation of pectin from Jerusalem artichoke tubers (Helianthus tuberosus L. and the analysis of its sorption characteristics Materials and methods. Research was carried out on the pectin content of the tubers of Jerusalem artichoke plants cultivated in Bulgaria. The polyuronide content (PUC was determined via the МсCready method. The static gravimetric method was used for analysis of the sorption characteristics of pectins. Results and discussion. The polysaccharide was extracted. The isolated pectins were analyzed in physical terms: the equilibrium sorption isotherms, belonging to type II in Brunauer’s classification, were obtained experimentally. The entire isotherm length demonstrated statistically significant hysteresis. The Henderson and Chung-Pfost models provided adequate isotherm description. The pectin content of the three Jerusalem artichoke samples is 14.8, 9.2 and 11.9 % a.d.m., respectively. The monomolecular moisture content of pectin was within the 7.42 – 7.92% dry basis range, its corresponding water activity value –within the 0.14 –0.16 range. Conclusion. The resultsof research are advisablefor use indevelop of functional food ingredient which is used pectin as a gelling agent and a stabilizer.

  18. Ultrastructure and autoradiography of dormant and activated parenchyma of Helianthus tuberosus

    Favali, M.A.; Sartorato, P.; Serafini-Fracassini, D.

    1984-01-01

    Parenchyma cells of dormant tubers of Helianthus tuberosus L. cv. OB 1 (Jerusalem artichoke) contain a very low amount of hormones, therefore they respond to 2.4-D or IAA treatment by dividing and synthesizing RNA, DNA, and polyamines. In particular the activation of the dormant tissues induces an early synthesis of DNA, which reaches the maximum at 3 hours, much before the beginning of the S phase (12 hours). By supplying [6- 3 H] thymidine and carrying out electron microscopic autoradiography, we were able to determine that plastids and mitochondria were the organelles responsible for this early synthesis while the DNA in the nucleus first appeared labeled at 15 hours. In addition, ultrastructural observations carried out to compare the dormant cells with activated ones, showed an increase in the nucleolar volume, a different organization of the tubular complex of the plastids and several other ultrastructural changes which indicate that at 3 hours some fundamental metabolic processes are already active; they become even more evident later on. The implication of these results in the physiology of the tuber cells during activation are discussed. (Author)

  19. Ultrastructure and autoradiography of dormant and activated parenchyma of Helianthus tuberosus

    Favali, M.A.; Sartorato, P. (Padua Univ. (Italy)); Serafini-Fracassini, D. (Bologna Univ. (Italy))

    1984-01-01

    Parenchyma cells of dormant tubers of Helianthus tuberosus L. cv. OB/sup 1/ (Jerusalem artichoke) contain a very low amount of hormones, therefore they respond to 2.4-D or IAA treatment by dividing and synthesizing RNA, DNA, and polyamines. In particular the activation of the dormant tissues induces an early synthesis of DNA, which reaches the maximum at 3 hours, much before the beginning of the S phase (12 hours). By supplying (6-/sup 3/H) thymidine and carrying out electron microscopic autoradiography, we were able to determine that plastids and mitochondria were the organelles responsible for this early synthesis while the DNA in the nucleus first appeared labeled at 15 hours. In addition, ultrastructural observations carried out to compare the dormant cells with activated ones, showed an increase in the nucleolar volume, a different organization of the tubular complex of the plastids and several other ultrastructural changes which indicate that at 3 hours some fundamental metabolic processes are already active; they become even more evident later on. The implication of these results in the physiology of the tuber cells during activation are discussed.

  20. Direct Analyses of Secondary Metabolites by Mass Spectrometry Imaging (MSI) from Sunflower (Helianthus annuus L.) Trichomes.

    Brentan Silva, Denise; Aschenbrenner, Anna-Katharina; Lopes, Norberto Peporine; Spring, Otmar

    2017-05-10

    Helianthus annuus (sunflower) displays non-glandular trichomes (NGT), capitate glandular trichomes (CGT), and linear glandular trichomes (LGT), which reveal different chemical compositions and locations in different plant tissues. With matrix-assisted laser desorption/ionization (MALDI) and laser desorption/ionization (LDI) mass spectrometry imaging (MSI) techniques, efficient methods were developed to analyze the tissue distribution of secondary metabolites (flavonoids and sesquiterpenes) and proteins inside of trichomes. Herein, we analyzed sesquiterpene lactones, present in CGT, from leaf transversal sections using the matrix 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxycinnamic acid (CHCA) (mixture 1:1) with sodium ions added to increase the ionization in positive ion mode. The results observed for sesquiterpenes and polymethoxylated flavones from LGT were similar. However, upon desiccation, LGT changed their shape in the ionization source, complicating analyses by MSI mainly after matrix application. An alternative method could be applied to LGT regions by employing LDI (without matrix) in negative ion mode. The polymethoxylated flavones were easily ionized by LDI, producing images with higher resolution, but the sesquiterpenes were not observed in spectra. Thus, the application and viability of MALDI imaging for the analyses of protein and secondary metabolites inside trichomes were confirmed, highlighting the importance of optimization parameters.

  1. Phomopsis Stem Canker: A Reemerging Threat to Sunflower (Helianthus annuus) in the United States.

    Mathew, Febina M; Alananbeh, Kholoud M; Jordahl, James G; Meyer, Scott M; Castlebury, Lisa A; Gulya, Thomas J; Markell, Samuel G

    2015-07-01

    Phomopsis stem canker causes yield reductions on sunflower (Helianthus annuus L.) on several continents, including Australia, Europe, and North America. In the United States, Phomopsis stem canker incidence has increased 16-fold in the Northern Great Plains between 2001 and 2012. Although Diaporthe helianthi was assumed to be the sole causal agent in the United States, a newly described species, D. gulyae, was found to be the primary cause of Phomopsis stem canker in Australia. To determine the identity of Diaporthe spp. causing Phomopsis stem canker in the Northern Great Plains, 275 infected stems were collected between 2010 and 2012. Phylogenetic analyses of sequences of the ribosomal DNA internal transcribed spacer region, elongation factor subunit 1-α, and actin gene regions of representative isolates, in comparison with those of type specimens, confirmed two species (D. helianthi and D. gulyae) in the United States. Differences in aggressiveness between the two species were determined using the stem-wound method in the greenhouse; overall, D. helianthi and D. gulyae did not vary significantly (P≤0.05) in their aggressiveness at 10 and 14 days after inoculation. These findings indicate that both Diaporthe spp. have emerged as sunflower pathogens in the United States, and have implications on the management of this disease.

  2. Combined linkage and association mapping of flowering time in Sunflower (Helianthus annuus L.).

    Cadic, Elena; Coque, Marie; Vear, Felicity; Grezes-Besset, Bruno; Pauquet, Jerôme; Piquemal, Joël; Lippi, Yannick; Blanchard, Philippe; Romestant, Michel; Pouilly, Nicolas; Rengel, David; Gouzy, Jerôme; Langlade, Nicolas; Mangin, Brigitte; Vincourt, Patrick

    2013-05-01

    Association mapping and linkage mapping were used to identify quantitative trait loci (QTL) and/or causative mutations involved in the control of flowering time in cultivated sunflower Helianthus annuus. A panel of 384 inbred lines was phenotyped through testcrosses with two tester inbred lines across 15 location × year combinations. A recombinant inbred line (RIL) population comprising 273 lines was phenotyped both per se and through testcrosses with one or two testers in 16 location × year combinations. In the association mapping approach, kinship estimation using 5,923 single nucleotide polymorphisms was found to be the best covariate to correct for effects of panel structure. Linkage disequilibrium decay ranged from 0.08 to 0.26 cM for a threshold of 0.20, after correcting for structure effects, depending on the linkage group (LG) and the ancestry of inbred lines. A possible hitchhiking effect is hypothesized for LG10 and LG08. A total of 11 regions across 10 LGs were found to be associated with flowering time, and QTLs were mapped on 11 LGs in the RIL population. Whereas eight regions were demonstrated to be common between the two approaches, the linkage disequilibrium approach did not detect a documented QTL that was confirmed using the linkage mapping approach.

  3. Sunflower (Helianthus annuus L.) as a pre-Columbian domesticate in Mexico

    Lentz, David L.; Pohl, Mary DeLand; Alvarado, José Luis; Tarighat, Somayeh; Bye, Robert

    2008-01-01

    Mexico has long been recognized as one of the world's cradles of domestication with evidence for squash (Cucurbita pepo) cultivation appearing as early as 8,000 cal B.C. followed by many other plants, such as maize (Zea mays), peppers (Capsicum annuum), common beans (Phaseolus vulgaris), and cotton (Gossypium hirsutum). We present archaeological, linguistic, ethnographic, and ethnohistoric data demonstrating that sunflower (Helianthus annuus) had entered the repertoire of Mexican domesticates by ca. 2600 cal B.C., that its cultivation was widespread in Mexico and extended as far south as El Salvador by the first millennium B.C., that it was well known to the Aztecs, and that it is still in use by traditional Mesoamerican cultures today. The sunflower's association with indigenous solar religion and warfare in Mexico may have led to its suppression after the Spanish Conquest. The discovery of ancient sunflower in Mexico refines our knowledge of domesticated Mesoamerican plants and adds complexity to our understanding of cultural evolution. PMID:18443289

  4. Effects of sewage sludge fertilizer on heavy metal accumulation and consequent responses of sunflower (Helianthus annuus).

    Belhaj, Dalel; Elloumi, Nada; Jerbi, Bouthaina; Zouari, Mohamed; Abdallah, Ferjani Ben; Ayadi, Habib; Kallel, Monem

    2016-10-01

    Use of sewage sludge, a biological residue produced from sewage treatment processes in agriculture, is an alternative disposal technique of waste. To study the usefulness of sewage sludge amendment for Helianthus annuus, a pot experiment was conducted by mixing sewage sludge at 2.5, 5, and 7.5 % (w/w) amendment ratios to the agricultural soil. Soil pH decreased whereas electrical conductivity, organic matter, total N, available P, and exchangeable Na, K, and Ca increased in soil amended with sewage sludge in comparison to unamended soil. Sewage sludge amendment led to significant increase in Pb, Ni, Cu, Cr, and Zn concentrations of soil. The increased concentration of heavy metals in soil due to sewage sludge amendment led to increases in shoot and root concentrations of Cr, Cu, Ni, and Zn in plant as compared to those grown on unamended soil. Accumulation was more in roots than shoots for most of the heavy metals. Moreover, high metal removal for the harvestable parts of the crops was recorded. Sewage sludge amendment increased root and shoot length, leaves number, biomass, and antioxidant activities of sunflower. Significant increases in the activities of antioxidant enzymes and in the glutathione, proline, and soluble sugar content in response to amendment with sewage sludge may be defense mechanisms induced in response to heavy metal stress. Graphical abstract Origin, fate and behavior of sewage sludge fertilizer.

  5. Biosurfactant-assisted phytoremediation of multi-contaminated industrial soil using sunflower (Helianthus annuus L.).

    Liduino, Vitor S; Servulo, Eliana F C; Oliveira, Fernando J S

    2018-02-01

    This study evaluated the use of commercial rhamnolipid biosurfactant supplementation in the phytoremediation of a soil via sunflower (Helianthus annuus L.) cultivation. The soil, obtained from an industrial area, was co-contaminated with heavy metals and petroleum hydrocarbons. The remediation tests were monitored for 90 days. The best results for removal of contaminants were obtained from the tests in which the sunflower plants were cultivated in soil with 4 mg kg -1 of the rhamnolipid. Under these conditions, reductions of 58% and 48% were obtained in the total petroleum hydrocarbon (TPH) and polycyclic aromatic hydrocarbon (PAH) concentrations, respectively; reductions in the concentrations of the following metals were also achieved: Ni (41%), Cr (30%), Pb (29%), and Zn (20%). The PCR-DGGE analysis of soil samples collected before and after the treatments verified that the plant cultivation and biosurfactants supplementation had little effect on the structure of the dominant bacterial community in the soil. The results indicated that sunflower cultivation with the addition of a biosurfactant is a viable and efficient technology to treat soils co-contaminated with heavy metals and petroleum hydrocarbons.

  6. Alleviation of adverse impact of cadmium stress in sunflower (helianthus annuus l.) by arbuscular mycorrhizal fungi

    ALLAH, E.F.; Alqarawi, A.A.; Hend, A.

    2015-01-01

    Sunflower (Helianthus annuus L.) is an important ornamental plant and good source of vegetable oil, widely accepted as potential promising plant for phytoremediation. A pot experiment was conducted to evaluate the impact of cadmium on the growth and some biochemical attributes of sunflower and role of arbuscular mycorrhizal fungi (AMF) in assuaging the cadmium stress induced changes. Cadmium treatment reduced growth, chlorophyll contents and cell membrane stability. AMF inoculated plants showed increased growth, chlorophyll contents and cell membrane stability and also mitigated changes caused due to cadmium. Cadmium caused increase in lipid peroxidation, and hydrogen peroxide production. An increase in antioxidant enzyme activity was observed due to cadmium treatment which was further enhanced by inoculation of AMF. Increase in proline and total phenols due to cadmium stress was obvious. Cadmium stressed plants showed enhanced fatty acid content. AMF inoculated plants showed higher activities of acid and alkaline phosphatases which were reduced by cadmium stress. However palmitoleic acid (C16:1), oleic (C18:1), linoleic (C18:2) and linolenic acid (C18:3) reduced in cadmium treated plants and the negative impact of cadmium was mitigated by AMF. (author)

  7. A time-series phytoremediation experiment with sunflowers (Helianthus annuus on a former uranium mining site

    Kötschau A.

    2013-04-01

    Full Text Available On a test field situated at a former uranium mining site near Ronneburg (Thuringia, Germany a small scale time-series field experiment with sunflowers (Helianthus annuus was carried out. This area ghas elevated contents for the heavy metals Cd, Co, Cr, Cu, Ni, Zn including the radionuclides U and Th. Over a time period of 24 weeks the sunflowers were cultivated on homogenized soil substrate and regularly harvested. The aim was to find the ideal moment to harvest the sunflowers, being defined as having the best balance between the extraction of the contaminants and a high biomass produced. The contents of the elements were determined in soil, roots and above-ground plant parts. The contents in the above-ground plant showed no clear increasing or decreasing trend over time, so they were not the appropriate values to determine the best moment to harvest. Instead the total extracted masses (content in μg/g x biomass in g of the contaminants in the above-ground plant parts were calculated. According to this the best moment to harvest the sunflower plants was reached after 24 weeks of vegetation, because the highest extracted masses for all contaminants were calculated to this time. Additionally the biomass, which could be used e.g. for bio-fuel production, was highest at this time.

  8. IN VITRO PHYTOREMEDIATION OF PERSISTENT ORGANIC POLLUTANTS BY Helianthus annuus L. PLANTS

    Marcos V. de Almeida

    Full Text Available Plant model systems are needed to properly conduct basic laboratory studies prior to field applications of phytoremediation. In vitro plant cultures are a useful tool for such research. This study focuses on the removal and/or degradation of 24 persistent organic pollutants under in vitro conditions by Helianthus annuus L (sunflower. The main purpose of exploiting this plant for phytoremediation process is due to its strong adaptability to adverse environments conditions such as resistance to pests, disease, and others. The study of bioremediation effects of all chemical molecules under in vitro conditions showed promising results. Sixteen out of twenty-four compounds evaluated reached up to 87% for remediation. The highest accumulation of pollutants was observed in the roots, showing that these results are consistent with the current literature. Through the study, it was observed effective absorption of POPs with logKow ranging from 4.50 to 6.91. Sunflower phytoremediation process efficiently detected heptachlor, aldrin, heptachlor epoxide, trans-chlordane, chlordane, dieldrin, DDE, DDT, methoxychlor, mirex and decachlorobiphenyl.

  9. The 134Cs uptake by sunflower (Helianthus anuus, Less) cultivated on soil contaminated with 134Cs

    Poppy Intan Tjahaja; Putu Sukmabuana

    2008-01-01

    One of the methods for remediation of contaminated environment is phytoremediation techniques, i.e. the environmental remediation using plants. In this research the bioavailability of sunflower plant (Helianthus anuus, Less) in radiocaesium uptake from soil was studied for being considered as a phytoremediator later. Sunflower plants were cultivated on soil contaminated with 134 Cs with the concentrations of 29,3 kBq/kg ; 117,2 kBq/kg ; 557 kBq/kg for 45 days. As control the sunflowers were also cultivated on non contaminated soil. Observation was carried out every 5 days by sampling 3 plants and soils. The plant and soil samples were dried using infra red lamp for 24 hours, and then counted using gamma spectrometer. The counting results i.e. 134 Cs concentration on soil and plant parts were then analyzed to obtain transfer factor (TF) values. The highest TF values was reached on 26 th day, i.e. 0,87; 1,89 ; 2,82 for initial soil 134 Cs concentrations of 29,3 Bq/g ; 117,2 Bq/g ; 557 Bq/g, respectively. The TF values obtained expressed the capability of plants to accumulate 134 Cs from soils. The observation to the plants growth showed that the plants grew normally on the 134 Cs contaminated soil until the concentration of 557 Bq/g. The sunflower can be considered to be phytoremediator of andosol soil contaminated with Cs radionuclides. (author)

  10. Hairy roots of Helianthus annuus: a model system to study phytoremediation of tetracycline and oxytetracycline.

    Gujarathi, Ninad P; Haney, Bryan J; Park, Heidi J; Wickramasinghe, S Ranil; Linden, James C

    2005-01-01

    The release of antibiotics to the environment has to be controlled because of serious threats to human health. Hairy root cultures of Helianthus annuus (sunflower), along with their inherent rhizospheric activity, provide a fast growing, microbe-free environment for understanding plant-pollutant interactions. The root system catalyzes rapid disappearance of tetracycline (TC) and oxytetracycline (OTC) from aqueous media, which suggests roots have potential for phytoremediation of the two antibiotics in vivo. In addition, in vitro modifications of the two antibiotics by filtered, cell- and microbe-free root exudates suggest involvement of root-secreted compounds. The modification is confirmed from changes observed in UV spectra of exudate-treated OTC. Modification appears to be more dominant at the BCD chromophore of the antibiotic molecule. Kinetic analyses dismiss direct enzyme catalysis; the modification rates decrease with increasing OTC concentrations. The rates increase with increasing age of cultures from which root exudates are prepared. The decrease in modification rates upon addition of the antioxidant ascorbic acid (AA) suggests involvement of reactive oxygen species (ROS) in the antibiotic modification process.

  11. Visitantes florales diurnos del girasol (Helianthus annuus, Asterales: Asteraceae en la Argentina

    Juan P. TORRETTA

    2010-01-01

    Full Text Available El girasol ( Helianthus annuus L. es un importante cultivo oleaginoso en la Argentina. Durante tres campañas agrícolas, se determinaron la diversidad y la abundancia del elenco de los visitantes florales diurnos de capítulos de girasol, en ocho sitios que cubren gran parte del área cultivada en Argentina. Setenta y seis morfo-especies de visitantes florales, pertenecientes a ocho órdenes, fueron capturados sobre capítulos de este cultivo. El principal orden fue Hymenoptera, con 37 especies o morfo- especies, de las cuales 32 fueron abejas (Apoidea. Las familias de abejas más representadas fueron Apidae (13, Megachilidae (11 y Halictidae (7. La abeja doméstica ( Apis mellifera L. realizó el 93% de las visitas. La composición del elenco de visitantes no mostró un patrón de variación identificable a lo largo del día, ni con respecto a la distancia al borde del cultivo, pero varió entre sitios de muestreo. Se concluye que la abeja doméstica es el principal polinizador del girasol en la Argentina, aunque varias especies nativas de abejas ( Melissodes tintinnans (Holmberg, M. rufithorax Brèthes, Melissoptila tandilensis Holmberg, y Megachile spp. podrían ser consideradas como potenciales polinizadores del cultivo.

  12. Μetal Uptake by Sunflower (Helianthus annuus) Irrigated with Water Polluted with Chromium and Nickel.

    Stoikou, Vasiliki; Andrianos, Vangelis; Stasinos, Sotiris; Kostakis, Marios G; Attiti, Sofia; Thomaidis, Nikolaos S; Zabetakis, Ioannis

    2017-07-17

    The water aquifers of the regions of Asopos River in Viotia and Messapia in Evia (Greece) have been contaminated with hexavalent chromium (Cr (VI)) and bivalent nickel (Ni (II)). Given that these areas are the two biggest tuber producing regions of Greece, in our previous work, the cross-contamination of the food chain with these two heavy metals was quantified. In the present study, the potential of sunflower ( Helianthus annuus ) cultivation in these regions is evaluated. The scope of our study was to investigate the uptake of chromium and nickel by sunflower, in a greenhouse experiment. The study included two cultivation periods of plants in six irrigation lines with different levels of Cr (VI) and Ni (II) ranging from 0 μg/L (control) to 10,000 μg/L. In all plant parts, statistically significant increased levels of Cr (VI) and Ni (II) were found when compared to control ones. Also, a positive correlation, both for Cr and Ni, between levels of heavy metals in irrigation water and plants was observed. Following European Food Safety Authority recommendations, the obtained oil was evaluated as safe for consumption, therefore, sunflower cultivation could be a valid bioremediation solution for the Asopos and Messapia regions.

  13. Evidence of correlated evolution and adaptive differentiation of stem and leaf functional traits in the herbaceous genus, Helianthus.

    Pilote, Alex J; Donovan, Lisa A

    2016-12-01

    Patterns of plant stem traits are expected to align with a "fast-slow" plant economic spectrum across taxa. Although broad patterns support such tradeoffs in field studies, tests of hypothesized correlated trait evolution and adaptive differentiation are more robust when taxa relatedness and environment are taken into consideration. Here we test for correlated evolution of stem and leaf traits and their adaptive differentiation across environments in the herbaceous genus, Helianthus. Stem and leaf traits of 14 species of Helianthus (28 populations) were assessed in a common garden greenhouse study. Phylogenetically independent contrasts were used to test for evidence of correlated evolution of stem hydraulic and biomechanical properties, correlated evolution of stem and leaf traits, and adaptive differentiation associated with source habitat environments. Among stem traits, there was evidence for correlated evolution of some hydraulic and biomechanical properties, supporting an expected tradeoff between stem theoretical hydraulic efficiency and resistance to bending stress. Population differentiation for suites of stem and leaf traits was found to be consistent with a "fast-slow" resource-use axis for traits related to water transport and use. Associations of population traits with source habitat characteristics supported repeated evolution of a resource-acquisitive "drought-escape" strategy in arid environments. This study provides evidence of correlated evolution of stem and leaf traits consistent with the fast-slow spectrum of trait combinations related to water transport and use along the stem-to-leaf pathway. Correlations of traits with source habitat characteristics further indicate that the correlated evolution is associated, at least in part, with adaptive differentiation of Helianthus populations among native habitats differing in climate. © 2016 Botanical Society of America.

  14. Fitoextracción De Plomo, Zinc y Cadmio de Relaves Mineros Utilizando Helianthus annuus L. (Girasol)

    Lizarbe Asmat, Katherine; Rivera López, Yaslin; Mendoza Bobadilla, Jorge; Vera Herrera, Manuel; Rodríguez Espinoza, Ronald

    2017-01-01

    Objetivo: Evaluar el crecimiento de Helianthus annuus L. (girasol), especie bioacumuladora de metales pesados, mediante la adición de acondicionadores orgánicos e inorgánicos al relave minero artesanal, para la fitoextracción de plomo, zinc y cadmio. Métodos: Se probaron cuatro tratamientos de diferentes proporciones relave – acondicionador (100 - 0%, 75 - 25%, 50 – 50%, 25 – 75% respectivamente), con seis repeticiones cada uno, para periodos de tiempo de 30, 60 y 90 días y mediante dos métod...

  15. The sensitivity of sunflower (Helianthus annuus L.) plants to UV-B radiation is altered by nitrogen status

    Cechin, Inês; Gonzalez, Gisely Cristina; Corniani, Natália; Fumis, Terezinha de Fátima

    2018-01-01

    ABSTRACT: Interaction effects between nitrogen and UV-B radiation were studied in sunflower (Helianthus annuus L. variety IAC-Iarama) plants grown in a greenhouse under natural photoperiod conditions. Plants were irradiated with 0.8W m-2 (control) or 8.0W m-2 (+UV-B) of UV-B radiation for 7h per day. The plants were grown in pots containing vermiculite and watered with 70% of full strength nitrogen-free Long Ashton solution, containing either low (42.3ppm) or high (282ppm) nitrogen as ammoniu...

  16. Ectopic expression of the HAM59 gene causes homeotic transformations of reproductive organs in sunflower (Helianthus annuus L.).

    Shulga, O A; Neskorodov, Ya B; Shchennikova, A V; Gaponenko, A K; Skryabin, K G

    2015-01-01

    The function of the HAM59 MADS-box gene in sunflower (Helianthus annuus L.) was studied to clarify homeotic C activity in the Asteraceae plant family. For the first time, transgenic sunflower plants with a modified pattern of HAM59 expression were obtained. It was shown that the HAM59 MADS-box transcription factor did mediate C activity in sunflower. In particular, it participated in termination of the floral meristem, repression of the cadastral function of A-activity, and together with other C-type sunflower protein HAM45-in the specification of the identity of stamens and pistils.

  17. Evolutionary Divergences in Root Exudate Composition among Ecologically-Contrasting Helianthus Species.

    Bowsher, Alan W; Ali, Rifhat; Harding, Scott A; Tsai, Chung-Jui; Donovan, Lisa A

    2016-01-01

    Plant roots exude numerous metabolites into the soil that influence nutrient availability. Although root exudate composition is hypothesized to be under selection in low fertility soils, few studies have tested this hypothesis in a phylogenetic framework. In this study, we examined root exudates of three pairs of Helianthus species chosen as phylogenetically-independent contrasts with respect to native soil nutrient availability. Under controlled environmental conditions, seedlings were grown to the three-leaf-pair stage, then transferred to either high or low nutrient treatments. After five days of nutrient treatments, we used gas chromatography-mass spectrometry for analysis of root exudates, and detected 37 metabolites across species. When compared in the high nutrient treatment, species native to low nutrient soils exhibited overall higher exudation than their sister species native to high nutrient soils in all three species pairs, providing support for repeated evolutionary shifts in response to native soil fertility. Species native to low nutrient soils and those native to high nutrient soils responded similarly to low nutrient treatments with increased exudation of organic acids (fumaric, citric, malic acids) and glucose, potentially as a mechanism to enhance nutrition acquisition. However, species native to low nutrient soils also responded to low nutrient treatments with a larger decrease in exudation of amino acids than species native to high nutrient soils in all three species pairs. This indicates that species native to low nutrient soils have evolved a unique sensitivity to changes in nutrient availability for some, but not all, root exudates. Overall, these repeated evolutionary divergences between species native to low nutrient soils and those native to high nutrient soils provide evidence for the adaptive value of root exudation, and its plasticity, in contrasting soil environments.

  18. Vulnerability of photosynthesis and photosystem I in Jerusalem artichoke (Helianthus tuberosus L.) exposed to waterlogging.

    Yan, Kun; Zhao, Shijie; Cui, Mingxing; Han, Guangxuan; Wen, Pei

    2018-04-01

    Jerusalem artichoke (Helianthus tuberosus L.) is an important energy crop for utilizing coastal marginal land. This study was to investigate waterlogging tolerance of Jerusalem artichoke through photosynthetic diagnose with emphasis on photosystem II (PSII) and photosystem I (PSI) performance. Potted plants were subjected to severe (liquid level 5 cm above vermiculite surface) and moderate (liquid level 5 cm below vermiculite surface) waterlogging for 9 days. Large decreased photosynthetic rate suggested photosynthesis vulnerability upon waterlogging. After 7 days of severe waterlogging, PSII and PSI photoinhibition arose, indicated by significant decrease in the maximal photochemical efficiency of PSII (Fv/Fm) and PSI (△MR/MR 0 ), and PSI seemed more vulnerable because of greater decrease in △MR/MR 0 than Fv/Fm. In line with decreased △MR/MR 0 and unchanged Fv/Fm after 9 days of moderate waterlogging, the amount of PSI reaction center protein rather than PSII reaction center protein was lowered, confirming greater PSI vulnerability. According to positive correlation between △MR/MR 0 and efficiency that an electron moves beyond primary quinone and negative correlation between △MR/MR 0 and PSII excitation pressure, PSI inactivation elevated PSII excitation pressure by depressing electron transport at PSII acceptor side. Thus, PSI vulnerability induced PSII photoinhibition and endangered the stability of whole photosynthetic apparatus under waterlogging. In agreement with photosystems photoinhibition, elevated H 2 O 2 concentration and lipid peroxidation in the leaves corroborated waterlogging-induced oxidative stress. In conclusion, Jerusalem artichoke is a waterlogging sensitive species in terms of photosynthesis and PSI vulnerability. Consistently, tuber yield was tremendously reduced by waterlogging, confirming waterlogging sensitivity of Jerusalem artichoke. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

  19. Sugar yield and composition of tubers from Jerusalem Artichoke (Helianthus tuberosus) irrigated with saline waters.

    Bhagia, Samarthya; Ferreira, Jorge F S; Kothari, Ninad; Nunez, Angelica; Liu, Xuan; da Silva Dias, Nildo; Suarez, Donald L; Kumar, Rajeev; Wyman, Charles E

    2018-06-01

    Currently, major biofuel crops are also food crops that demand fertile soils and good-quality water. Jerusalem artichoke (Helianthus tuberosus, Asteraceae) produces high tonnage of tubers that are rich in sugars, mainly in the form of inulin. In this study, plants of the cultivar "White Fuseau" grown under five salinity levels were evaluated for tuber yield. Results indicated that this cultivar is moderately salt-tolerant if the goal is tuber production. Hydraulic pressings of the tubers produced juice that contained 15% (wet weight) or 55% (dry weight) free sugars, with 70% of these in the form of inulin and the rest as fructose, sucrose, and glucose. Importantly, salinity did not affect the total free sugar or inulin content of the tubers. Tubers were composed of about 12% dry washed bagasse (wet weight) or 44% (dry matter basis) and bagasse retained such high quantities of free sugars after pressing that washing was required for complete sugar recovery. Chemical composition analysis of tuber bagasse suggested that it had low lignin content (11-13 wt%), and its structural sugar composition was similar to chicory root bagasse. Because of the high hemicellulose and pectin content of the bagasse, adding xylanase and pectinase to cellulase substantially improved sugar yields from enzymatic hydrolysis compared to at the same protein loading as cellulase alone. In addition to the high total sugar yield of tuber, these first findings on the sugar and lignin content and enzymatic hydrolysis of tuber bagasse can lead to low-cost production of ethanol for transportation fuels. © 2018 Wiley Periodicals, Inc.

  20. Response of sunflower (Helianthus annuus L.) leaf surface defenses to exogenous methyl jasmonate.

    Rowe, Heather C; Ro, Dae-kyun; Rieseberg, Loren H

    2012-01-01

    Helianthus annuus, the common sunflower, produces a complex array of secondary compounds that are secreted into glandular trichomes, specialized structures found on leaf surfaces and anther appendages of flowers. The primary components of these trichome secretions are sesquiterpene lactones (STL), a diverse class of compounds produced abundantly by the plant family Compositae and believed to contribute to plant defense against herbivory. We treated wild and cultivated H. annuus accessions with exogenous methyl jasmonate, a plant hormone that mediates plant defense against insect herbivores and certain classes of fungal pathogens. The wild sunflower produced a higher density of glandular trichomes on its leaves than the cultivar. Comparison of the profiles of glandular trichome extracts obtained by liquid chromatography-mass spectroscopy (LC-MS) showed that wild and cultivated H. annuus were qualitatively similar in surface chemistry, although differing in the relative size and proportion of various compounds detected. Despite observing consistent transcriptional responses to methyl jasmonate treatment, we detected no significant effect on glandular trichome density or LC-MS profile in cultivated or wild sunflower, with wild sunflower exhibiting a declining trend in overall STL production and foliar glandular trichome density of jasmonate-treated plants. These results suggest that glandular trichomes and associated compounds may act as constitutive defenses or require greater levels of stimulus for induction than the observed transcriptional responses to exogenous jasmonate. Reduced defense investment in domesticated lines is consistent with predicted tradeoffs caused by selection for increased yield; future research will focus on the development of genetic resources to explicitly test the ecological roles of glandular trichomes and associated effects on plant growth and fitness.

  1. Pollen aroma fingerprint of two sunflower (Helianthus annuus L.) genotypes characterized by different pollen colors.

    Bertoli, Alessandra; Fambrini, Marco; Doveri, Silvia; Leonardi, Michele; Pugliesi, Claudio; Pistelli, Luisa

    2011-09-01

    Samples of fresh pollen grains, collected from capitula in full bloom from two genotypes of sunflower (Helianthus annuus L.) and characterized by a different color, i.e., white-cream (WC) and orange (O), were analyzed by the HS-SPME (headspacesolid phase microextraction)/GC/MS technique. This study defined for the first time the fingerprint of the sunflower pollen, separated from the disc flowers, to define its contribution to the inflorescence aroma. In the GC/MS fingerprints of the WC and O genotypes, 61 and 62 volatile compounds were identified, respectively. Monoterpene hydrocarbons (34% in O vs. 28% in WC) and sesquiterpene hydrocarbons (37% in O vs. 31% in WC) were ubiquitous in all samples analyzed and represented the main chemical classes. α-Pinene (21% in O vs. 20% in WC) and sabinene (11% in O vs. 6% in WC) were the dominant volatiles, but also a full range of aliphatic hydrocarbons and their oxygenated derivatives gave a decisive contribution to the aroma composition (10% in O vs. 12% in WC). In addition, dendrolasin (3% in O vs. 4% in WC) and some minor constituents such as (E)-hex-2-en-1-ol (0.4% in O vs. 0.1% in WC) were pointed out not only for their contribution to the pollen scent, but also for their well-known role in the plant ecological relationships. Having evaluated two pollen morphs with different carotenoid-based colors, the study sought to highlight also the presence of some volatile precursors or derivatives of these pigments in the aroma. However, the pollen aroma of the two selected genotypes made a specific chemical contribution to the sunflower inflorescence scent without any influence on carotenoid derivatives. 2011 Verlag Helvetica Chimica Acta AG, Zürich.

  2. Physiology and proteomics of drought stress acclimation in sunflower (Helianthus annuus L.).

    Fulda, S; Mikkat, S; Stegmann, H; Horn, R

    2011-07-01

    An easy and manageable in vitro screening system for drought tolerance of sunflower seedlings based on MS media supplemented with polyethylene glycol 6000 was evaluated. Morphological and physiological parameters were compared between control (-0.05 MPa) and drought-stressed (-0.6 MPa) seedlings of Helianthus annuus L. cv. Peredovick. There was a significant growth deficit in drought-stressed plants compared to control plants in terms of hypocotyl length, and shoot and root fresh mass. Shoot growth was more restricted than root growth, resulting in an increased root/shoot ratio of drought-stressed plants. Accumulation of osmolytes such as inositol (65-fold), glucose (58-fold), proline (55-fold), fructose (11-fold) and sucrose (eightfold), in leaves of drought-stressed plants could be demonstrated by gas-liquid chromatography. Soluble protein patterns of leaves were analysed with two-dimensional gel electrophoresis (2D-PAGE) and MALDI-TOF mass spectrometry. A set of 46 protein spots allowed identification of 19 marker proteins. Quantitative changes in protein expression of drought-stressed versus control plants were detected. In leaves of drought-stressed sunflower seedlings six proteins were significantly up-regulated more than twofold: a putative caffeoyl-CoA 3-O-methyltransferase (4.5-fold), a fructokinase 3 (3.3-fold), a vegetative storage protein (2.5-fold), a glycine-rich RNA binding protein (2.2-fold), a CuZn-superoxide dismutase (2.1-fold) and an unknown low molecular weight protein (2.3-fold). These proteins represent general stress proteins induced under drought conditions or proteins contributing to basic carbon metabolism. The up-regulated proteins are interesting candidates for further physiological and molecular investigations regarding drought tolerance in sunflower. © 2011 German Botanical Society and The Royal Botanical Society of the Netherlands.

  3. Metal accumulation by sunflower (Helianthus annuus L. and the efficacy of its biomass in enzymatic saccharification.

    Saurabh Sudha Dhiman

    Full Text Available Accumulation of metal contaminants in soil as a result of various industrial and anthropogenic activities has reduced soil fertility significantly. Phytoextraction of metal contaminants can improve soil fertility and provide inexpensive feedstock for biorefineries. We investigated the hyperaccumulation capacity of sunflower (Helianthus annuus biomass by cultivating these plants in various concentrations of metal contaminants. Sunflowers were grown in soils contaminated with various levels of heavy metals (10-2,000 mg/kg dry soil. The degree of metal uptake by different parts of the biomass and the residual concentration in the soil were estimated through inductively coupled plasma mass spectrometry. An almost 2.5-fold hyperaccumulation of Zn2+ was observed in the leaf and flower biomass compared with the concentration in the soil. For the subsequent saccharification of biomass with hyperaccumulated contaminants, a fungal lignocellulosic consortium was used. The fungal consortium cocktail retained more than 95% filter paper activity with 100 mM Ni2+ ions even after 36 h. The highest saccharification yield (SY, 87.4% was observed with Ni2+ as the contaminant (10 mg/kg dry wt, whereas Pb2+ (251.9 mg/kg dry wt was the strongest inhibitor of biomass hydrolysis, resulting in only a 30% SY. Importantly, the enzyme cocktail produced by the fungal consortium resulted in almost the same SY (% as that obtained from a combination of commercial cellulase and β-glucosidase. Significant sugar conversion (61.7% from H. annuus biomass hydrolysate occurred, resulting in the production of 11.4 g/L of bioethanol. This is the first study to assess the suitability of phytoremediated sunflower biomass for bioethanol production.

  4. Metal accumulation by sunflower (Helianthus annuus L.) and the efficacy of its biomass in enzymatic saccharification.

    Dhiman, Saurabh Sudha; Zhao, Xin; Li, Jinglin; Kim, Dongwook; Kalia, Vipin C; Kim, In-Won; Kim, Jae Young; Lee, Jung-Kul

    2017-01-01

    Accumulation of metal contaminants in soil as a result of various industrial and anthropogenic activities has reduced soil fertility significantly. Phytoextraction of metal contaminants can improve soil fertility and provide inexpensive feedstock for biorefineries. We investigated the hyperaccumulation capacity of sunflower (Helianthus annuus) biomass by cultivating these plants in various concentrations of metal contaminants. Sunflowers were grown in soils contaminated with various levels of heavy metals (10-2,000 mg/kg dry soil). The degree of metal uptake by different parts of the biomass and the residual concentration in the soil were estimated through inductively coupled plasma mass spectrometry. An almost 2.5-fold hyperaccumulation of Zn2+ was observed in the leaf and flower biomass compared with the concentration in the soil. For the subsequent saccharification of biomass with hyperaccumulated contaminants, a fungal lignocellulosic consortium was used. The fungal consortium cocktail retained more than 95% filter paper activity with 100 mM Ni2+ ions even after 36 h. The highest saccharification yield (SY, 87.4%) was observed with Ni2+ as the contaminant (10 mg/kg dry wt), whereas Pb2+ (251.9 mg/kg dry wt) was the strongest inhibitor of biomass hydrolysis, resulting in only a 30% SY. Importantly, the enzyme cocktail produced by the fungal consortium resulted in almost the same SY (%) as that obtained from a combination of commercial cellulase and β-glucosidase. Significant sugar conversion (61.7%) from H. annuus biomass hydrolysate occurred, resulting in the production of 11.4 g/L of bioethanol. This is the first study to assess the suitability of phytoremediated sunflower biomass for bioethanol production.

  5. Root water transport of Helianthus annuus L. under iron oxide nanoparticle exposure.

    Martínez-Fernández, Domingo; Barroso, Didac; Komárek, Michael

    2016-01-01

    The application of nanomaterials in commercially available products is increasing rapidly for agriculture, phytoremediation and biotechnology. Since plants suppose the first sink for the accumulation of nanoparticles from the environment, emerging studies have focused on the general consequences for plants and their effects on the biomass production. However, effects on the root surface, as well as blockage of nutrients and water uptake by the roots, may also occur. This experiment was designed to prove if the plant water relations can be affected by the adsorption of nanoparticles on the root surface, causing a consequent stress for the plants. With this goal, plants of Helianthus annuus were previously grown in a hydroponic culture, and at age of 55 days, their roots were exposed to three different concentrations of nanomaghemite (NM) in the hydroponic solution for 5 days: control without NM; 50 and 100 mg l(-1) NM. The main effect was related to the reduction of the root hydraulic conductivity (Lo) and the nutrients uptake. The concentrations of the macronutrients Ca, K, Mg and S in the shoot were reduced relative to the control plants, which resulted in lower contents of chlorophyll pigments. Although stress was not detected in the plants, after the analysis of stress markers like the accumulation of proline or ascorbate in the tissues, reduction of the root functionality by nanoparticles has been identified here, manifested as the effect of NM on Lo. The treatment with 50 mg l(-1) NM significantly reduced the Lo, by up to 57% of its control value, and it was reduced by up to 26% at 100 mg l(-1) NM. These results will be an important factor to take into account with regard to the applicability of NM for long-term use in crops, particularly during privative water conditions.

  6. Visitantes florales nocturnos del girasol (Helianthus annuus, Asterales: Asteraceae en la Argentina

    Juan P TORRETTA

    2009-01-01

    Full Text Available El girasol (Helianthus annuus es un cultivo oleaginoso, polinizado por Apis mellifera L. y otras abejas en distintas regiones del mundo. Sin embargo, sus flores también son visitadas por insectos de actividad nocturna. Durante tres campañas agrícolas, se determinó la diversidad de los visitantes nocturnos de capítulos de girasol, en cinco sitios de Argentina. También se estudió el comportamiento de forrajeo de los principales visitantes y la variación de la receptividad estigmática a lo largo del día, con el fin de establecer si estos visitantes contribuyen a la polinización. Al menos 67 especies o morfoespecies pertenecientes a cuatro órdenes de visitantes nocturnos fueron colectadas. El orden más rico y abundante fue Lepidoptera (44 especies o morfoespecies, cinco familias, seguido por Coleoptera (18 especies o morfoespecies, nueve familias, Orthoptera (tres morfoespecies, una familia y Blattaria (dos especies, una familia. Los lepidópteros forrajearon exclusivamente por néctar, mientras que los individuos de los demás órdenes consumieron polen y/o partes florales. El estigma se encontró receptivo durante las horas de luz, con una receptividad máxima al mediodía (12:00 - 14:00. Llamativamente, las flores del girasol son visitadas por mayor número de polillas que de abejas. Debido a que las polillas consumen néctar y potencialmente transportan polen entre flores, en un momento del día en que los estigmas se encuentran menos receptivos, es improbable que polinicen efectivamente el cultivo.

  7. Analysis of Phenolic Acids of Jerusalem Artichoke (Helianthus tuberosus L. Responding to Salt-Stress by Liquid Chromatography/Tandem Mass Spectrometry

    Fujia Chen

    2014-01-01

    Full Text Available Plant phenolics can have applications in pharmaceutical and other industries. To identify and quantify the phenolic compounds in Helianthus tuberosus leaves, qualitative analysis was performed by a reversed phase high-performance liquid chromatography coupled with tandem mass spectrometry (HPLC-MS/MS and quantitative analysis by HPLC. Ten chlorogenic acids (CGAs were identified (3-o-caffeoylquinic acid, two isomers of caffeoylquinic acid, caffeic acid, p-coumaroyl-quinic acid, feruloylquinic acid, 3,4-dicaffeoyquinic acid, 3,5-dicaffeoylquinic acid, 1,5-dicaffeoylquinic acid, and 4,5-dicaffeoylquinic acid by comparing their retention times, UV-Vis absorption spectra, and MS/MS spectra with standards. In addition, four other phenolic compounds, including caffeoyl glucopyranose, isorhamnetin glucoside, kaempferol glucuronide, and kaempferol-3-o-glucoside, were tentatively identified in Helianthus tuberosus leaves for the first time. The 3-o-caffeoylquinic acid (7.752 mg/g DW, 4,5-dicaffeoylquinic acid (5.633 mg/g DW, and 3,5-dicaffeoylquinic acid (4.900 mg/g DW were the major phenolic compounds in leaves of Helianthus tuberosus cultivar NanYu in maturity. The variations in phenolic concentrations and proportions in Helianthus tuberosus leaves were influenced by genotype and plant growth stage. Cultivar NanYu had the highest concentration of phenolic compounds, in particular 3-o-caffeoylquinic acid and 4,5-dicaffeoylquinic acid compared with the other genotypes (wild accession and QingYu. Considering various growth stages, the concentration of total phenolics in cultivar NanYu was higher at flowering stage (5.270 mg/g DW than at budding and tuber swelling stages. Cultivar NanYu of Helianthus tuberosus is a potential source of natural phenolics that may play an important role in the development of pharmaceuticals.

  8. Association Mapping and the Genomic Consequences of Selection in Sunflower

    Mandel, Jennifer R.; Nambeesan, Savithri; Bowers, John E.; Marek, Laura F.; Ebert, Daniel; Rieseberg, Loren H.; Knapp, Steven J.; Burke, John M.

    2013-01-01

    The combination of large-scale population genomic analyses and trait-based mapping approaches has the potential to provide novel insights into the evolutionary history and genome organization of crop plants. Here, we describe the detailed genotypic and phenotypic analysis of a sunflower (Helianthus annuus L.) association mapping population that captures nearly 90% of the allelic diversity present within the cultivated sunflower germplasm collection. We used these data to characterize overall patterns of genomic diversity and to perform association analyses on plant architecture (i.e., branching) and flowering time, successfully identifying numerous associations underlying these agronomically and evolutionarily important traits. Overall, we found variable levels of linkage disequilibrium (LD) across the genome. In general, islands of elevated LD correspond to genomic regions underlying traits that are known to have been targeted by selection during the evolution of cultivated sunflower. In many cases, these regions also showed significantly elevated levels of differentiation between the two major sunflower breeding groups, consistent with the occurrence of divergence due to strong selection. One of these regions, which harbors a major branching locus, spans a surprisingly long genetic interval (ca. 25 cM), indicating the occurrence of an extended selective sweep in an otherwise recombinogenic interval. PMID:23555290

  9. Identification of candidate genes associated with leaf senescence in cultivated sunflower (Helianthus annuus L..

    Sebastian Moschen

    Full Text Available Cultivated sunflower (Helianthus annuus L., an important source of edible vegetable oil, shows rapid onset of senescence, which limits production by reducing photosynthetic capacity under specific growing conditions. Carbon for grain filling depends strongly on light interception by green leaf area, which diminishes during grain filling due to leaf senescence. Transcription factors (TFs regulate the progression of leaf senescence in plants and have been well explored in model systems, but information for many agronomic crops remains limited. Here, we characterize the expression profiles of a set of putative senescence associated genes (SAGs identified by a candidate gene approach and sunflower microarray expression studies. We examined a time course of sunflower leaves undergoing natural senescence and used quantitative PCR (qPCR to measure the expression of 11 candidate genes representing the NAC, WRKY, MYB and NF-Y TF families. In addition, we measured physiological parameters such as chlorophyll, total soluble sugars and nitrogen content. The expression of Ha-NAC01, Ha-NAC03, Ha-NAC04, Ha-NAC05 and Ha-MYB01 TFs increased before the remobilization rate increased and therefore, before the appearance of the first physiological symptoms of senescence, whereas Ha-NAC02 expression decreased. In addition, we also examined the trifurcate feed-forward pathway (involving ORE1, miR164, and ethylene insensitive 2 previously reported for Arabidopsis. We measured transcription of Ha-NAC01 (the sunflower homolog of ORE1 and Ha-EIN2, along with the levels of miR164, in two leaves from different stem positions, and identified differences in transcription between basal and upper leaves. Interestingly, Ha-NAC01 and Ha-EIN2 transcription profiles showed an earlier up-regulation in upper leaves of plants close to maturity, compared with basal leaves of plants at pre-anthesis stages. These results suggest that the H. annuus TFs characterized in this work could

  10. Comparative uptake of plutonium from soils by Brassica juncea and Helianthus annuus

    Lee, J.H.; Hossner, L.R.; Attrep, M.; Kung, K.S.

    2002-01-01

    Extractability of Pu from soils was most affected by pH and amounts of clay, salts, and carbonates. - Plutonium uptake by Brassica juncea (Indian mustard) and Helianthus annuus (sunflower) from soils with varying chemical composition and contaminated with Pu complexes (Pu-nitrate [ 239 Pu(NO 3 ) 4 ], Pu-citrate [ 239 Pu(C 6 H 5 O 7 ) + ], and Pu-diethylenetriaminepentaacetic acid (Pu-DTPA [ 239 Pu-C 14 H 23 O 10 N 3 ]) was investigated. Sequential extraction of soils incubated with applied Pu was used to determine the distribution of Pu in the various soil fractions. The initial Pu activity levels in soils were 44.40-231.25 Bq g -1 as Pu-nitrate , Pu-citrate, or Pu-DTPA. A difference in Pu uptake between treatments of Pu-nitrate and Pu-citrate without chelating agent was observed only with Indian mustard in acidic Crowley soil. The uptake of Pu by plants was increased with increasing DTPA rates, however, the Pu concentration of plants was not proportionally increased with increasing application rate of Pu to soil. Plutonium uptake from Pu-DTPA was significantly higher from the acid Crowley soil than from the calcareous Weswood soil. The uptake of Pu from the soils was higher in Indian mustard than in sunflower. Sequential extraction of Pu showed that the ion-exchangeable Pu fraction in soils was dramatically increased with DTPA treatment and decreased with time of incubation. Extractability of Pu in all fractions was not different when Pu-nitrate and Pu-citrate were applied to the same soil. More Pu was associated with the residual Pu fraction without DTPA application. Consistent trends with time of incubation for other fractions were not apparent. The ion-exchangeable fraction, assumed as plant-available Pu, was significantly higher in acid soil compared with calcareous soil with or without DTPA treatment. When the calcareous soil was treated with DTPA, the ion-exchangeable Pu was comparatively less influenced. This fraction in the soil was more affected with time

  11. Molecular tagging of a novel rust resistance gene R(12) in sunflower (Helianthus annuus L.).

    Gong, L; Hulke, B S; Gulya, T J; Markell, S G; Qi, L L

    2013-01-01

    Sunflower production in North America has recently suffered economic losses in yield and seed quality from sunflower rust (Puccinia helianthi Schwein.) because of the increasing incidence and lack of resistance to new rust races. RHA 464, a newly released sunflower male fertility restorer line, is resistant to both of the most predominant and most virulent rust races identified in the Northern Great Plains of the USA. The gene conditioning rust resistance in RHA 464 originated from wild Helianthus annuus L., but has not been molecularly marked or determined to be independent from other rust loci. The objectives of this study are to identify molecular markers linked to the rust resistance gene and to investigate the allelism of this gene with the unmapped rust resistance genes present in HA-R6, HA-R8 and RHA 397. Virulence phenotypes of seedlings for the F(2) population and F(2:3) families suggested that a single dominant gene confers rust resistance in RHA 464, and this gene was designated as R(12). Bulked segregant analysis identified ten markers polymorphic between resistant and susceptible bulks. In subsequent genetic mapping, the ten markers covered 33.4 cM of genetic distance on linkage group 11 of sunflower. A co-dominant marker CRT275-11 is the closest marker distal to R(12) with a genetic distance of 1.0 cM, while ZVG53, a dominant marker linked in the repulsion phase, is proximal to R(12) with a genetic distance of 9.6 cM. The allelism test demonstrated that R(12) is not allelic to the rust resistance genes in HA-R6, HA-R8 and RHA 397, and it is also not linked to any previously mapped rust resistance genes. Discovery of the R(12) novel rust resistance locus in sunflower and associated markers will potentially support the molecular marker-assisted introgression and pyramiding of R(12) into sunflower breeding lines.

  12. Identification of candidate genes associated with leaf senescence in cultivated sunflower (Helianthus annuus L.).

    Moschen, Sebastian; Bengoa Luoni, Sofia; Paniego, Norma B; Hopp, H Esteban; Dosio, Guillermo A A; Fernandez, Paula; Heinz, Ruth A

    2014-01-01

    Cultivated sunflower (Helianthus annuus L.), an important source of edible vegetable oil, shows rapid onset of senescence, which limits production by reducing photosynthetic capacity under specific growing conditions. Carbon for grain filling depends strongly on light interception by green leaf area, which diminishes during grain filling due to leaf senescence. Transcription factors (TFs) regulate the progression of leaf senescence in plants and have been well explored in model systems, but information for many agronomic crops remains limited. Here, we characterize the expression profiles of a set of putative senescence associated genes (SAGs) identified by a candidate gene approach and sunflower microarray expression studies. We examined a time course of sunflower leaves undergoing natural senescence and used quantitative PCR (qPCR) to measure the expression of 11 candidate genes representing the NAC, WRKY, MYB and NF-Y TF families. In addition, we measured physiological parameters such as chlorophyll, total soluble sugars and nitrogen content. The expression of Ha-NAC01, Ha-NAC03, Ha-NAC04, Ha-NAC05 and Ha-MYB01 TFs increased before the remobilization rate increased and therefore, before the appearance of the first physiological symptoms of senescence, whereas Ha-NAC02 expression decreased. In addition, we also examined the trifurcate feed-forward pathway (involving ORE1, miR164, and ethylene insensitive 2) previously reported for Arabidopsis. We measured transcription of Ha-NAC01 (the sunflower homolog of ORE1) and Ha-EIN2, along with the levels of miR164, in two leaves from different stem positions, and identified differences in transcription between basal and upper leaves. Interestingly, Ha-NAC01 and Ha-EIN2 transcription profiles showed an earlier up-regulation in upper leaves of plants close to maturity, compared with basal leaves of plants at pre-anthesis stages. These results suggest that the H. annuus TFs characterized in this work could play important

  13. Linearity assumption in soil-to-plant transfer factors of natural uranium and radium in Helianthus annuus L

    Rodriguez, P. Blanco; Tome, F. Vera; Fernandez, M. Perez; Lozano, J.C.

    2006-01-01

    The linearity assumption of the validation of soil-to-plant transfer factors of natural uranium and 226 Ra was tested using Helianthus annuus L. (sunflower) grown in a hydroponic medium. Transfer of natural uranium and 226 Ra was tested in both the aerial fraction of plants and in the overall seedlings (roots and shoots). The results show that the linearity assumption can be considered valid in the hydroponic growth of sunflowers for the radionuclides studied. The ability of sunflowers to translocate uranium and 226 Ra was also investigated, as well as the feasibility of using sunflower plants to remove uranium and radium from contaminated water, and by extension, their potential for phytoextraction. In this sense, the removal percentages obtained for natural uranium and 226 Ra were 24% and 42%, respectively. Practically all the uranium is accumulated in the roots. However, 86% of the 226 Ra activity concentration in roots was translocated to the aerial part

  14. [Adaptability of Helianthus annuus seedlings to crude oil pollution in soil and its improvement measures under salinization stress].

    Zhang, Jing-lei; Ci, Hua-cong; He, Xing-dong; Liang, Yu-ting; Zhao, Xuan; Sun, Hui-ting; Xie, Hong-tao

    2015-11-01

    To explore the adaptability of plant under salt stress to crude oil pollution of soil and improvement measures, a pot experiment of Helianthus annuus seedlings was conducted using orthogonal experiment method with crude oil-sodium chloride-desulfurization gypsum and cinder-zeolite-desulfurization gypsum-sawdust. The results showed that, with the increase of soil crude oil concentration, the relative growth rate (RGR) of plant height, RGR of aboveground biomass and root N: P ratios of H. annuus seedlings decreased significantly, while the activity of SOD and CAT increased at first and then decreased significantly. The RGR of plant height and aboveground biomass significantly increased (P pollution of soil could decrease the relative growth rate of H. annuus seedling, and sawdust could reduce the influence of crude oil pollution on plant growth under salt stress.

  15. Linearity assumption in soil-to-plant transfer factors of natural uranium and radium in Helianthus annuus L

    Rodriguez, P. Blanco [Departamento de Fisica, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz (Spain); Tome, F. Vera [Departamento de Fisica, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz (Spain)]. E-mail: fvt@unex.es; Fernandez, M. Perez [Area de Ecologia, Departamento de Fisica, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz (Spain); Lozano, J.C. [Laboratorio de Radiactividad Ambiental, Facultad de Ciencias, Universidad de Salamanca, 37008 Salamanca (Spain)

    2006-05-15

    The linearity assumption of the validation of soil-to-plant transfer factors of natural uranium and {sup 226}Ra was tested using Helianthus annuus L. (sunflower) grown in a hydroponic medium. Transfer of natural uranium and {sup 226}Ra was tested in both the aerial fraction of plants and in the overall seedlings (roots and shoots). The results show that the linearity assumption can be considered valid in the hydroponic growth of sunflowers for the radionuclides studied. The ability of sunflowers to translocate uranium and {sup 226}Ra was also investigated, as well as the feasibility of using sunflower plants to remove uranium and radium from contaminated water, and by extension, their potential for phytoextraction. In this sense, the removal percentages obtained for natural uranium and {sup 226}Ra were 24% and 42%, respectively. Practically all the uranium is accumulated in the roots. However, 86% of the {sup 226}Ra activity concentration in roots was translocated to the aerial part.

  16. effect of gamma irradiation, antitranspirants and packages on the storage ability of jerusalem artichoke tubers (Helianthus Tuberosus,L.)

    Abd-Elhak, T.S.F.E.

    2005-01-01

    two experiments were carried out in the summer seasons of 2001 and 2002 on the cultivar Fuseau of jerusalem artichoke (Helianthus Tuberosus,L.) to follow the models of changes that occurred in the vegetative growth and tubers during development to determine the most suitable age for harvesting . irradiation, antitranspirant and package size either provided with polyethylene sheets or not were examined to improve the storage ability of tubers. studies on the models of developmental stages showed that the plant height and fresh weight increased till the last examined age of 180 days while the number of stems increased till the age of 150 days. the total carbohydrates and inulin contents accumulated up to the age of 120 days then decreased till the age of 180 days whereas the protein percentage increased up to the age of 180 days

  17. The potential of Zea mays, Commelina bengelensis, Helianthus annuus and Amaranthus hybridus for phytoremediation of waste water

    Chacha Joseph Sarima

    2012-12-01

    Full Text Available Waste-water from domestic use and from industrial effluent burden the water systems with high levels of heavy metal hence there is need to remove these heavy metals so that the waste water can be recycled for use for household or irrigation. The present study has screened Zea mays (maize, Commelina bengelensis (wondering jew, Helianthus annuus (sunflower and Amaranthus hybridus (amaranthus for their ability to bioaccumulate Pb, Cu, Cd and Zn metals. The results obtained show that the H. annuus and C. bengelensis plant have promising potential for removal of Pb, Cu and Cd from wastewater though their ability to remove Zn from contaminated solutions is not much different from that of Z. mays and A. hybridus.

  18. Influence of silver and titanium nanoparticles on arbuscular mycorrhizal colonization and accumulation of radiocaesium in Helianthus annuus

    Dubchak, S.; Ogar, A.; Mietelski, J. W.; Turnau, K.

    2010-01-01

    The influence of arbuscular mycorrhizal fungus on 1 34Cs uptake by Helianthus annuus was studied in a pilot study under growth chamber conditions. Mycorrhizal plants took up five times more 1 34Cs (up to 250,000 Bq kg - 1 dry weight) than non mycorrhizal plants. Silver and titanium nanoparticles, supplied into the surface soil layer decreased both the mycorrhizal colonization and Cs uptake by mycorrhizal plants. The application of activated carbon attenuated the effect of nanoparticles and increased 1 34Cs uptake in the presence of mycorrhizal fungi (up to 400,000 Bq kg - 1 dry weight). The results underline the possible application of phyto remediation techniques based on mycorrhizas assisted plants in decontamination of both radionuclides and nanoparticles. (Author) 27 refs.

  19. Influence of silver and titanium nanoparticles on arbuscular mycorrhizal colonization and accumulation of radiocaesium in Helianthus annuus

    Dubchak, S.; Ogar, A.; Mietelski, J. W.; Turnau, K.

    2010-07-01

    The influence of albacore's mycorrhizal fungus on {sup 1}34Cs uptake by Helianthus annuus was studied in a pilot study under growth chamber conditions. Mycorrhizal plants took up five times more {sup 1}34Cs (up to 250,000 Bq kg{sup -}1 dry weight) than non mycorrhizal plants. Silver and titanium nanoparticles, supplied into the surface soil layer decreased both the mycorrhizal colonization and Cs uptake by mycorrhizal plants. The application of activated carbon attenuated the effect of nanoparticles and increased {sup 1}34Cs uptake in the presence of mycorrhizal fungi (up to 400,000 Bq kg{sup -}1 dry weight). The results underline the possible application of phyto remediation techniques based on mycorrhizas assisted plants in decontamination of both radionuclides and nanoparticles. (Author) 27 refs.

  20. The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution.

    Badouin, Hélène; Gouzy, Jérôme; Grassa, Christopher J; Murat, Florent; Staton, S Evan; Cottret, Ludovic; Lelandais-Brière, Christine; Owens, Gregory L; Carrère, Sébastien; Mayjonade, Baptiste; Legrand, Ludovic; Gill, Navdeep; Kane, Nolan C; Bowers, John E; Hubner, Sariel; Bellec, Arnaud; Bérard, Aurélie; Bergès, Hélène; Blanchet, Nicolas; Boniface, Marie-Claude; Brunel, Dominique; Catrice, Olivier; Chaidir, Nadia; Claudel, Clotilde; Donnadieu, Cécile; Faraut, Thomas; Fievet, Ghislain; Helmstetter, Nicolas; King, Matthew; Knapp, Steven J; Lai, Zhao; Le Paslier, Marie-Christine; Lippi, Yannick; Lorenzon, Lolita; Mandel, Jennifer R; Marage, Gwenola; Marchand, Gwenaëlle; Marquand, Elodie; Bret-Mestries, Emmanuelle; Morien, Evan; Nambeesan, Savithri; Nguyen, Thuy; Pegot-Espagnet, Prune; Pouilly, Nicolas; Raftis, Frances; Sallet, Erika; Schiex, Thomas; Thomas, Justine; Vandecasteele, Céline; Varès, Didier; Vear, Felicity; Vautrin, Sonia; Crespi, Martin; Mangin, Brigitte; Burke, John M; Salse, Jérôme; Muños, Stéphane; Vincourt, Patrick; Rieseberg, Loren H; Langlade, Nicolas B

    2017-06-01

    The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought. Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives, including numerous extremophile species. Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs. The genome mostly consists of highly similar, related sequences and required single-molecule real-time sequencing technologies for successful assembly. Genome analyses enabled the reconstruction of the evolutionary history of the Asterids, further establishing the existence of a whole-genome triplication at the base of the Asterids II clade and a sunflower-specific whole-genome duplication around 29 million years ago. An integrative approach combining quantitative genetics, expression and diversity data permitted development of comprehensive gene networks for two major breeding traits, flowering time and oil metabolism, and revealed new candidate genes in these networks. We found that the genomic architecture of flowering time has been shaped by the most recent whole-genome duplication, which suggests that ancient paralogues can remain in the same regulatory networks for dozens of millions of years. This genome represents a cornerstone for future research programs aiming to exploit genetic diversity to improve biotic and abiotic stress resistance and oil production, while also considering agricultural constraints and human nutritional needs.

  1. The content of protein and of amino acids in Jerusalem artichoke tubers (Helianthus tuberosus L.) of red variety Rote Zonenkugel.

    Cieślik, Ewa; Gębusia, Agnieszka; Florkiewicz, Adam; Mickowska, Barbara

    2011-01-01

    Jerusalem artichoke (Helianthus tuberosus L.) is grown primarily for its edible tubers, which were first cultivated by native Americans before the arrival of the Europeans. Unlike most tubers, but in common with other members of the Asteraceae, the tubers store fructans instead of starch. Fructans are non-digestible carbohydrates considered functional food ingredients because they affect body processes in ways that result in better health and in many diseases prevention. However, the Jerusalem artichoke deserves attention not only because of the content of fructans, recent studies also indicate a high protein content, including essential amino acids. The aim of the work was to establish the content of protein and amino acids in Jerusalem artichoke tubers (Helianthus tuberosus L.) of red variety--Rote Zonenkugel. The content of protein was estimated by Dumas method. The amino acids composition was analysed with ion-change chromatography with postcolumn derivatisation and detection of ninhydryn reaction with automatic amino acids analyser. The assessed liophylisate was characterised by high protein content (6.36%) in comparison to chicory (which is the main industrial source of fructans) and to commonly consumed potatoes. There was shown a few times higher content of essential amino acids (also of methionine) in comparison to chicory and potato. The examined essential amino acids were present in very advantagenous proportions. In Jerusalem artichoke tubers of Rote Zonenkugel variety of the high content of protein was established in comparison to other plant sources. The high content was found of amino acids with special stress on essential amino acids (esp. sulphur ones).

  2. Pattern of cross-sensitivity between 4 Compositae plants, Parthenium hysterophorus, Xanthium strumarium, Helianthus annuus and Chrysanthemum coronarium, in Indian patients.

    Nandakishore, T; Pasricha, J S

    1994-03-01

    To assess the pattern of cross-sensitivity between 4 members of the Compositae family, namely Parthenium hysterophorus L., Xanthium strumarium L., Helanthus annuus L. and Chrysanthemum coronarium L., 63 patients clinically diagnosed to have airborne contact dermatitis, and 51 controls having well-defined patterns of contact dermatitis caused by agents other than plants, were patch tested with measured amounts of standardized aqueous extracts of these plants. Positive reactions were obtained in 62 patients and 13 controls with Parthenium hysterophorus, in 47 patients and 9 controls with Xanthium strumarium, in 7 patients and 2 controls with Helianthus annuus, and in 13 of the 57 patients and one out of 28 controls tested with Chrysanthemum coronarium. 2 patients were allergic to all 4 of the plants; 14 patients to 3 plants, namely Parthenium, Xanthium and Chrysanthemum in 9 cases and Parthenium, Xanthium and Helianthus in 5 cases; 32 patients to 2 plants, namely Parthenium and Xanthium in 30 cases, and Parthenium and Chrysanthemum, and Xanthium and Chrysanthemum in 1 case each; 15 patients were allergic to 1 plant only, that being Parthenium. All the 47 patients allergic to Xanthium, 13 patients allergic to Chrysanthemum and 7 patients allergic to Helianthus were positive with some other plant as well. There was 1 patient who was allergic to Xanthium and Chrysanthemum but not to Parthenium. The titre of contact hypersensitivity (TCH) determined in the patients allergic to Parthenium, Xanthium and Helianthus showed values that varied widely with each plant in different patients, and there was no parallelism between the TCH with various plants.(ABSTRACT TRUNCATED AT 250 WORDS)

  3. The complete chloroplast genome sequence of Aster spathulifolius (Asteraceae); genomic features and relationship with Asteraceae.

    Choi, Kyoung Su; Park, SeonJoo

    2015-11-10

    Aster spathulifolius, a member of the Asteraceae family, is distributed along the coast of Japan and Korea. This plant is used for medicinal and ornamental purposes. The complete chloroplast (cp) genome of A. sphathulifolius consists of 149,473 bp that include a pair of inverted repeats of 24,751 bp separated by a large single copy region of 81,998 bp and a small single copy region of 17,973 bp. The chloroplast genome contains 78 coding genes, four rRNA genes and 29 tRNA genes. When compared to other cpDNA sequences of Asteraceae, A. spathulifolius showed the closest relationship with Jacobaea vulgaris, and its atpB gene was found to be a pseudogene, unlike J. vulgaris. Furthermore, evaluation of the gene compositions of J. vulgaris, Helianthus annuus, Guizotia abyssinica and A. spathulifolius revealed that 13.6-kb showed inversion from ndhF to rps15, unlike Lactuca of Asteraceae. Comparison of the synonymous (Ks) and nonsynonymous (Ka) substitution rates with J. vulgaris revealed that synonymous genes related to a small subunit of the ribosome showed the highest value (0.1558), while nonsynonymous rates of genes related to ATP synthase genes were highest (0.0118). These findings revealed that substitution has occurred at similar rates in most genes, and the substitution rates suggested that most genes is a purified selection. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Extreme genomes

    DeLong, Edward F

    2000-01-01

    The complete genome sequence of Thermoplasma acidophilum, an acid- and heat-loving archaeon, has recently been reported. Comparative genomic analysis of this 'extremophile' is providing new insights into the metabolic machinery, ecology and evolution of thermophilic archaea.

  5. Grass genomes

    Bennetzen, Jeffrey L.; SanMiguel, Phillip; Chen, Mingsheng; Tikhonov, Alexander; Francki, Michael; Avramova, Zoya

    1998-01-01

    For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that in...

  6. Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke.

    Bock, Dan G; Kane, Nolan C; Ebert, Daniel P; Rieseberg, Loren H

    2014-02-01

    The perennial sunflower Helianthus tuberosus, known as Jerusalem Artichoke or Sunchoke, was cultivated in eastern North America before European contact. As such, it represents one of the few taxa that can support an independent origin of domestication in this region. Its tubers were adopted as a source of food and forage when the species was transferred to the Old World in the early 1600s, and are still used today. Despite the cultural and economic importance of this tuber crop species, its origin is debated. Competing hypotheses implicate the occurrence of polyploidization with or without hybridization, and list the annual sunflower H. annuus and five distantly related perennial sunflower species as potential parents. Here, we test these scenarios by skimming the genomes of diverse populations of Jerusalem Artichoke and its putative progenitors. We identify relationships among Helianthus taxa using complete plastomes (151 551 bp), partial mitochondrial genomes (196 853 bp) and 35S (8196 bp) and 5S (514 bp) ribosomal DNA. Our results refute the possibility that Jerusalem Artichoke is of H. annuus ancestry. We provide the first genetic evidence that this species originated recursively from perennial sunflowers of central-eastern North America via hybridization between tetraploid Hairy Sunflower and diploid Sawtooth Sunflower. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

  7. Cancer genomics

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  8. Aseptic hydroponics to assess rhamnolipid-Cd and rhamnolipid-Zn bioavailability for sunflower (Helianthus annuus): a phytoextraction mechanism study.

    Wen, Jia; McLaughlin, Mike J; Stacey, Samuel P; Kirby, Jason K

    2016-11-01

    The availability of cadmium (Cd) and zinc (Zn) to sunflower (Helianthus annuus) was investigated in rhamnolipid- and ethylenediaminetetraacetic acid (EDTA)-buffered solutions in order to evaluate the influence of aqueous speciation of the metals on their uptake by the plant, in relation to predictions of uptake by the free ion activity model (FIAM). Free metal ion activity was estimated using the chemical equilibrium program MINTEQ or measured by Donnan dialysis. The uptake of Cd followed the FIAM for the EDTA-buffered solution at EDTA concentrations below 0.4 μM; for the rhamnolipid-buffered solution, the uptake of both metals in roots was not markedly affected by increasing rhamnolipid concentrations in solution. This suggests rhamnolipid enhanced metal accumulation in plant roots (per unit free metal in solution) possibly through formation and uptake of lipophilic complexes. The addition of normal Ca concentrations (low millimetre range) to the rhamnolipid uptake solutions reduced Cd accumulation in shoots by inhibiting Cd translocation, whereas it significantly increased Zn accumulation in shoots. This study confirms that although rhamnolipid could enhance accumulation of Cd in plants roots at low Ca supply, it is not suitable for Cd phytoextraction in contaminated soil environments where Ca concentrations in soil solution are orders of magnitude greater than those of Cd.

  9. Rhizofiltration using sunflower (Helianthus annuus L.) and bean (Phaseolus vulgaris L. var. vulgaris) to remediate uranium contaminated groundwater

    Lee, Minhee, E-mail: heelee@pknu.ac.kr [Department of Environmental Geosciences, Pukyong National University, 599-1 Daeyondong, Namgu, Busan 608-737 (Korea, Republic of); Yang, Minjune [Department of Environmental Geosciences, Pukyong National University, 599-1 Daeyondong, Namgu, Busan 608-737 (Korea, Republic of)

    2010-01-15

    The uranium removal efficiencies of rhizofiltration in the remediation of groundwater were investigated in lab-scale experiments. Sunflower (Helianthus annuus L.) and bean (Phaseolus vulgaris L. var. vulgaris) were cultivated and an artificially uranium contaminated solution and three genuine groundwater samples were used in the experiments. More than 80% of the initial uranium in solution and genuine groundwater, respectively, was removed within 24 h by using sunflower and the residual uranium concentration of the treated water was lower than 30 {mu}g/L (USEPA drinking water limit). For bean, the uranium removal efficiency of the rhizofiltration was roughly 60-80%. The maximum uranium removal via rhizofiltration for the two plant cultivars occurred at pH 3-5 of solution and their uranium removal efficiencies exceeded 90%. The lab-scale continuous rhizofiltration clean-up system delivered over 99% uranium removal efficiency, and the results of SEM and EDS analyses indicated that most uranium accumulated in the roots of plants. The present results suggested that the uranium removal capacity of two plants evaluated in the clean-up system was about 25 mg/kg of wet plant mass. Notably, the removal capacity of the root parts only was more than 500 mg/kg.

  10. Effects of Azospirillum lipoferum on seedling characteristics derived from sunflower (Helianthus annus L. seed water deficit conditions

    H. Hadi

    2016-05-01

    Full Text Available Seedling characteristics of different sunflower (Helianthus annus L. cultivars under drought stress and inoculation with the Azospirillum lipoferum in a spilt-factorial layout based on randomized complete block design with three replications were evaluated. Treatments included dehydration stress (seed produced on maternal plants which irrigated after 60 (desirable irrigation, 120 (medium stress, 180 mm (severe stress evaporation from evaporation pan class A, different sunflower cultivars (Lakomka, Master, Favorite, Soor and Armavirosky and inoculation with bacteria (Azospirillum lipoferum and control. Bacteria allocated in the main plots and seeds which derived from dehydration stress conditions and different cultivars were allocated in sub plots as a factorial layout. Results showed that the time of seedling emergence, seedling vigor index, leaf petiole, stem and seedling dry weight were increased 14, 44, 30, 31, 22 and 27 percent by inoculating with bacteria, respectively. The percent of Seedling emergence of seeds derived from medium stress 48 percent was more than optimal irrigation conditions. Final appearance, speed of emergence, emergence index, dry weight and stamina seedling resulting from severe stress conditions were decreased compared with optimal irrigation. Seedling emergence of seeds derived from medium stress which inoculated with bacteria increased by 9 percent. Emergence speed index, appearance, stamina and seedling dry weights of seeds which inoculated with bacteria increased at medium and sever water stress. With consideration of the effect of dehydration stress on germination and seedling emergence, seed inoculation with bacteria improved seedling emergence and seedling vigor of seeds derived from dehydration stress conditions.

  11. The Comparison of Effects of Gamma Radiation of Crude Oil Yield on Some Sunflower (Helianthus Annuus Seeds

    Havser ERTEM VAİZOĞULLAR

    2015-01-01

    Full Text Available This study compares the effects of different doses gamma radiation on crude oil yield and moisture of different six variety sunflower (Helianthus annuus L. seeds. As materials, sunflower variety Ege-2001, Turay, AS-508, Tunca, TR-3080 and Tarsan-1018 seeds were used and irradiated with doses of 0 (control, 100, 200, 300, 400 and 500 Gy gamma radiation. Irradiation was performed in a cesium (Ce137 Gammacell 3000 Elan source, dose rate about 9.75 Gy/min (2900 Ci in the Pamukkale University Faculty of Medicine in the department of the radiological. Moisture amount of seeds were also measured by AOCS standarts. Extraction of the seeds was done with soxhlet apparatus using petroleum ether by hot continuous extraction for 6 hours.  It was found that the highest moisture rate in 100 Gy for all seeds variety. The moisture rate ranged between 3.00 and 9.68% in TR-3080 and Ege-2001, respectively. According to the our results, seed moisture content was affected by gamma radiation in a significant negative one-way. The significant reduction in seed moisture content (9.68% began at 100 Gy of gamma rays and continued to decline to up to 4.04% at 500 Gy. The crude oil yield showed not a important increase in 100 and 200 Gy doses. The result showed that the highest crude oil yield was also obtained from 400 Gy and 33.49% in Ege-2001 seeds.

  12. In vitro mutagenicity assay (Ames test and phytochemical characterization of seeds oil of Helianthus annuus Linné (sunflower

    Nelma de Mello Silva Oliveira

    Full Text Available The objective of this research was to investigate the genotoxic potential of the oil of H. annuus L. (sunflower seeds via the Ames test as well as its oxidative properties and lipid composition. The pre-incubation method, system metabolic activation (S9 fraction and five S. typhimurium strains (TA97, TA98, TA100, TA1535 and TA102 were employed for the Ames test. The oxidative stability and fatty acid composition were analyzed by standard methods and gas chromatography. A revertant analysis showed no significant differences between the treatment doses (10–200 μl/plate and the negative controls, regardless of S9+ and S9−, and included all of the S. typhimurium strains. Chromatographic analysis showed high levels of polyunsaturated fatty acids, followed by monounsaturated, saturated and total trans-isomers. Among the polyunsaturated, monounsaturated and saturated fatty acids, linoleic, oleic and palmitic acids predominated. The results suggest that the sunflower oil is not genotoxic as indicated by frameshift mutations and base pair substitutions regardless of the treatment dose, but shows dose-dependent toxicity. The oxidative properties of the sunflower oil were consistent with the requirements of national and international standards. However, its composition could also indicate phytotherapeutic properties. Keywords: Helianthus annuus L., Sunflower oil, Genetic toxicity, Gas chromatography

  13. Seed yield, N-uptake and oil quality in Helianthus annuus as affected by N-fertilizer

    Kurdali, F.; Al-Ain, F.; Attar, J.

    2008-11-01

    A field experiment was conducted to study the impact of different nitrogen fertilizer rates (0, 50, 100 and 150 kg N/ha as urea) on dry matter yield, N uptake, seed yield, grain oil content and properties of sunflower Helianthus annuus using the 15 N labeling technique. Sunflower plants responded strongly to increasing N supply with respect to growth performance. Dry matter yield and total N uptake were significantly increased with increasing N-supply. Partitioning of N yield in different plant parts showed that capitulum was the principle sink of N (60%) followed by leaves (30%) and stem (10%) regardless of N-fertilizer rates. Seed yield of sunflower was significantly increased at higher N-supply. However, oil concentration was significantly reduced in the N-fertilized treatments. Decreasing of grain oil content due to N addition was overcompensated by the seed yield increase. Consequently, no significant effect of N supply on oil yield was observed. The effect of N supply on iodine number was small, and only a small trend towards lower iodine value in the N100 was observed. No clear trend of the effect of N supply on other oil quality parameters was observed. Nitrogen derived from fertilizer (Ndff) was significantly increased with increasing N-supply. Recovery of fertilizer 15 N was of 64% regardless of N-rates. This efficiency was less pronounced in stem and leaves than that in capitulum which had a greater value at higher N-supply. (Author)

  14. Analysis of Essential Oil in Jerusalem Artichoke (Helianthus tuberosus L.) Leaves and Tubers by Gas Chromatography-Mass Spectrometry.

    Helmi, Zead; Al Azzam, Khaldun Mohammad; Tsymbalista, Yuliya; Ghazleh, Refat Abo; Shaibah, Hassan; Aboul-Enein, Hassan

    2014-12-01

    To investigate, for the first time, the chemical composition of essential oil of the tubers and leaves of Jerusalem artichoke (Helianthus tuberosus L.), a species of sunflower native to eastern North America, growing in Ukraine. A hydrodistillation apparatus was used for the extraction of volatile components and then it was analysed by gas chromatography equipped with a split-splitless injector (split ratio, 1:50) and flame ionization detector (FID). The oil was analyzed under linear temperature programming applied at 4°C/min from 50°C - 340°C. Temperatures of the injector and FID detector were maintained at 280°C and 300°C, respectively. The chemical analysis of the oil was carried out using gas chromatography coupled to mass spectrometry (GC-MS), to determine the chemical composition of the volatile fraction. The essential oils content ranged from 0.00019 to 0.03486 and 0.00011 to 0.00205 (g/100g), in leaves and tubers, respectively. The qualitative and quantitative analysis led to the identification of 17 components in both species samples. The major component found in leaves and tubers was (-)-β-bisabolene with 70.7% and 63.1%, respectively. Essential oil profile of Jerusalem artichoke species showed significant differences between leaves and tubers species. Additionally, the leaves of Jerusalem artichoke are a promising source of natural β-bisabolene.

  15. The sensitivity of sunflower (Helianthus annuus L. plants to UV-B radiation is altered by nitrogen status

    Inês Cechin

    2018-02-01

    Full Text Available ABSTRACT: Interaction effects between nitrogen and UV-B radiation were studied in sunflower (Helianthus annuus L. variety IAC-Iarama plants grown in a greenhouse under natural photoperiod conditions. Plants were irradiated with 0.8W m-2 (control or 8.0W m-2 (+UV-B of UV-B radiation for 7h per day. The plants were grown in pots containing vermiculite and watered with 70% of full strength nitrogen-free Long Ashton solution, containing either low (42.3ppm or high (282ppm nitrogen as ammonium nitrate. High nitrogen increased dry matter of stem, leaves and shoot, photosynthetic pigments and photosynthesis (A without any alteration in stomatal conductance (gs nor transpiration (E while it reduced the intercellular CO2 (Ci concentration, and malondialdehyde (MDA content. High UV-B radiation had negative effects on dry matter production, A, gs and E with the effects more marked under high nitrogen, whereas it increased Ci under high nitrogen. Activity of PG-POD was reduced by high UV-B radiation under low nitrogen but it was not changed under high nitrogen. The UV-B radiation increased the MDA content independently of nitrogen level. Results indicate that the effects of UV-B radiation on sunflower plants are dependent of nitrogen supply with high nitrogen making their physiological processes more sensitive to UV-B radiation.

  16. Identification and characterization of two bisabolene synthases from linear glandular trichomes of sunflower (Helianthus annuus L., Asteraceae).

    Aschenbrenner, Anna-Katharina; Kwon, Moonhyuk; Conrad, Jürgen; Ro, Dae-Kyun; Spring, Otmar

    2016-04-01

    Sunflower is known to produce a variety of bisabolene-type sesquiterpenes and accumulates these substances in trichomes of leaves, stems and flowering parts. A bioinformatics approach was used to identify the enzyme responsible for the initial step in the biosynthesis of these compounds from its precursor farnesyl pyrophosphate. Based on sequence similarity with a known bisabolene synthases from Arabidopsis thaliana AtTPS12, candidate genes of Helianthus were searched in EST-database and used to design specific primers. PCR experiments identified two candidates in the RNA pool of linear glandular trichomes of sunflower. Their sequences contained the typical motifs of sesquiterpene synthases and their expression in yeast functionally characterized them as bisabolene synthases. Spectroscopic analysis identified the stereochemistry of the product of both enzymes as (Z)-γ-bisabolene. The origin of the two sunflower bisabolene synthase genes from the transcripts of linear trichomes indicates that they may be involved in the synthesis of sesquiterpenes produced in these trichomes. Comparison of the amino acid sequences of the sunflower bisabolene synthases showed high similarity with sesquiterpene synthases from other Asteracean species and indicated putative evolutionary origin from a β-farnesene synthase. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Translatome profiling in dormant and nondormant sunflower (Helianthus annuus) seeds highlights post-transcriptional regulation of germination.

    Layat, Elodie; Leymarie, Juliette; El-Maarouf-Bouteau, Hayat; Caius, José; Langlade, Nicolas; Bailly, Christophe

    2014-12-01

    Seed dormancy, which blocks germination in apparently favourable conditions, is a key regulatory control point of plant population establishment. As germination requires de novo translation, its regulation by dormancy is likely to be related to the association of individual transcripts to polysomes. Here, the polysome-associated mRNAs, that is, the translatome, were fractionated and characterized with microarrays in dormant and nondormant sunflower (Helianthus annuus) embryos during their imbibition at 10°C, a temperature preventing germination of dormant embryos. Profiling of mRNAs in polysomal complexes revealed that the translatome differs between germinating and nongerminating embryos. Association of transcripts with polysomes reached a maximum after 15 h of imbibition; at this time-point 194 polysome-associated transcripts were specifically found in nondormant embryos and 47 in dormant embryos only. The proteins corresponding to the polysomal mRNAs in nondormant embryos appeared to be very pertinent for germination and were involved mainly in transport, regulation of transcription or cell wall modifications. This work demonstrates that seed germination results from a timely regulated and selective recruitment of mRNAs to polysomes, thus opening novel fields of investigation for the understanding of this developmental process. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

  18. Molecular cloning and biochemical characterization of three phosphoglycerate kinase isoforms from developing sunflower (Helianthus annuus L.) seeds.

    Troncoso-Ponce, M A; Rivoal, J; Venegas-Calerón, M; Dorion, S; Sánchez, R; Cejudo, F J; Garcés, R; Martínez-Force, E

    2012-07-01

    Three cDNAs encoding different phosphoglycerate kinase (PGK, EC 2.7.2.3) isoforms, two cytosolic (HacPGK1 and HacPGK2) and one plastidic (HapPGK), were cloned and characterized from developing sunflower (Helianthus annuus L.) seeds. The expression profiles of these genes showed differences in heterotrophic tissues, such as developing seeds and roots, where HacPGK1 was predominant, while HapPGK was highly expressed in photosynthetic tissues. The cDNAs were expressed in Escherichia coli, and the corresponding proteins purified to electrophoretic homogeneity, using immobilized metal ion affinity chromatography, and biochemically characterized. Despite the high level of identity between sequences, the HacPGK1 isoform showed strong differences in terms of specific activity, temperature stability and pH sensitivity in comparison to HacPGK2 and HapPGK. A polyclonal immune serum was raised against the purified HacPGK1 isoform, which showed cross-immunoreactivity with the other PGK isoforms. This serum allowed the localization of high expression levels of PGK isozymes in embryo tissues. Copyright © 2012 Elsevier Ltd. All rights reserved.

  19. Phytotoxic effects of nickel on yield and concentration of macro- and micro-nutrients in sunflower (Helianthus annuus L.) achenes.

    Ahmad, Muhammad Sajid Aqeel; Ashraf, Muhammad; Hussain, Mumtaz

    2011-01-30

    The phytotoxic effects of varying levels of nickel (0, 10, 20, 30, and 40 mg L(-1)) on growth, yield and accumulation of macro- and micro-nutrients in leaves and achenes of sunflower (Helianthus annuus L.) were appraised in this study. A marked reduction in root and shoot fresh biomass was recorded at higher Ni levels. Nickel stress also caused a substantial decrease in all macro- and micro-nutrients in leaves and achenes. The lower level of Ni (10 mg L(-1)) had a non-significant effect on various yield attributes, but higher Ni levels considerably decreased these parameters. Higher Ni levels decreased the concentrations of Ca, Mn and Fe in achenes. In contrast, achene N, K, Zn, Mn and Cu decreased consistently with increasing level of Ni, even at lower level (10 mg L(-1)). Sunflower hybrid Hysun-33 had better yield and higher most of the nutrients in achenes as compared with SF-187. The maximum reduction in all parameters was observed at the maximum level of nickel (40 mg L(-1)) where almost all parameters were reduced more than 50% of those of control plants. In conclusion, the pattern of uptake and accumulation of different nutrients in sunflower plants were nutrient- and cultivar-specific under Ni-stress. Copyright © 2010 Elsevier B.V. All rights reserved.

  20. Fine mapping of the sunflower resistance locus Pl(ARG) introduced from the wild species Helianthus argophyllus.

    Wieckhorst, S; Bachlava, E; Dussle, C M; Tang, S; Gao, W; Saski, C; Knapp, S J; Schön, C-C; Hahn, V; Bauer, E

    2010-11-01

    Downy mildew, caused by Plasmopara halstedii, is one of the most destructive diseases in cultivated sunflower (Helianthus annuus L.). The dominant resistance locus Pl(ARG) originates from silverleaf sunflower (H. argophyllus Torrey and Gray) and confers resistance to all known races of P. halstedii. We mapped Pl(ARG) on linkage group (LG) 1 of (cms)HA342 × ARG1575-2, a population consisting of 2,145 F(2) individuals. Further, we identified resistance gene candidates (RGCs) that cosegregated with Pl(ARG) as well as closely linked flanking markers. Markers from the target region were mapped with higher resolution in NDBLOS(sel) × KWS04, a population consisting of 2,780 F(2) individuals that does not segregate for Pl(ARG). A large-insert sunflower bacterial artificial chromosome (BAC) library was screened with overgo probes designed for markers RGC52 and RGC151, which cosegregated with Pl(ARG). Two RGC-containing BAC contigs were anchored to the Pl(ARG) region on LG 1.

  1. Modelled hydraulic redistribution by sunflower (Helianthus annuus L.) matches observed data only after including night-time transpiration.

    Neumann, Rebecca B; Cardon, Zoe G; Teshera-Levye, Jennifer; Rockwell, Fulton E; Zwieniecki, Maciej A; Holbrook, N Michele

    2014-04-01

    The movement of water from moist to dry soil layers through the root systems of plants, referred to as hydraulic redistribution (HR), occurs throughout the world and is thought to influence carbon and water budgets and ecosystem functioning. The realized hydrologic, biogeochemical and ecological consequences of HR depend on the amount of redistributed water, whereas the ability to assess these impacts requires models that correctly capture HR magnitude and timing. Using several soil types and two ecotypes of sunflower (Helianthus annuus L.) in split-pot experiments, we examined how well the widely used HR modelling formulation developed by Ryel et al. matched experimental determination of HR across a range of water potential driving gradients. H. annuus carries out extensive night-time transpiration, and although over the last decade it has become more widely recognized that night-time transpiration occurs in multiple species and many ecosystems, the original Ryel et al. formulation does not include the effect of night-time transpiration on HR. We developed and added a representation of night-time transpiration into the formulation, and only then was the model able to capture the dynamics and magnitude of HR we observed as soils dried and night-time stomatal behaviour changed, both influencing HR. © 2013 John Wiley & Sons Ltd.

  2. Rhizofiltration using sunflower (Helianthus annuus L.) and bean (Phaseolus vulgaris L. var. vulgaris) to remediate uranium contaminated groundwater

    Lee, Minhee; Yang, Minjune

    2010-01-01

    The uranium removal efficiencies of rhizofiltration in the remediation of groundwater were investigated in lab-scale experiments. Sunflower (Helianthus annuus L.) and bean (Phaseolus vulgaris L. var. vulgaris) were cultivated and an artificially uranium contaminated solution and three genuine groundwater samples were used in the experiments. More than 80% of the initial uranium in solution and genuine groundwater, respectively, was removed within 24 h by using sunflower and the residual uranium concentration of the treated water was lower than 30 μg/L (USEPA drinking water limit). For bean, the uranium removal efficiency of the rhizofiltration was roughly 60-80%. The maximum uranium removal via rhizofiltration for the two plant cultivars occurred at pH 3-5 of solution and their uranium removal efficiencies exceeded 90%. The lab-scale continuous rhizofiltration clean-up system delivered over 99% uranium removal efficiency, and the results of SEM and EDS analyses indicated that most uranium accumulated in the roots of plants. The present results suggested that the uranium removal capacity of two plants evaluated in the clean-up system was about 25 mg/kg of wet plant mass. Notably, the removal capacity of the root parts only was more than 500 mg/kg.

  3. Plant domestication and the assembly of bacterial and fungal communities associated with strains of the common sunflower, Helianthus annuus.

    Leff, Jonathan W; Lynch, Ryan C; Kane, Nolan C; Fierer, Noah

    2017-04-01

    Root and rhizosphere microbial communities can affect plant health, but it remains undetermined how plant domestication may influence these bacterial and fungal communities. We grew 33 sunflower (Helianthus annuus) strains (n = 5) that varied in their extent of domestication and assessed rhizosphere and root endosphere bacterial and fungal communities. We also assessed fungal communities in the sunflower seeds to investigate the degree to which root and rhizosphere communities were influenced by vertical transmission of the microbiome through seeds. Neither root nor rhizosphere bacterial communities were affected by the extent of sunflower domestication, but domestication did affect the composition of rhizosphere fungal communities. In particular, more modern sunflower strains had lower relative abundances of putative fungal pathogens. Seed-associated fungal communities strongly differed across strains, but several lines of evidence suggest that there is minimal vertical transmission of fungi from seeds to the adult plants. Our results indicate that plant-associated fungal communities are more strongly influenced by host genetic factors and plant breeding than bacterial communities, a finding that could influence strategies for optimizing microbial communities to improve crop yields. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  4. Fine mapping of the sunflower resistance locus PlARG introduced from the wild species Helianthus argophyllus

    Wieckhorst, S.; Bachlava, E.; Dußle, C. M.; Tang, S.; Gao, W.; Saski, C.; Knapp, S. J.; Schön, C.-C.; Hahn, V.

    2010-01-01

    Downy mildew, caused by Plasmopara halstedii, is one of the most destructive diseases in cultivated sunflower (Helianthus annuus L.). The dominant resistance locus PlARG originates from silverleaf sunflower (H. argophyllus Torrey and Gray) and confers resistance to all known races of P. halstedii. We mapped PlARG on linkage group (LG) 1 of (cms)HA342 × ARG1575-2, a population consisting of 2,145 F2 individuals. Further, we identified resistance gene candidates (RGCs) that cosegregated with PlARG as well as closely linked flanking markers. Markers from the target region were mapped with higher resolution in NDBLOSsel × KWS04, a population consisting of 2,780 F2 individuals that does not segregate for PlARG. A large-insert sunflower bacterial artificial chromosome (BAC) library was screened with overgo probes designed for markers RGC52 and RGC151, which cosegregated with PlARG. Two RGC-containing BAC contigs were anchored to the PlARG region on LG 1. Electronic supplementary material The online version of this article (doi:10.1007/s00122-010-1416-4) contains supplementary material, which is available to authorized users. PMID:20700574

  5. Influence of nitrogen fertilization on diazotrophic communities in the rhizosphere of the Jerusalem artichoke (Helianthus tuberosus L.).

    Meng, Xianfa; Wang, Lin; Long, Xiaohua; Liu, Zhaopu; Zhang, Zhenhua; Zed, Rengel

    2012-06-01

    Diazotrophs in the soil may be influenced by plant factors as well as nitrogen (N) fertilization. In this study, we investigated potential diazotrophic communities in the rhizosphere of the Jerusalem artichoke (Helianthus tuberosus L.) supplied with differing amounts of N. The community structure of N(2)-fixing bacteria was profiled using the length heterogeneity polymerase chain reaction (LH-PCR) and terminal restriction fragment length polymorphism (T-RFLP) based on a variation in the nifH gene. Higher numbers of diazotrophs were detected by T-RFLP compared to LH-PCR. The lowest number of N(2)-fixing bacteria was observed in the rhizosphere soil with high N fertilization. T-RFLP was a better method than LH-PCR for profiling microbial diversity of diazotrophs using multidimensional scaling (MDS) and analysis of similarity (ANOSIM) of fingerprints as well as diversity measures. The supply of N fertilizer appeared to negatively influence the abundance of diazotrophs in the rhizophere of the Jerusalem artichoke. Copyright © 2012 Institut Pasteur. All rights reserved.

  6. Cultivar and Metal-Specific Effects of Endophytic Bacteria in Helianthus tuberosus Exposed to Cd and Zn

    Blanca Montalbán

    2017-09-01

    Full Text Available Plant growth promoting endophytic bacteria (PGPB isolated from Brassica napus were inoculated in two cultivars of Helianthus tuberosus (VR and D19 growing on sand supplemented with 0.1 mM Cd or 1 mM Zn. Plant growth, concentrations of metals and thiobarbituric acid (TBA reactive compounds were determined. Colonization of roots of H. tuberosus D19 by Pseudomonas sp. 262 was evaluated using confocal laser scanning microscopy. Pseudomonas sp. 228, Serratia sp. 246 and Pseudomonas sp. 262 significantly enhanced growth of H. tuberosus D19 exposed to Cd or Zn. Pseudomonas sp. 228 significantly increased Cd concentrations in roots. Serratia sp. 246, and Pseudomonas sp. 256 and 228 resulted in significantly decreased contents of TBA reactive compounds in roots of Zn exposed D19 plants. Growth improvement and decrease of metal-induced stress were more pronounced in D19 than in VR. Pseudomonas sp. 262-green fluorescent protein (GFP colonized the root epidermis/exodermis and also inside root hairs, indicating that an endophytic interaction was established. H. tuberosus D19 inoculated with Pseudomonas sp. 228, Serratia sp. 246 and Pseudomonas sp. 262 holds promise for sustainable biomass production in combination with phytoremediation on Cd and Zn contaminated soils.

  7. Root biomass response to foliar application of imazapyr for two imidazolinone tolerant alleles of sunflower (Helianthus annuus L.).

    Sala, Carlos A; Bulos, Mariano; Altieri, Emiliano; Ramos, María Laura

    2012-09-01

    Imisun and CLPlus are two imidazolinone tolerance traits in sunflower (Helianthus annuus L.) determined by the expression of two alleles at the locus Ahasl1. Both traits differed in their tolerance level to imazapyr -a type of imidazolinone herbicide- when aboveground biomass is considered, but the concomitant herbicide effect over the root system has not been reported. The objective of this work was to quantify the root biomass response to increased doses of imazapyr in susceptible (ahasl1/ahasl1), Imisun (Ahasl1-1/Ahasl1-1) and CLPlus (Ahasl1-3/Ahasl1-3) homozygous sunflower genotypes. These materials were sprayed at the V2-V4 stage with increased doses of imazapyr (from 0 to 480 g active ingredient ha(-1)) and 14 days after treatment root biomass of each plant was assessed. Genotype at the Ahasl1 locus, dose of imazapyr and their interaction significantly contributed (P < 0.001) to explain the reduction in root biomass accumulation after herbicide application. Estimated dose of imazapyr required to reduce root biomass accumulation by fifty percent (GR(50)) differed statistically for the three genotypes under study (P < 0.001). CLPlus genotypes showed the highest values of GR(50), 300 times higher on average than the susceptible genotypes, and almost 8 times higher than Imisun materials, demonstrating that both alleles differ in their root biomass response to foliar application of increased doses of imazapyr.

  8. The effect of EDTA and citric acid on phytoremediation of Cd, Cr, and Ni from soil using Helianthus annuus

    Turgut, Cafer; Katie Pepe, M.; Cutright, Teresa J.

    2004-01-01

    The possibility to clean heavy metal contaminated soils with hyperaccumulator plants has shown great potential. One of the most recently studied species used in phytoremediation applications are sunflowers. In this study, two cultivars of Helianthus annuus were used in conjunction with ethylene diamine tetracetic acid (EDTA) and citric acid (CA) as chelators. Two different concentrations of the chelators were studied for enhancing the uptake and translocation of Cd, Cr, and Ni from a silty-clay loam soil. When 1.0 g/kg CA was used, the highest total metal uptake was only 0.65 mg. Increasing the CA concentration posed a severe phytotoxicity to both cultivars as evidenced by stunted growth and diminished uptake rates. Decreasing the CA concentration to 0.1 and 0.3 g/kg yielded results that were not statistically different from the control. EDTA at a concentration of 0.1 g/kg yielded the best results for both cultivars achieving a total metal uptake of ∼0.73 mg compared to ∼0.40 mg when EDTA was present at 0.3 g/kg

  9. Enhanced Pb Absorption by Hordeum vulgare L. and Helianthus annuus L. Plants Inoculated with an Arbuscular Mycorrhizal Fungi Consortium.

    Arias, Milton Senen Barcos; Peña-Cabriales, Juan José; Alarcón, Alejandro; Maldonado Vega, María

    2015-01-01

    The effect of an arbuscular mycorrhizal fungi (AMF) consortium conformed by (Glomus intraradices, Glomus albidum, Glomus diaphanum, and Glomus claroideum) on plant growth and absorption of Pb, Fe, Na, Ca, and (32)P in barley (Hordeum vulgare L.) and sunflower (Helianthus annuus L.) plants was evaluated. AMF-plants and controls were grown in a substrate amended with powdered Pb slag at proportions of 0, 10, 20, and 30% v/v equivalent to total Pb contents of 117; 5,337; 13,659, and 19,913 mg Pb kg(-1) substrate, respectively. Mycorrhizal root colonization values were 70, 94, 98, and 90%, for barley and 91, 97, 95, and 97%, for sunflower. AMF inoculum had positive repercussions on plant development of both crops. Mycorrhizal barley absorbed more Pb (40.4 mg Pb kg(-1)) shoot dry weight than non-colonized controls (26.5 mg Pb kg(-1)) when treated with a high Pb slag dosage. This increase was higher in roots than shoots (650.0 and 511.5 mg Pb kg(-1) root dry weight, respectively). A similar pattern was found in sunflower. Plants with AMF absorbed equal or lower amounts of Fe, Na and Ca than controls. H. vulgare absorbed more total P (1.0%) than H. annuus (0.9%). The arbuscular mycorrizal consortium enhanced Pb extraction by plants.

  10. The effect of EDTA and citric acid on phytoremediation of Cd, Cr, and Ni from soil using Helianthus annuus.

    Turgut, Cafer; Katie Pepe, M; Cutright, Teresa J

    2004-09-01

    The possibility to clean heavy metal contaminated soils with hyperaccumulator plants has shown great potential. One of the most recently studied species used in phytoremediation applications are sunflowers. In this study, two cultivars of Helianthus annuus were used in conjunction with ethylene diamine tetracetic acid (EDTA) and citric acid (CA) as chelators. Two different concentrations of the chelators were studied for enhancing the uptake and translocation of Cd, Cr, and Ni from a silty-clay loam soil. When 1.0 g/kg CA was used, the highest total metal uptake was only 0.65 mg. Increasing the CA concentration posed a severe phytotoxicity to both cultivars as evidenced by stunted growth and diminished uptake rates. Decreasing the CA concentration to 0.1 and 0.3 g/kg yielded results that were not statistically different from the control. EDTA at a concentration of 0.1 g/kg yielded the best results for both cultivars achieving a total metal uptake of approximately 0.73 mg compared to approximately 0.40 mg when EDTA was present at 0.3 g/kg.

  11. Comparative effect of Al, Se, and Mo toxicity on NO3(-) assimilation in sunflower (Helianthus annuus L.) plants.

    Ruiz, Juan M; Rivero, Rosa M; Romero, Luis

    2007-04-01

    Here, we study the effect caused by three trace elements--Al, Se, and Mo--applied at the same concentration (100 microM) and in their oxyanionic forms--NaAl(OH)(4), Na(2)SeO(4), and Na(2)MoO(4)--on NO(3)(-) assimilation (NO(3)(-), nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), and glutamate synthase (GOGAT) activities, and concentrations of amino acids and proteins) in sunflower (Helianthus annuus L. var. Kasol) plants. The most harmful element for sunflower plants proved to be selenate, followed by aluminate. On the contrary, the application of molybdate had no negative effect on the growth of this plant, suggesting the possibility of using sunflower for the phytoremediation of this metal, mainly in agricultural zones used for grazing where the excess of this element can provoke problems of molybdenosis in ruminants (particularly in cattle). In addition, we found that the alteration of NO(3)(-) assimilation by SeO(4)(2-) and Al(OH)(4)(-) directly influences the growth and development of plants, foliar inhibition of NR activity by SeO(4)(2-) being more harmful than the decrease in foliar availability of NO(3)(-) provoked by Al(OH)(4)(-).

  12. The effect of EDTA and citric acid on phytoremediation of Cd, Cr, and Ni from soil using Helianthus annuus

    Turgut, Cafer; Katie Pepe, M.; Cutright, Teresa J

    2004-09-01

    The possibility to clean heavy metal contaminated soils with hyperaccumulator plants has shown great potential. One of the most recently studied species used in phytoremediation applications are sunflowers. In this study, two cultivars of Helianthus annuus were used in conjunction with ethylene diamine tetracetic acid (EDTA) and citric acid (CA) as chelators. Two different concentrations of the chelators were studied for enhancing the uptake and translocation of Cd, Cr, and Ni from a silty-clay loam soil. When 1.0 g/kg CA was used, the highest total metal uptake was only 0.65 mg. Increasing the CA concentration posed a severe phytotoxicity to both cultivars as evidenced by stunted growth and diminished uptake rates. Decreasing the CA concentration to 0.1 and 0.3 g/kg yielded results that were not statistically different from the control. EDTA at a concentration of 0.1 g/kg yielded the best results for both cultivars achieving a total metal uptake of {approx}0.73 mg compared to {approx}0.40 mg when EDTA was present at 0.3 g/kg.

  13. Comparative analysis of tannery-effluent contaminated soil and mixed culture bacterial inoculation on helianthus annuus L. growth

    Yasin, M.; Faisal, M.

    2012-01-01

    Here we reported the effect of four strains Bacillus pumilus-CrK08, Cellulosimicrobium cellulans-CrK16, Exiguobacterium-CrK19 and Bacillus cereus-CrK20 and tannery contaminated soil on Helianthus annuus L. var Hysun-33 growth parameters. Plants growing in tannery effluent contaminated soil have shown slowed leaf growth, reduced shoot length, burning of leaf margins and tips compared to plants growing in normal garden soil. The inoculated plants had shown overall increase in root length (15%), shoot length (33%) and fresh weight shoot (135%) compared to un-inoculated plants growing in stress conditions. Plants growing in tannery contaminated soil have shown increase in soluble proteins contents (9%), acid phosphatase activity (200%), peroxidase activity (203%) and decrease in chlorophyll a (39%), chlorophyll b (23%) and carotenoids contents (28%) compare to plants growing in normal control soil. Inoculated plants grown in contaminated soil have shown an increased in peroxidase activity, soluble proteins contents, acid phosphatase activity, chlorophyll a, b and carotenoid contents compare to respective un-inoculated plants. (author)

  14. Elimination of natural uranium and {sup 226}Ra from contaminated waters by rhizofiltration using Helianthus annuus L

    Vera Tome, F. [Departamento de Fisica Aplicada, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz (Spain)], E-mail: fvt@unex.es; Blanco Rodriguez, P. [Departamento de Fisica, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz (Spain); Lozano, J.C. [Laboratorio de Radiactividad Ambiental, Facultad de Ciencias, Universidad de Salamanca, 37008 Salamanca (Spain)

    2008-04-15

    The elimination of natural uranium and {sup 226}Ra from contaminated waters by rhizofiltration was tested using Helianthus annuus L. (sunflower) seedlings growing in a hydroponic medium. Different experiments were designed to determine the optimum age of the seedlings for the remediation process, and also to study the principal way in which the radionuclides are removed from the solution by the sunflower roots. In every trial a precipitate appeared which contained a major fraction of the natural uranium and {sup 226}Ra. The results indicated that the seedlings themselves induced the formation of this precipitate. When four-week-old seedlings were exposed to contaminated water, a period of only 2 days was sufficient to remove the natural uranium and {sup 226}Ra from the solution: about 50% of the natural uranium and 70% of the {sup 226}Ra were fixed in the roots, and essentially the rest was found in the precipitate, with only very small percentages fixed in the shoots and left in solution.

  15. Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray.

    Fernandez, Paula; Soria, Marcelo; Blesa, David; DiRienzo, Julio; Moschen, Sebastian; Rivarola, Maximo; Clavijo, Bernardo Jose; Gonzalez, Sergio; Peluffo, Lucila; Príncipi, Dario; Dosio, Guillermo; Aguirrezabal, Luis; García-García, Francisco; Conesa, Ana; Hopp, Esteban; Dopazo, Joaquín; Heinz, Ruth Amelia; Paniego, Norma

    2012-01-01

    Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST (>130,000 ESTs) curation, assembly and sequence annotation was performed using Blast2GO (www.blast2go.de). The EST assembly comprises 41,013 putative transcripts (12,924 contigs and 28,089 singletons). The resulting Sunflower Unigen Resource (SUR version 1.0) was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. This microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower replicated 10 times (740 controls) and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit. Pre-processing and differential expression analysis of Agilent microarrays was performed using the Bioconductor limma package. The analyses based on p-values calculated by eBayes (psunflower unigene collection, and a custom, validated sunflower oligonucleotide-based microarray using Agilent technology. Both the curated unigene collection and the validated oligonucleotide microarray provide key resources for sunflower genome analysis, transcriptional studies, and molecular breeding for crop improvement.

  16. 2,3-butanediol production from Jerusalem artichoke, Helianthus tuberosus, by Bacillus polymyxa ATCC 12321. Optimization of k/sub L/ a profile

    Fages, J.; Mulard, D.; Rouquet, J.J.; Wilhelm, J.L.

    1986-12-01

    Optimization of D-(-)-2,3-butanediol production from the Jerusalem artichoke, Helianthus tuberosus, by Bacillus polymyxa ATCC 12 321 is described. The effects of initial sugar concentration and oxygen transfer rate were examined. The latter appears to be the most important parameter affecting the kinetics of the process. The best results (44 g.l/sup -1/ 2,3-butanediol, productivity of 0.79 g.l/sup -1/.h/sup -1/) were obtained by setting an optimal k/sub L/a profile during batch culture.

  17. Genome Imprinting

    the cell nucleus (mitochondrial and chloroplast genomes), and. (3) traits governed ... tively good embryonic development but very poor development of membranes and ... Human homologies for the type of situation described above are naturally ..... imprint; (b) New modifications of the paternal genome in germ cells of each ...

  18. Baculovirus Genomics

    Oers, van M.M.; Vlak, J.M.

    2007-01-01

    Baculovirus genomes are covalently closed circles of double stranded-DNA varying in size between 80 and 180 kilobase-pair. The genomes of more than fourty-one baculoviruses have been sequenced to date. The majority of these (37) are pathogenic to lepidopteran hosts; three infect sawflies

  19. Genomic Testing

    ... this database. Top of Page Evaluation of Genomic Applications in Practice and Prevention (EGAPP™) In 2004, the Centers for Disease Control and Prevention launched the EGAPP initiative to establish and test a ... and other applications of genomic technology that are in transition from ...

  20. Ancient genomes

    Hoelzel, A Rus

    2005-01-01

    Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has instead undertaken to clone and sequence a portion of the ancient genome of the cave bear.

  1. Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L. gene expression oligonucleotide microarray.

    Paula Fernandez

    Full Text Available Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST (>130,000 ESTs curation, assembly and sequence annotation was performed using Blast2GO (www.blast2go.de. The EST assembly comprises 41,013 putative transcripts (12,924 contigs and 28,089 singletons. The resulting Sunflower Unigen Resource (SUR version 1.0 was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. This microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower replicated 10 times (740 controls and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit. Pre-processing and differential expression analysis of Agilent microarrays was performed using the Bioconductor limma package. The analyses based on p-values calculated by eBayes (p<0.01 allowed the detection of 558 differentially expressed genes between water stress and control conditions; from these, ten genes were further validated by qPCR. Over-represented ontologies were identified using FatiScan in the Babelomics suite. This work generated a curated and trustable sunflower unigene collection, and a custom, validated sunflower oligonucleotide-based microarray using Agilent technology. Both the curated unigene collection and the validated oligonucleotide microarray provide key resources for sunflower genome analysis, transcriptional studies, and molecular breeding for crop improvement.

  2. Comparisons of Photosynthetic Responses of Xanthium strumarium and Helianthus annuus to Chronic and Acute Water Stress in Sun and Shade.

    Ben, G Y; Osmond, C B; Sharkey, T D

    1987-06-01

    We have examined the effects of mild, chronic water stress and acute water stress on two water stress sensitive plants, Xanthium strumarium and Helianthus annuus. Using a combination of the leaf disc O(2) electrode to measure the light responses of photosynthesis and 77 K fluorescence to monitor damage to the primary photochemistry, we have found the following: (a) The CO(2) saturated rate of photosynthesis at high light is the most water stress sensitive parameter measured. (b) The apparent quantum yield (moles O(2) per mole photons) was slightly, if at all, affected by mild water stress (>-1.5 megapascals). (c) Severe water stress (<-1.5 megapascals) reduced the quantum yield of photosynthesis regardless of whether the stress was applied in sun or shade. The light independent reduction of quantum yield was not associated with a reduction in 77 K fluorescence (F(v)/F(m)) indicating that the quantum yield reduction was not the result of damage to primary photochemistry. (d) The diel fluctuation in 77 K fluorescence seen in sun-exposed control leaves was greatly exaggerated in water stressed leaves because of enhanced decline in 77 K fluorescence in the morning. The rate of recovery was similar in both control and water stressed leaves. Shaded leaves showed no change in 77 K fluorescence regardless of whether water stress was imposed or not. (e) The water stress sensitive plants used in these experiments did not recover from acute water stress severe enough to reduce the quantum yield or chronic water stress which lasted long enough that light dependent damage to primary photochemistry occurred.

  3. Genetic diversity and population structure in cultivated sunflower and a comparison to its wild progenitor, Helianthus annuus L.

    Mandel, J R; Dechaine, J M; Marek, L F; Burke, J M

    2011-09-01

    Crop germplasm collections are valuable resources for ongoing plant breeding efforts. To fully utilize such collections, however, researchers need detailed information about the amount and distribution of genetic diversity present within collections. Here, we report the results of a population genetic analysis of the primary gene pool of sunflower (Helianthus annuus L.) based on a broad sampling of 433 cultivated accessions from North America and Europe, as well as a range-wide collection of 24 wild sunflower populations. Gene diversity across the cultivars was 0.47, as compared with 0.70 in the wilds, indicating that cultivated sunflower harbors roughly two-thirds of the total genetic diversity present in wild sunflower. Population structure analyses revealed that wild sunflower can be subdivided into four genetically distinct population clusters throughout its North American range, whereas the cultivated sunflower gene pool could be split into two main clusters separating restorer lines from the balance of the gene pool. Use of a maximum likelihood method to estimate the contribution of the wild gene pool to the cultivated sunflower germplasm revealed that the bulk of the cultivar diversity is derived from two wild sunflower population genetic clusters that are primarily composed of individuals from the east-central United States, the same general region in which sunflower domestication is believed to have occurred. We also identified a nested subset of accessions that capture as much of the allelic diversity present within the sampled cultivated sunflower germplasm collection as possible. At the high end, a core set of 288 captured nearly 90% of the alleles present in the full set of 433, whereas a core set of just 12 accessions was sufficient to capture nearly 50% of the total allelic diversity present within this sample of cultivated sunflower.

  4. Effect of Chlorocholine Chloride (CCC on the Plants’ Height and Inulin Content in Jerusalem Artichoke (Helianthus tuberosus L.

    Mikołaj Wawrzyniak

    2016-11-01

    Full Text Available Jerusalem artichoke (Helianthus tuberosus L. is herbaceous perennial plant rich in inulin and useful source of biomass. Due to its low agricultural requirements and high adaptability, it can provide very high biomass yields even on low quality sites. The plant is used in food industry, bio-fuel production, forage, pharmacy and nutrition. Its tubers accumulate approx. 10-20% of inulin in fresh weight. Currently, the use of the Helianthius tuberosus L. as a potential dietary strategy in patients affected by type 2 Diabetes is challenge. Moreover, deep understanding of the relationship between diet and composition of gut microbiota can bring the new insight in the treatment of inflammatory dependent diseases. The aim of this study was to examine an effect of plant growth retardant Chlorocholine Chloride (CCC on the plants’ height of H. tuberosus and inulin content in the tubers. We examined in the field a procedure for its shoots reduction. Material for the experiment were bought in a Polish commercial company and 528 tubers were planted in field in the middle of April 2014. Then, half of them were sprayed with 0.75% retardant of CCC . Furthermore, every week for 12 following weeks, the plants’ heights were measured. After the vegetation was over, 6 tubers for each treatment were dug out and chemically analyzed for inulin content using High Pressure Size Exclusion Chromatography. After first week of CCC use, 16% decrease of the heights plants was observed. Height of plants sprayed with CCC were significantly different comparing to Control. Weekly growth was significantly  slower in plants sprayed with CCC on first three weeks after applying retardant. Differences in plants height sustain to the end of measurements. Used retardant and its concentration did not affect the inulin content of the tubers.

  5. Selectivity and stability of herbicides and their tank mixtures for the seed yield of sunflower (Helianthus Annuus L.

    G. Delchev

    2016-12-01

    Full Text Available Abstract. The research was conducted during 2012 – 2014 on pellic vertisol soil type. Under investigation were 4 sunflower hybrids (Helianthus annuus L.: hybrid Bacardy (an imitolerant hybrid by ClearField plus technology, hybrid Estiva (an imitolerant hybrid by ClearField technology, hybrid Sumico (a tribenuron-methyl tolerant hybrid by ExpessSun technology and hybrid Arizona (a hybrid by conventional technology. Factor A included the years of investigation. Factor B, herbicides and tank mixtures, included 20 rates. It includes 3 variants by ClearField plus technology, 5 variants by ClearField technology, 5 variants by ExpessSun technology and 7 variants by conventional technology. All variants are on herbicide Gardoprim plus gold 500 SC (Smetolachlor + terbuthylazine – 3.5 l/ha, which treated after sowing before emergence of the sunflower. It is found that the highest seed yield is obtained at herbicide tank mixture Pulsar plus + Stomp aqua by ClearField plus technology. Tank mixture Listego + Dash + Sharpen by ClearField technology and Express + Trend + Select super by ExpressSun technology also lead to obtaining high seed yields. The most unstable are secondary weed infested checks by the fourth technologies for sunflower growing which are treated with soil-applied herbicide Gardoprim plus gold only. Technologically the most valuable are herbicide combination Pulsar plus + Stomp aqua and herbicide Pulsar by ClearField plus technology, tank mixtures Listego + Dash + Sharpen and Listego + Dash by ClearField technology and Express + Trend + Select super and Express + Lactofol B + Select super by ExpressSun technology. Tank mixtures of herbicides Smerch, Pendigan, Wing, Raft, Pledge and Modown with Amalgerol premium by conventional technology have low estimates due to insufficient control of some weeds in sunflower crops.

  6. Development and characterization of novel EST-SSR markers and their application for genetic diversity analysis of Jerusalem artichoke (Helianthus tuberosus L.).

    Mornkham, T; Wangsomnuk, P P; Mo, X C; Francisco, F O; Gao, L Z; Kurzweil, H

    2016-10-24

    Jerusalem artichoke (Helianthus tuberosus L.) is a perennial tuberous plant and a traditional inulin-rich crop in Thailand. It has become the most important source of inulin and has great potential for use in chemical and food industries. In this study, expressed sequence tag (EST)-based simple sequence repeat (SSR) markers were developed from 40,362 Jerusalem artichoke ESTs retrieved from the NCBI database. Among 23,691 non-redundant identified ESTs, 1949 SSR motifs harboring 2 to 6 nucleotides with varied repeat motifs were discovered from 1676 assembled sequences. Seventy-nine primer pairs were generated from EST sequences harboring SSR motifs. Our results show that 43 primers are polymorphic for the six studied populations, while the remaining 36 were either monomorphic or failed to amplify. These 43 SSR loci exhibited a high level of genetic diversity among populations, with allele numbers varying from 2 to 7, with an average of 3.95 alleles per loci. Heterozygosity ranged from 0.096 to 0.774, with an average of 0.536; polymorphic index content ranged from 0.096 to 0.854, with an average of 0.568. Principal component analysis and neighbor-joining analysis revealed that the six populations could be divided into six clusters. Our results indicate that these newly characterized EST-SSR markers may be useful in the exploration of genetic diversity and range expansion of the Jerusalem artichoke, and in cross-species application for the genus Helianthus.

  7. Molecular evolution of candidate genes for crop-related traits in sunflower (Helianthus annuus L.).

    Mandel, Jennifer R; McAssey, Edward V; Nambeesan, Savithri; Garcia-Navarro, Elena; Burke, John M

    2014-01-01

    Evolutionary analyses aimed at detecting the molecular signature of selection during crop domestication and/or improvement can be used to identify genes or genomic regions of likely agronomic importance. Here, we describe the DNA sequence-based characterization of a pool of candidate genes for crop-related traits in sunflower. These genes, which were identified based on homology to genes of known effect in other study systems, were initially sequenced from a panel of improved lines. All genes that exhibited a paucity of sequence diversity, consistent with the possible effects of selection during the evolution of cultivated sunflower, were then sequenced from a panel of wild sunflower accessions an outgroup. These data enabled formal tests for the effects of selection in shaping sequence diversity at these loci. When selection was detected, we further sequenced these genes from a panel of primitive landraces, thereby allowing us to investigate the likely timing of selection (i.e., domestication vs. improvement). We ultimately identified seven genes that exhibited the signature of positive selection during either domestication or improvement. Genetic mapping of a subset of these genes revealed co-localization between candidates for genes involved in the determination of flowering time, seed germination, plant growth/development, and branching and QTL that were previously identified for these traits in cultivated × wild sunflower mapping populations.

  8. Assessment of RAPD Markers to Analyse the Genetic Diversity among Sunflower (Helianthus annuus L. Genotypes

    Ali Raza

    2018-02-01

    Full Text Available Genetic diversity estimation among different species is an important tool for genetic improvement to maximize the yield, desirable quality, wider adaptation, pest and insect resistance that ultimately boosting traditional plant breeding methods. The most efficient way of diversity estimation is application of molecular markers. In this study, twenty random amplified polymorphic DNA (RAPD primers were utilized to estimate the genetic diversity between ten sunflower genotypes. Overall 227 bands were amplified by 20 primers with an average of 11.35 bands per primer. RAPD data showed 86.34% polymorophic bands and 13.65% of monomorophic bands. Genetic similarity was ranged from 50.22% to 87.22%. The lowest similarity (50.22% was observed between FH-352 and FH-359 and the maximum similarity 87.22% was observed between A-23 and G-46. Polymorphic information content (PIC values were varying from 0.05 to 0.12 with a mean of 0.09. Cluster analysis based on RAPD results displayed two major distinct groups 1 and 2. Group-2 contains FH-352 which was the most diverse genotype, while group-1 consists of few sub groups with all other genotypes. Ample diversity was found in all the genotypes. Present study reveals novel information about sunflower genome which can be used in future studies for sunflower improvement.

  9. Herbarium genomics

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  10. Elicitation of Jerusalem artichoke (Helianthus tuberosus L.) cell suspension culture for enhancement of inulin production and altered degree of polymerisation.

    Ma, Chunquan; Zhou, Dong; Wang, Haitao; Han, Dongming; Wang, Yang; Yan, Xiufeng

    2017-01-01

    Plant cell suspension cultures have emerged as a potential source of secondary metabolites for food additives and pharmaceuticals. In this study inulin accumulation and its degree of polymerisation (DP) in the treated cells in the same medium were investigated after treatment with six types of elicitors. An in vitro cell suspension culture of Jerusalem artichoke (Helianthus tuberosus L.) was optimised by adding an extra nitrogen source. According to the growth kinetics, a maximum biomass of 5.48 g L -1 was obtained from the optimal cell suspension medium consisted of Murashige and Skoog basic medium (MS) + 1.0 mg L -1 α-naphthalene acetic acid (NAA) + 1.0 mg L -1 6-benzylaminopurine (6-BA) + 0.5 mg L -1 proline + 1.0 mg L -1 glutamine. Methyl jasmonate (MeJA, 250 µmol L -1 ) treatment for 15 days led to the highest levels of inulin (2955.27 ± 9.81 mg L -1 compared to control of 1217.46 ± 0.26 mg L -1 ). The elicited effect of five elicitors to the suspension cells of Jerusalem artichoke is as follows: AgNO 3 (Ag, 10 µmol L -1 ), salicylic acid (SA, 75 µmol L -1 ), chitosan (KJT, 40 mg L -1 ), Trichoderma viride (Tv, 90 mg L -1 ), yeast extract (YE, 0.25 mg L -1 ), and the corresponding content of inulin is increased by 2.05-, 1.93-, 1.76-, 1.44- and 1.18-fold compared to control, respectively. The obvious effect on the percentage of lower DP in inulin was observed in cells treated with 40 mg L -1 KJT, 0.25 mg L -1 YE and 10 µmol L -1 Ag. Among the six types of elicitors, the descending order of inulin content is MeJA > Ag > SA > KJT > Tv > YE. For the purpose inulin with lower DP and its application to prebiotic food, three elicitors, including KJT, YE and Ag, can be used for the elicitation. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  11. Cephalopod genomics

    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...

  12. Genome Sequencing

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  13. Comparative Genomics

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 8. Comparative Genomics - A Powerful New Tool in Biology. Anand K Bachhawat. General Article Volume 11 Issue 8 August 2006 pp 22-40. Fulltext. Click here to view fulltext PDF. Permanent link:

  14. Effect of Irrigation with Contaminated Water by Cloth Detergent on Seed Germination Traits and Early Growth of Sunflower (Helianthus annuus L.

    Hassan HEIDARI

    2013-02-01

    Full Text Available One of the sources for irrigation is sewage. Contaminated water may affect seed germination and plant growth. A laboratory experiment and a pot experiment were conducted in 2012 to determine the effect of different doses of detergent on seed germination traits and early growth of sunflower (Helianthus annuus L.. The experiments included eight doses of cloth detergent (0, 0.00002, 0.0002, 0.002, 0.02, 0.2, 2, 20 g/L. Results showed that 20 and 2 g/L of detergent severely reduced seed germination, plant height, leaf number per plant, total biomass and stem weight. 20 g/L of detergent reduced shoot length, root length, seedling weight and seed vigor. Seed germination stage was more sensitive to contaminated water than early growth stage. The results demonstrated that irrigating sunflower by contaminated water with household cleaning products at high concentration should be avoided.

  15. Personal genomics services: whose genomes?

    Gurwitz, David; Bregman-Eschet, Yael

    2009-07-01

    New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below.

  16. Visualization for genomics: the Microbial Genome Viewer.

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a

  17. Helianthus annuus L

    moj

    Maximum and minimum reductions were observed in the cases ... markers were identified (P≤0.05) for the studied characters under natural and ..... characters did not provide sufficient information about the functional relations between the.

  18. Ancient genomics

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained...... by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans...

  19. Marine genomics

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew David; Kupczok, Anne

    2017-01-01

    Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...

  20. Evaluating the Competitive Ability of Sunflower (Helianthus annuus L. Cultivars against Tumble Pigweed (Amaranthus albus L. in Birjand Region

    mohammad javad babaie zarch

    2017-09-01

    Full Text Available Introduction Using crop species and cultivars with high competitive ability against weeds is one of the effective strategies for sustainable weed management. Emergence rate, rapid root growth, seed vigor, development rate of leaves, rapid root and shoot biomass accumulation, rapid canopy closure and plant height are important traits in relation to the competitiveness between different cultivars of crops. Competitive ability is measured using two indices including the weed growth prevention ability or weed biomass reduction index and crop tolerance to weed or yield reduction preventing index. The purpose of this study is to evaluate the competitive ability of six oilseed sunflower (Helianthus annuus L. cultivars and also introducing the most important morpho-physiological attributes affecting their competitive ability with tumble pigweed (Amaranthus albus L. in Birjand. Materials and methods This experiment was carried out as factorial layout based on randomized complete block design with three replications at the Agricultural Research Station, University of Birjand in 2012. Treatments were included six sunflower oilseed cultivars (Azargol, Jame esfehan, Farrokh, Syrna, Progress, Euroflor and tumble pigweed densities in four levels (zero (control, 5, 10 and 15 plants per square meter. The number of days and cumulative degree days were recorded from sowing to emergence. Plant height, leaf area and dry matter were recorded at four stages from emergence to 75 days after it. Sunflower seeds were harvested after physiological maturity. Preventing indices were used to evaluate the competitive ability of cultivars, competitive tolerance (Watson et al., 2002 and weed biomass. Data were analyzed with the SAS software and cluster analysis was performed using SPSS software. FLSD test was employed for comparison of the means at the 5% significance level. The graphs were prepared by Excel. Results and Discussion Analysis of variance showed that there was a

  1. Whole-plant utilization of sunflowers

    Adams, R P [Univ. of Texas, Austin; Seiler, G J

    1984-01-01

    Forty-eight accessions representing 39 taxa of the genus Helianthus (sunflower) were collected from a common garden and whole plants examined for yields of non-polar extractables. (hydrocarbons, rubber, etc.), polar extractables (resins, sugars, etc.) and crude protein. This study revealed several promising species for obtaining hydrocarbons: H. agrestis, H. annuus, H. argophyllus, and H. arizonensis. Species highest in methanol extractables were H. ciliaris, H. leavigtus, H. occidentalis ssp. plantagineus, H. paradoxus, H. petiolaris, and H. silphioides. Species with greater than 16% protein yields were H. arizonensis, H. grosseserratus, H. neglectus, H. petiolaris ssp. fallax, and H. simulans. Since this genus is well known agronomically, the development of one of the species for whole-plant utilization may be easier than the domestication of some lesser-known genera. 42 references, 3 tables

  2. Ensembl Genomes 2016: more genomes, more complexity.

    Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

    2016-01-04

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. Rodent malaria parasites : genome organization & comparative genomics

    Kooij, Taco W.A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P.

  4. Funding Opportunity: Genomic Data Centers

    Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

  5. ROLE OF SOME CHEMICAL MATERIALS ON THE PHYTO-EXTRACTION OF HEAVY METALS FROM CONTAMINATED SOILS WITH SUNFLOWER PLANTS (HELIANTHUS ANNUUS)

    ABD EL-BARY, S.A.; EL-NAKA, E.A.; RIZK, M.A.; LOTFY, S.M.

    2009-01-01

    Chelation and complexation of heavy metals were evaluated as practical ways to solubilize, detoxify and enhance heavy metals accumulation by plants. Sunflower (Helianthus annuus) was selected as potential heavy metals accumulator for metals phyto-extraction in two selected soils (clayey and sandy). To enhance metals phyto-extraction, ammonium nitrate and organic chelates such as EDTA and citric acid were added to soils at the rates from 0 to 20 mmol/kg soil as extracting solutions and applied to the soil by mixing thoroughly before planting. Dry matter production and metals concentrations in shoots and roots and soil pH were measured after 60 days.Plant dry matter production and metals accumulation were varied with soil contamination, chelate / organic acid form and rate, and soil type. The highest metals concentration was obtained in plants grown on clayey soil, however, the lowest content was observed in case of sandy soil. Addition of citric acid increased metals accumulation and translocation to the shoots significantly. Addition of 20 mmol/kg of citric acid to clayey soils increased metals concentration in shoots several folds of magnitude, but addition of ammonium nitrate had little effect on metal translocation to shoots. Citric acid was the most effective chelate in plant accumulation of tested metals.

  6. Effect of polyethylene and organic mulches in different intervals of irrigation on morphological characteristics and grain yield of sunflower (Helianthus annus L.

    R. Mahdipour Afra

    2016-05-01

    Full Text Available In order to investigate the effects of polyethylene and organic mulches in different Irrigation intervals on morphological characteristics and seed grain of sunflower (Helianthus annus L. hybrid Azrgol, an experiment was conducted in split-plot design based on randomized complete blocks with three replications at research farm of college of Aboureihan, University of Tehran during year of 2009. Main factor was three irrigation interval including of 7, 12 and 17 days and sub-factors were treatments without mulch as control and different types of mulch (polyethylene, cow manure including of 8.5 t.ha-1,17 t.ha-1, 25 t.ha-1, wheat stubble mulch in three levels of 2.5, 5.5 and 7.5 t.ha-1. Plant height, head diameter, seed number in each head, 1000-seed weight, seed yield, oil yield, harvest index were investigated. The results indicated that the effect of irrigation period and the effect of mulches for all measured traits were significant. Highest seed yield with average of 2.965 t.ha-1 was obtained from 7 days irrigation and also polyethylene mulch and stubble mulch level three in different irrigation periods, had the highest yield. The overall results showed that, using mulches by reducing irrigation water use can increases the quality and quantity seed yield. Regarding the results of the study and non-toxic effects of stubble mulches in agriculture, we suggest their usage.

  7. THE EFFECT OF SPRUCE BARK POLYPHENOLS EXTRACT IN COMBINATION WITH DEUTERIUM DEPLETED WATER (DDW ON GLYCINE MAX L. AND HELIANTHUS ANNUUS L. DEVELOPMENT

    Corneliu Tanase

    2010-09-01

    Full Text Available The aim of this study was to evaluate the effect of spruce bark aqueous extract and deuterium depleted water (DDW as bioregulators on the plant growth Glycine max L. and Helianthus annuus. The following specific parameteres were closely monitorised: germination energy and germination capacity, plants vegetative organelles growth and development and photoassimilatory pigments concentrations. The results have shown that DDW presents different effects depending on tested plant species. In the case of soybean, DDW presented stimulatory effects on both germination energy and capacity, radicles elongation, primary leaves growth and development but inhibitory effects on photoassimilatory pigments. Spruce bark extract reduced the germination capacity of soybean seeds, but accelerated the germination process of sunflower seeds and present stimulatory effects on plantlets biomass accumulation. The combination of DDW with Picea abies polyphenolic extract promoted soybean plantlet elongation, especially the rootlets ones and stimulated green biomass accumulation for both soybean and sunflower plantlets. Analyzing the photoassimilatory pigments concentration for sunflower, it can be observed an increasing trend (almost 100% comparing with control when introduce into the growth medium DDW and P. abies polyphenolic extract. DDW and P. abies bark extract have shown an important role in plant growth and development, improving photoassimiliation process.

  8. Effect of feeding low-fiber fraction of air-classified sunflower (Helianthus annus L.) meal on laying hen productive performance and egg yolk cholesterol.

    Laudadio, V; Ceci, E; Lastella, N M B; Tufarelli, V

    2014-11-01

    The present study was designed to determine the effect on laying performance and egg quality resulting from total substitution of soybean meal (SBM) with low-fiber sunflower meal (SFM; Helianthus annus L.) meal in diet of hens. ISA Brown layers, 28 wk of age, were randomly allocated to 2 dietary treatments and fed for 10 wk. The hens were kept in a free-range environment and fed 2 wheat middling-based diets consisting of a control diet, which contained SBM (153 g/kg of diet), and a test diet containing low-fiber SFM (160 g/kg of diet) as the main protein source. Each dietary treatment was replicated 4 times. Low-fiber SFM was obtained by a combination of sieving and air classification processes. Feed consumption was recorded daily and egg production was calculated on a hen-day basis; eggs from each group were collected weekly to evaluate egg components and quality. The total substitution of SBM with low-fiber SFM had no adverse effect on growth performance of laying hens. Egg production and none of egg quality traits examined were influenced by dietary treatment, except for yolk color (P eggs (P egg yolk total cholesterol and low-density lipoprotein cholesterol concentrations (P egg quality and to develop low-cholesterol eggs. ©2014 Poultry Science Association Inc.

  9. Comparative study of SOS2 and a novel PMP3-1 gene expression in two sunflower (Helianthus annuus L.) lines differing in salt tolerance.

    Saadia, Mubshara; Jamil, Amer; Ashraf, Muhammad; Akram, Nudrat Aisha

    2013-06-01

    Gene expression pattern of two important regulatory proteins, salt overly sensitive 2 (SOS2) and plasma membrane protein 3-1 (PMP3-1), involved in ion homeostasis, was analyzed in two salinity-contrasting sunflower (Helianthus annuus L.) lines, Hysun-38 (salt tolerant) and S-278 (moderately salt tolerant). The pattern was studied at selected time intervals (24 h) under 150 mM NaCl treatment. Using reverse transcription PCR, SOS2 gene fragment was obtained from young leaf and root tissues of opposing lines while that for PMP3-1 was obtained only from young root tissues. Both tolerant and moderately tolerant lines showed a gradual increase in SOS2 expression in sunflower root tissues. Leaf tissues showed the gradually increasing pattern of SOS2 expression in tolerant plants as compared to that for moderately tolerant ones that showed a relatively lower level of expression for this gene. We found the highest level of PMP 3-1 expression in the roots of tolerant sunflower line at 6 and 12 h postsalinity treatment. The moderately tolerant line showed higher expression of PMP3-1 at 12 and 24 h after salt treatment. Overall, the expression of genes for both the regulator proteins varied significantly in the two sunflower lines differing in salinity tolerance.

  10. [Analysis of mineral elements of sunflower (Helianthus annuus L.) grown on saline land in Hetao Irrigation District by ICP-AES].

    Tong, Wen-Jie; Chen, Fu; Wen, Xin-Ya

    2014-01-01

    The absorption and accumulation of ten mineral elements in four kinds of organs (root, steam, leaf and flower disc) in Helianthus annuus L. plants cultured in Hetao Irrigation District under different level of salinity stress were determined by ICP-AES with wet digestion (HNO3 + HClO4). The results showed that: (1) The contents of Fe, Mn, Zn, Ca, and Na were highest in roots, so was K in stems, B and Mg in leaves and P in flower discs, while no significant difference was detected in the content of Cu among these organs; (2) The cumulants of Ca, Mg, P, Cu, B and Zn were highest in flower discs, so were Na, Fe and Mn in roots and K in stems; (3) In sunflower plants, the proportion of mineral element cumulant for K : Ca : Mg : P : Na was 16.71 : 5.23 : 3.86 : 1.23 : 1.00, and for Zn : Fe : B : Mn: Cu was 56.28 : 27.75 : 1.93 : 1.17 : 1.00, respectively; (4) The effect of salinity stress on absorption of mineral elements differed according to the kind of organ and element, root was the most sensitive to soil salt content, followed by stem and leaf, and the effect on flower disc seemed complex.

  11. Effects of untreated and treated oilfield-produced water on seed germination, seedling development, and biomass production of sunflower (Helianthus annuus L.).

    da Costa Marques, Mônica Regina; de Souza, Paulo Sérgio Alves; Rigo, Michelle Machado; Cerqueira, Alexandre Andrade; de Paiva, Julieta L; Merçon, Fábio; Perez, Daniel Vidal

    2015-10-01

    This study aims to evaluate possible toxic effects of oil and other contaminants from oilfield-produced water from oil exploration and production, on seed germination, and seedling development of sunflower (Helianthus annuus L.). In comparison, as treated by electroflocculation, oilfield-produced water, with lower oil and organic matter content, was also used. Electroflocculation treatment of oilfield-produced water achieved significant removals of chemical oxygen demand (COD) (94 %), oil and grease (O&G) (96 %), color (97 %), and turbidity (99 %). Different O&G, COD, and salt levels of untreated and treated oilfield-produced water did not influence germination process and seedling biomass production. Normal seedlings percentage and vigor tended to decrease more intensely in O&G and COD levels, higher than 337.5 mg L(-1) and 1321 mg O2 L(-1), respectively, using untreated oilfield-produced water. These results indicate that this industrial effluent must be treated, in order to not affect adversely seedling development. This way, electroflocculation treatment appears as an interesting alternative to removing oil and soluble organic matter in excess from oilfield-produced water improving sunflower's seedling development and providing a friendly environmental destination for this wastewater, reducing its potential to harm water resources, soil, and biota.

  12. Comparison of MP AES and ICP-MS for analysis of principal and selected trace elements in nitric acid digests of sunflower (Helianthus annuus).

    Karlsson, Stefan; Sjöberg, Viktor; Ogar, Anna

    2015-04-01

    The use of nitrogen as plasma gas for microwave plasma atomic emission spectroscopy (MP AES) is an interesting development in analytical science since the running cost can be significantly reduced in comparison to the inductively coupled argon plasma. Here, we evaluate the performance of the Agilent 4100 MP AES instrument for the analysis of principal metals (Ca, K, Mg, and Na), lithogenic metals (Al, Fe, and Mn) and selected trace metals (As, Ba, Cd, Co, Cr, Cu, Mo, Ni, Pb, V, and Zn) in nitric acid plant digests. The digests were prepared by microwave-assisted dissolution of dry plant material from sunflower (Helianthus annuus) in concentrated nitric acid. Comparisons are made with analysis of the same solutions with ICP-MS (Agilent 7500cx) using the octopole reaction system (ORS) in the collision mode for As, Fe, and V. The limits of detection were usually in the low µg L(-1) range and all principal and lithogenic metals were successfully determined with the MP AES and provided almost identical results with the ICP-MS. The same applies for the selected trace metals except for As, Co and Mo where the concentrations were below the detection limit with the MP AES. For successful analysis we recommend that (i) only atom lines are used, (ii) ionization is minimized (e.g. addition of CsNO3) and (iii) the use of internal standards should be considered to resolve spectral interferences. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. A new method for in-situ monitoring of the underground development of Orobanche cumana in sunflower (Helianthus annuus) with a mini-rhizotron.

    Eizenberg, H; Shtienberg, D; Silberbush, M; Ephrath, J E

    2005-11-01

    To develop an in-situ, non-destructive method for observation and monitoring of the underground developmental stages of the root parasite Orobanche cumana. The parasitic weed Orobanche causes severe damage to vegetables and field crops. Most of the damage caused to the crops occurs during the underground, unobservable parasitism stage. Sunflower (Helianthus annuus 'Adi') plants were planted in soil that was artificially inoculated with O. cumana seeds. Clear Plexiglas mini-rhizotron plastic observation tubes were inserted into the soil. Seed germination, early stage of penetration, and formation of tubercles and spikes were observed non-destructively and were monitored throughout the growing season by mean of a mini-rhizotron camera. Use of this technology enabled the complete individual parasite life cycle from the very early development (including germination) to Orobanche shoot to be monitored. In addition, the effect of the systemic herbicide Cadre (imazapic) on the development of O. cumana was inspected and quantified. This novel methodology facilitates the in-situ study of major aspects of the host-parasite interaction and of parasite suppression, such as parasitism dynamics, parasite growth rate, and the effect of chemical treatments on the parasite.

  14. Effect of different levels of foliar application of potassium on hysun-33 and ausigold-4 sunflower (helianthus annuus l.) cultivars under salt stress

    Arshadullah, M.; Ali, A.; Hyder, I.; Mahmood, I.A.; Zaman, B.U.

    2014-01-01

    A hydroponic study was conducted to see the growth response of two cultivars of sunflower (Hysun-33 and Ausigold-4) to K+ nutrition under salt stress during the growing season 2011, at National Agriculture Research Centre, Islamabad, Pakistan. Nursery of Helianthus annuus was raised in sand and ten-day old seedlings per hole were transplanted in each pot having four holes per pot lid. Half strength Hoagland's nutrient solution was filled in each pot. After the establishment of seedlings, salt stress (6 dS/m) was developed artificially. The treatments were, control, 2 and 4 % K + as K/sub 2/SO/sub 4/ foliar applications. Salt present in the growing medium caused a significant (P<0.00l), reduction in fresh and dry weights of sunflower. Salt stress suppresses the K uptake from pot. Application of varying levels of K/sub 2/SO/sub 4/ improved the fresh and dry weights of sunflower under both control and saline conditions. However, the highest increase in fresh and dry weight of control and stressed plants was observed when 2% K was applied. Further increase in the level of K application did not improve fresh and dry weights of salt stress and unstressed plants. The growth medium salts reduced sunflower growth. (author)

  15. SOIL CHEMICAL PROPERTIES AND GROWTH OF SUNFLOWER (HELIANTHUS ANNUUS L. AS AFFECTED BY THE APPLICATION OF ORGANIC FERTILIZERS AND INOCULATION WITH ARBUSCULAR MYCORRHIZAL FUNGI

    Apolino José Nogueira da Silva

    2015-02-01

    Full Text Available The use of organic fertilizers and the inoculation of mycorrhizal fungi in the cultivation of oil crops is essential to reduce production costs and minimize negative impacts on natural resources. A field experiment was conducted in an Argissolo Amarelo (Ultisol with the aim of evaluating the effects of fertilizer application and inoculation of arbuscular mycorrhizal fungi on the growth attributes of sunflower (Helianthus annuus L. and on soil chemical properties. The experiment was conducted at the Federal University of Rio Grande do Norte, Brazil, using a randomized block design with three replicates in a 4 × 2 factorial arrangement consisting of four treatments in regard to application of organic fertilizer (liquid biofertilizer, cow urine, mineral fertilizer, and unfertilized control and two treatments in regard to arbuscular mycorrhizal fungi (with and without mycorrhizal fungi. The results showed that the physiological attributes of relative growth rate and leaf weight ratio were positively influenced by fertilization, compared to the control treatment, likely brought about by the supply of nutrients from the fertilizers applied. The growth and productivity attributes were positively affected by mycorrhization.

  16. Greenhouse gas emissions and plant characteristics from soil cultivated with sunflower (Helianthus annuus L.) and amended with organic or inorganic fertilizers.

    López-Valdez, F; Fernández-Luqueño, F; Luna-Suárez, S; Dendooven, L

    2011-12-15

    Agricultural application of wastewater sludge has become the most widespread method of disposal, but the environmental effects on soil, air, and crops must be considered. The effect of wastewater sludge or urea on sunflower's (Helianthus annuus L.) growth and yield, the soil properties, and the resulting CO(2) and N(2)O emissions are still unknown. The objectives of this study were to investigate: i) the effect on soil properties of organic or inorganic fertilizer added to agricultural soil cultivated with sunflower, ii) how urea or wastewater sludge increases CO(2) and N(2)O emissions from agricultural soil over short time periods, and iii) the effect on plant characteristics and yield of urea or wastewater sludge added to agricultural soil cultivated with sunflower. The sunflower was fertilized with wastewater sludge or urea or grown in unamended soil under greenhouse conditions while plant and soil characteristics, yield, and greenhouse gas emissions were monitored. Sludge and urea modified some soil characteristics at the onset of the experiment and during the first two months but not thereafter. Some plant characteristics were improved by sludge. Urea and sludge treatments increased the yield at similar rates, while sludge-amended soil significantly increased N(2)O emissions but not CO(2) emissions compared to the other amended or unamended soils. This implies that wastewater sludge increased the biomass and/or the yield; however, from a holistic point of view, using wastewater sludge as fertilizer should be viewed with concern. Copyright © 2011 Elsevier B.V. All rights reserved.

  17. Inoculating Helianthus annuus (sunflower) grown in zinc and cadmium contaminated soils with plant growth promoting bacteria--effects on phytoremediation strategies.

    Marques, Ana P G C; Moreira, Helena; Franco, Albina R; Rangel, António O S S; Castro, Paula M L

    2013-06-01

    Plant growth promoting bacteria (PGPR) may help reducing the toxicity of heavy metals to plants in polluted environments. In this work the effects of inoculating metal resistant and plant growth promoting bacterial strains on the growth of Helianthus annuus grown in Zn and Cd spiked soils were assessed. The PGPR strains Ralstonia eutropha (B1) and Chrysiobacterium humi (B2) reduced losses of weight in metal exposed plants and induced changes in metal bioaccumulation and bioconcentration - with strain B2 decreasing up to 67% Zn accumulation and by 20% Zn bioconcentration factor (BCF) in the shoots, up to 64% Zn uptake and 38% Zn BCF in the roots, and up to 27% Cd uptake and 27% Cd BCF in plant roots. The impact of inoculation on the bacterial communities in the rhizosphere of the plant was also assessed. Bacterial community diversity decreased with increasing levels of metal contamination in the soil, but in rhizosphere soil of plants inoculated with the PGPR strains, a higher bacterial diversity was kept throughout the experimental period. Inoculation of sunflower, particularly with C. humi (B2), appears to be an effective way of enhancing the short term stabilization potential of the plant in metal contaminated land, lowering losses in plant biomass and decreasing aboveground tissue contamination. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. Greenhouse gas emissions and plant characteristics from soil cultivated with sunflower (Helianthus annuus L.) and amended with organic or inorganic fertilizers

    López-Valdez, F.; Fernández-Luqueño, F.; Luna-Suárez, S.; Dendooven, L.

    2011-01-01

    Agricultural application of wastewater sludge has become the most widespread method of disposal, but the environmental effects on soil, air, and crops must be considered. The effect of wastewater sludge or urea on sunflower's (Helianthus annuus L.) growth and yield, the soil properties, and the resulting CO 2 and N 2 O emissions are still unknown. The objectives of this study were to investigate: i) the effect on soil properties of organic or inorganic fertilizer added to agricultural soil cultivated with sunflower, ii) how urea or wastewater sludge increases CO 2 and N 2 O emissions from agricultural soil over short time periods, and iii) the effect on plant characteristics and yield of urea or wastewater sludge added to agricultural soil cultivated with sunflower. The sunflower was fertilized with wastewater sludge or urea or grown in unamended soil under greenhouse conditions while plant and soil characteristics, yield, and greenhouse gas emissions were monitored. Sludge and urea modified some soil characteristics at the onset of the experiment and during the first two months but not thereafter. Some plant characteristics were improved by sludge. Urea and sludge treatments increased the yield at similar rates, while sludge-amended soil significantly increased N 2 O emissions but not CO 2 emissions compared to the other amended or unamended soils. This implies that wastewater sludge increased the biomass and/or the yield; however, from a holistic point of view, using wastewater sludge as fertilizer should be viewed with concern.

  19. Exploring Other Genomes: Bacteria.

    Flannery, Maura C.

    2001-01-01

    Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

  20. Pl(17) is a novel gene independent of known downy mildew resistance genes in the cultivated sunflower (Helianthus annuus L.).

    Qi, L L; Long, Y M; Jan, C C; Ma, G J; Gulya, T J

    2015-04-01

    Pl 17, a novel downy mildew resistance gene independent of known downy mildew resistance genes in sunflowers, was genetically mapped to linkage group 4 of the sunflower genome. Downy mildew (DM), caused by Plasmopara halstedii (Farl.). Berl. et de Toni, is one of the serious sunflower diseases in the world due to its high virulence and the variability of the pathogen. DM resistance in the USDA inbred line, HA 458, has been shown to be effective against all virulent races of P. halstedii currently identified in the USA. To determine the chromosomal location of this resistance, 186 F 2:3 families derived from a cross of HA 458 with HA 234 were phenotyped for their resistance to race 734 of P. halstedii. The segregation ratio of the population supported that the resistance was controlled by a single dominant gene, Pl 17. Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) primers were used to identify molecular markers linked to Pl 17. Bulked segregant analysis using 849 SSR markers located Pl 17 to linkage group (LG) 4, which is the first DM gene discovered in this linkage group. An F2 population of 186 individuals was screened with polymorphic SSR and SNP primers from LG4. Two flanking markers, SNP SFW04052 and SSR ORS963, delineated Pl 17 in an interval of 3.0 cM. The markers linked to Pl 17 were validated in a BC3 population. A search for the physical location of flanking markers in sunflower genome sequences revealed that the Pl 17 region had a recombination frequency of 0.59 Mb/cM, which was a fourfold higher recombination rate relative to the genomic average. This region can be considered amenable to molecular manipulation for further map-based cloning of Pl 17.

  1. Genomics With Cloud Computing

    Sukhamrit Kaur; Sandeep Kaur

    2015-01-01

    Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computin...

  2. Genome Maps, a new generation genome browser.

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

  3. A Comparison of the First Two Sequenced Chloroplast Genomes in Asteraceae: Lettuce and Sunflower

    Timme, Ruth E.; Kuehl, Jennifer V.; Boore, Jeffrey L.; Jansen, Robert K.

    2006-01-20

    Asteraceae is the second largest family of plants, with over 20,000 species. For the past few decades, numerous phylogenetic studies have contributed to our understanding of the evolutionary relationships within this family, including comparisons of the fast evolving chloroplast gene, ndhF, rbcL, as well as non-coding DNA from the trnL intron plus the trnLtrnF intergenic spacer, matK, and, with lesser resolution, psbA-trnH. This culminated in a study by Panero and Funk in 2002 that used over 13,000 bp per taxon for the largest taxonomic revision of Asteraceae in over a hundred years. Still, some uncertainties remain, and it would be very useful to have more information on the relative rates of sequence evolution among various genes and on genome structure as a potential set of phylogenetic characters to help guide future phylogenetic structures. By way of contributing to this, we report the first two complete chloroplast genome sequences from members of the Asteraceae, those of Helianthus annuus and Lactuca sativa. These plants belong to two distantly related subfamilies, Asteroideae and Cichorioideae, respectively. In addition to these, there is only one other published chloroplast genome sequence for any plant within the larger group called Eusterids II, that of Panax ginseng (Araliaceae, 156,318 bps, AY582139). Early chloroplast genome mapping studies demonstrated that H. annuus and L. sativa share a 22 kb inversion relative to members of the subfamily Barnadesioideae. By comparison to outgroups, this inversion was shown to be derived, indicating that the Asteroideae and Cichorioideae are more closely related than either is to the Barnadesioideae. Later sequencing study found that taxa that share this 22 kb inversion also contain within this region a second, smaller, 3.3 kb inversion. These sequences also enable an analysis of patterns of shared repeats in the genomes at fine level and of RNA editing by comparison to available EST sequences. In addition, since

  4. JGI Fungal Genomics Program

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  5. Genomic Encyclopedia of Fungi

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  6. Genomics With Cloud Computing

    Sukhamrit Kaur

    2015-04-01

    Full Text Available Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computing to genomics are like easy access and sharing of data security of data less cost to pay for resources but still there are some demerits like large time needed to transfer data less network bandwidth.

  7. Genetics and mapping of the R₁₁ gene conferring resistance to recently emerged rust races, tightly linked to male fertility restoration, in sunflower (Helianthus annuus L.).

    Qi, L L; Seiler, G J; Vick, B A; Gulya, T J

    2012-09-01

    Sunflower oil is one of the major sources of edible oil. As the second largest hybrid crop in the world, hybrid sunflowers are developed by using the PET1 cytoplasmic male sterility system that contributes to a 20 % yield advantage over the open-pollinated varieties. However, sunflower production in North America has recently been threatened by the evolution of new virulent pathotypes of sunflower rust caused by the fungus Puccinia helianthi Schwein. Rf ANN-1742, an 'HA 89' backcross restorer line derived from wild annual sunflower (Helianthus annuus L.), was identified as resistant to the newly emerged rust races. The aim of this study was to elucidate the inheritance of rust resistance and male fertility restoration and identify the chromosome location of the underlying genes in Rf ANN-1742. Chi-squared analysis of the segregation of rust response and male fertility in F(2) and F(3) populations revealed that both traits are controlled by single dominant genes, and that the rust resistance gene is closely linked to the restorer gene in the coupling phase. The two genes were designated as R ( 11 ) and Rf5, respectively. A set of 723 mapped SSR markers of sunflower was used to screen the polymorphism between HA 89 and the resistant plant. Bulked segregant analysis subsequently located R ( 11 ) on linkage group (LG) 13 of sunflower. Based on the SSR analyses of 192 F(2) individuals, R ( 11 ) and Rf5 both mapped to the lower end of LG13 at a genetic distance of 1.6 cM, and shared a common marker, ORS728, which was mapped 1.3 cM proximal to Rf5 and 0.3 cM distal to R ( 11 ) (Rf5/ORS728/R ( 11 )). Two additional SSRs were linked to Rf5 and R ( 11 ): ORS995 was 4.5 cM distal to Rf5 and ORS45 was 1.0 cM proximal to R ( 11 ). The advantage of such an introduced alien segment harboring two genes is its large phenotypic effect and simple inheritance, thereby facilitating their rapid deployment in sunflower breeding programs. Suppressed recombination was observed in LGs 2, 9

  8. Myco-phytoremediation of arsenic- and lead-contaminated soils by Helianthus annuus and wood rot fungi, Trichoderma sp. isolated from decayed wood.

    Govarthanan, M; Mythili, R; Selvankumar, T; Kamala-Kannan, S; Kim, H

    2018-04-30

    In the present study, Helianthus annuus grown in arsenic- (As) and lead- (Pb) contaminated soil were treated with plant-growth promoting fungi Trichoderma sp. MG isolated from decayed wood and assessed for their phytoremediation efficiency. The isolate MG exhibited a high tolerance to As (650mg/L) and Pb (500mg/L), and could remove > 70% of metals in aqueous solution with an initial concentration of 100mg/L each. In addition, the isolate MG was screened for plant-growth-promoting factors such as siderophores, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, indole acetic acid (IAA) synthesis, and phosphate solubilisation. Phytoremediation studies indicated that treatment of H. annuus with the isolate MG had the maximum metal-accumulation in shoots (As; 67%, Pb; 59%). Furthermore, a significant increase in the soil extracellular enzyme-activities was observed in myco-phytoremediated soils. The activities of phosphatase (35 U/g dry soil), dehydrogenase (41mg TPF/g soil), cellulase (37.2mg glucose/g/2h), urease (55.4mgN/g soil/2h), amylase (49.3mg glucose/g/2h) and invertase (45.3mg glucose/g/2h) significantly increased by 12%, 14%, 12%, 22%, 19% and 14% in As contaminated soil, respectively. Similarly, the activities of phosphatase (31.4U/g dry soil), dehydrogenase (39.3mg TPF/g soil), cellulase (37.1mg glucose/g/2h), urease (49.8mgN/g soil/2h), amylase (46.3mg glucose/g/2h), and invertase (42.1mg glucose/g/2h) significantly increased by 11%, 15%, 11%, 18%, 20% and 14% in Pb contaminated soil, respectively. Obtained results indicate that the isolate MG could be a potential strain for myco-phytoremediation of As and Pb contaminated soil. Copyright © 2018 Elsevier Inc. All rights reserved.

  9. Greenhouse gas emissions and plant characteristics from soil cultivated with sunflower (Helianthus annuus L.) and amended with organic or inorganic fertilizers

    Lopez-Valdez, F., E-mail: flopez2072@yahoo.com [Laboratory of Agricultural Biotechnology, CIBA, IPN, Tepetitla de Lardizabal, C.P. 90700, Tlaxcala (Mexico); Laboratory of Soil Ecology, GIB, Department of Biotechnology and Bioengineering, Cinvestav-Zacatenco, C.P. 07360, D.F. (Mexico); Fernandez-Luqueno, F. [Natural and Energetic Resources, Cinvestav-Saltillo, C.P. 25900, Coahuila (Mexico); Laboratory of Soil Ecology, GIB, Department of Biotechnology and Bioengineering, Cinvestav-Zacatenco, C.P. 07360, D.F. (Mexico); Luna-Suarez, S. [Laboratory of Agricultural Biotechnology, CIBA, IPN, Tepetitla de Lardizabal, C.P. 90700, Tlaxcala (Mexico); Dendooven, L. [Laboratory of Soil Ecology, GIB, Department of Biotechnology and Bioengineering, Cinvestav-Zacatenco, C.P. 07360, D.F. (Mexico)

    2011-12-15

    Agricultural application of wastewater sludge has become the most widespread method of disposal, but the environmental effects on soil, air, and crops must be considered. The effect of wastewater sludge or urea on sunflower's (Helianthus annuus L.) growth and yield, the soil properties, and the resulting CO{sub 2} and N{sub 2}O emissions are still unknown. The objectives of this study were to investigate: i) the effect on soil properties of organic or inorganic fertilizer added to agricultural soil cultivated with sunflower, ii) how urea or wastewater sludge increases CO{sub 2} and N{sub 2}O emissions from agricultural soil over short time periods, and iii) the effect on plant characteristics and yield of urea or wastewater sludge added to agricultural soil cultivated with sunflower. The sunflower was fertilized with wastewater sludge or urea or grown in unamended soil under greenhouse conditions while plant and soil characteristics, yield, and greenhouse gas emissions were monitored. Sludge and urea modified some soil characteristics at the onset of the experiment and during the first two months but not thereafter. Some plant characteristics were improved by sludge. Urea and sludge treatments increased the yield at similar rates, while sludge-amended soil significantly increased N{sub 2}O emissions but not CO{sub 2} emissions compared to the other amended or unamended soils. This implies that wastewater sludge increased the biomass and/or the yield; however, from a holistic point of view, using wastewater sludge as fertilizer should be viewed with concern.

  10. Agronomic performance and chemical response of sunflower ( Helianthus annuus L.) to some organic nitrogen sources and conventional nitrogen fertilizers under sandy soil conditions

    Helmy, A. M.; Fawzy Ramadan, M. F.

    2009-07-01

    Sunflower ( Helianthus annuus L.) is an option for oilseed production, particularly in dry land areas due to good root system development. In this study, two field experiments were performed in the El-Khattara region (Sharkia Governorate, Egypt) during the 2005 season. The objective of this research was to determine the effect of organic nitrogen (ON) sources and their combinations as well as to compare the effect of ON and ammonium sulfate (AS) as a conventional fertilizer added individually or in combination on growth, yield components, oil percentage and the uptake of some macro nutrients by sunflowers grown on sandy soil.The treatments of chicken manure (CM) and a mixture of farmyard manure (FYM) with CM were superior to the other treatments and gave the highest yield, dry matter yield, NPK uptake by plants at all growth stages along with seed yield at the mature stage. The effect of the different ON on crop yield and its components may follow the order; CM> palma residues (PR)> FYM. This was more emphasized when the materials were mixed with AS at a ratio of 3:1 and 1:1. The uptake of nitrogen (N), phosphorus (P) and potassium (K) by plants was affected by the addition of different N sources and treatments. The highest nutrient content and uptake by straw were obtained when treated with CM followed by PR at all growth stages, while it was PR followed by CM for seeds. Oil recovery was shown to respond to the N supply and the changes in individual fatty acids were not statistically different. However, it seems that the application of organic fertilizers resulted in an increase in total unsaturated fatty acids compared to the control. (Author) 58 refs.

  11. Comparisons of Photosynthetic Responses of Xanthium strumarium and Helianthus annuus to Chronic and Acute Water Stress in Sun and Shade 1

    Ben, Gui-Ying; Osmond, C. Barry; Sharkey, Thomas D.

    1987-01-01

    We have examined the effects of mild, chronic water stress and acute water stress on two water stress sensitive plants, Xanthium strumarium and Helianthus annuus. Using a combination of the leaf disc O2 electrode to measure the light responses of photosynthesis and 77 K fluorescence to monitor damage to the primary photochemistry, we have found the following: (a) The CO2 saturated rate of photosynthesis at high light is the most water stress sensitive parameter measured. (b) The apparent quantum yield (moles O2 per mole photons) was slightly, if at all, affected by mild water stress (>−1.5 megapascals). (c) Severe water stress (<−1.5 megapascals) reduced the quantum yield of photosynthesis regardless of whether the stress was applied in sun or shade. The light independent reduction of quantum yield was not associated with a reduction in 77 K fluorescence (Fv/Fm) indicating that the quantum yield reduction was not the result of damage to primary photochemistry. (d) The diel fluctuation in 77 K fluorescence seen in sun-exposed control leaves was greatly exaggerated in water stressed leaves because of enhanced decline in 77 K fluorescence in the morning. The rate of recovery was similar in both control and water stressed leaves. Shaded leaves showed no change in 77 K fluorescence regardless of whether water stress was imposed or not. (e) The water stress sensitive plants used in these experiments did not recover from acute water stress severe enough to reduce the quantum yield or chronic water stress which lasted long enough that light dependent damage to primary photochemistry occurred. PMID:16665465

  12. Ridge sowing of sunflower (Helianthus annuus L.) in a minimum till system improves the productivity, oil quality, and profitability on a sandy loam soil under an arid climate.

    Sher, Ahmad; Suleman, Muhammad; Qayyum, Abdul; Sattar, Abdul; Wasaya, Allah; Ijaz, Muhammad; Nawaz, Ahmad

    2018-04-01

    Sunflower (Helianthus annuus L.) is a major oilseed crop grown for its edible oil across the globe including Pakistan. In Pakistan, the production of edible oil is less than the required quantity; the situation is being worsened with the increasing population. Thus, there is dire need to grow those sunflower genotypes which perform better under a given set of agronomic practices. In this 2-year study, we compared four sunflower genotypes, viz., Armoni, Kundi, Sinji, and S-278 for their yield potential, oil contents, fatty acid composition, and profitability under three sowing methods, viz., bed sowing, line sowing, and ridge sowing and two tillage system, viz., plow till and minimum till. Among the sunflower genotypes, the genotype Armoni produced the highest plant height, number of leaves, head diameter, 1000-achene weight, and achene yield; the oil contents and oleic acid were the highest in genotype Sinji. Among the sowing methods, the highest number of leaves per plant, head diameter, number of achenes per head, achene yield, and oil contents were recorded in ridge sowing. Among the tillage systems, the highest head diameter 16. 2 cm, 1000-achene weight (57.2 g), achene yield (1.8 t ha -1 ), oil contents (35.2%), and oleic acid (15.2%) were recorded in minimum till sunflower. The highest net benefits and benefit to cost ratio were recorded in minimum till ridge sown Armoni genotype. In conclusion, the genotype Armoni should be grown on ridges to achieve the highest achene yield, oil contents, and net profitability.

  13. Osmotic and Salt Stresses Modulate Spontaneous and Glutamate-Induced Action Potentials and Distinguish between Growth and Circumnutation in Helianthus annuus Seedlings

    Maria Stolarz

    2017-10-01

    Full Text Available Action potentials (APs, i.e., long-distance electrical signals, and circumnutations (CN, i.e., endogenous plant organ movements, are shaped by ion fluxes and content in excitable and motor tissues. The appearance of APs and CN as well as growth parameters in seedlings and 3-week old plants of Helianthus annuus treated with osmotic and salt stress (0–500 mOsm were studied. Time-lapse photography and extracellular measurements of electrical potential changes were performed. The hypocotyl length was strongly reduced by the osmotic and salt stress. CN intensity declined due to the osmotic but not salt stress. The period of CN in mild salt stress was similar to the control (~164 min and increased to more than 200 min in osmotic stress. In sunflower seedlings growing in a hydroponic medium, spontaneous APs (SAPs propagating basipetally and acropetally with a velocity of 12–20 cm min−1 were observed. The number of SAPs increased 2–3 times (7–10 SAPs 24 h−1plant−1 in the mild salt stress (160 mOsm NaCl and KCl, compared to the control and strong salt stress (3–4 SAPs 24 h−1 plant−1 in the control and 300 mOsm KCl and NaCl. Glutamate-induced series of APs were inhibited in the strong salt stress-treated seedlings but not at the mild salt stress and osmotic stress. Additionally, in 3-week old plants, the injection of the hypo- or hyperosmotic solution at the base of the sunflower stem evoked series of APs (3–24 APs transmitted along the stem. It has been shown that osmotic and salt stresses modulate differently hypocotyl growth and CN and have an effect on spontaneous and evoked APs in sunflower seedlings. We suggested that potassium, sodium, and chloride ions at stress concentrations in the nutrient medium modulate sunflower excitability and CN.

  14. Prebiotic potential of Jerusalem artichoke (Helianthus tuberosus L.) in Wistar rats: effects of levels of supplementation on hindgut fermentation, intestinal morphology, blood metabolites and immune response.

    Samal, Lipismita; Chaturvedi, Vishwa Bandhu; Saikumar, Guttula; Somvanshi, Ramesh; Pattanaik, Ashok Kumar

    2015-06-01

    Many studies have been conducted using purified prebiotics such as inulin or fructooligosaccharides (FOS) as nutraceuticals, but there is very little information available on the prebiotic potential of raw products rich in inulin and FOS, such as Jerusalem artichoke (JA; Helianthus tuberosus L.). The present experiment aimed to evaluate the prebiotic effects of JA tubers in rats. Seventy-two Wistar weanling rats divided into four groups were fed for 12 weeks on a basal diet fortified with pulverized JA tubers at 0 (control), 20, 40 and 60 g kg(-1) levels. Enhanced cell-mediated immunity in terms of skin indurations (P = 0.082) and CD4+ T-lymphocyte population (P = 0.002) was observed in the JA-supplemented groups compared with the control group. Blood haemoglobin (P = 0.017), glucose (P = 0.001), urea (P = 0.004) and calcium (P = 0.048) varied favourably upon inclusion of JA. An increasing trend (P = 0.059) in the length of large intestine was apparent in the JA-fed groups. The tissue mass of caecum (P = 0.069) and colon (P = 0.003) was increased in the JA-supplemented groups, accompanied by higher (P = 0.007) caecal crypt depth. The pH and ammonia concentrations of intestinal digesta decreased and those of lactate and total volatile fatty acids increased in the JA-fed groups. The results suggest that JA had beneficial effects on immunity, blood metabolites, intestinal morphometry and hindgut fermentation of rats. © 2014 Society of Chemical Industry.

  15. Physiological and biochemical responses of sunflower (Helianthus annuus L.) exposed to nano-CeO2 and excess boron: Modulation of boron phytotoxicity.

    Tassi, E; Giorgetti, L; Morelli, E; Peralta-Videa, J R; Gardea-Torresdey, J L; Barbafieri, M

    2017-01-01

    Little is known about the interaction of nanoparticles (NPs) with soil constituents and their effects in plants. Boron (B), an essential micronutrient that reduces crop production at both deficiency and excess, has not been investigated with respect to its interaction with cerium oxide NPs (nano-CeO 2 ). Considering conflicting results on the nano-CeO 2 toxicity and protective role as antioxidant, their possible modulation on B toxicity in sunflower (Helianthus annuus L.) was investigated. Sunflower was cultivated for 30 days in garden pots containing original or B-spiked soil amended with nano-CeO 2 at 0-800 mg kg -1 . At harvest, Ce and B concentrations in tissues, biomass, and activities of stress enzymes in leaves were determined. Results showed that in the original soil, Ce accumulated mainly in roots, with little translocation to stems and leaves, while reduced root Ce was observed in plants from B-spiked soil. In the original soil, higher levels of nano-CeO 2 reduced plant B concentration. Although morphological effects were not visible, changes in biomass and oxidative stress response were observed. Sunflower leaves from B-spiked soil showed visible symptoms of B toxicity, such as necrosis and chlorosis in old leaves, as well as an increase of superoxide dismutase (SOD) activity. However, at high nano-CeO 2 level, SOD activity decreased reaching values similar to that of the control. This study has shown that nano-CeO 2 reduced both the B nutritional status of sunflower in original soil and the B phytotoxicity in B-spiked soil. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  16. Study of qualitative and quantitative yield and some agronomic characteristics of sunflower (Helianthus annus L. in response of seed inoculation with PGPR in various levels of nitrogen fertilizer

    H. Nazarly

    2016-05-01

    Full Text Available In order to study the qualitative and quantitative yield and some agronomic characteristics of sunflower (Helianthus annus L. in response to seed inoculation with PGPR under various levels of nitrogen fertilizer, a factorial experiment was conducted based on a randomized complete block design with three replications in field experimental University of Mohaghegh Ardabili during growing season of 2009-2010. Factors were nitrogen fertilizer in three levels (0, 80 and 160 kg N ha-1 as urea and seed inoculation with plant growth promoting rhizobacteria in four levels containing, without inoculation (as control, seed inoculation with Azotobacter chroococcum strain 5, Azospirillum lipoferum strain OF, Psedomunas strain 186. Results indicated that nitrogen levels and seed inoculation with Plant Growth Promoting Rhizobacteria (PGPR had significant effects on all of characteristics studied (except grain 1000 weight and stem diameter. Grain yield, plant height, head diameter, seed number per head, , yield and oil percentage, yield and protein percentage increased with increasing of nitrogen fertilizer and application of seed inoculation with PGPR. Response of grain yield wasn't the same for various levels of nitrogen fertilizer and seed inoculation with PGPR. The highest grain yield belonged to application of 160 kg N ha-1 and seed inoculation with Azotobacter. Means comparison showed that treatment compounds N160 × without inoculation with PGPR and N80 × seed inoculation with PGPR Azotobacter had similar grain yields. Thus, it can be suggested that in order to increasing of grain yield seed should be inoculated with Azotobacter bacteria × 80 kg N/ha in conditions of Ardabil region.

  17. Candidate gene association mapping of Sclerotinia stalk rot resistance in sunflower (Helianthus annuus L.) uncovers the importance of COI1 homologs.

    Talukder, Zahirul I; Hulke, Brent S; Qi, Lili; Scheffler, Brian E; Pegadaraju, Venkatramana; McPhee, Kevin; Gulya, Thomas J

    2014-01-01

    Functional markers for Sclerotinia basal stalk rot resistance in sunflower were obtained using gene-level information from the model species Arabidopsis thaliana. Sclerotinia stalk rot, caused by Sclerotinia sclerotiorum, is one of the most destructive diseases of sunflower (Helianthus annuus L.) worldwide. Markers for genes controlling resistance to S. sclerotiorum will enable efficient marker-assisted selection (MAS). We sequenced eight candidate genes homologous to Arabidopsis thaliana defense genes known to be associated with Sclerotinia disease resistance in a sunflower association mapping population evaluated for Sclerotinia stalk rot resistance. The total candidate gene sequence regions covered a concatenated length of 3,791 bp per individual. A total of 187 polymorphic sites were detected for all candidate gene sequences, 149 of which were single nucleotide polymorphisms (SNPs) and 38 were insertions/deletions. Eight SNPs in the coding regions led to changes in amino acid codons. Linkage disequilibrium decay throughout the candidate gene regions declined on average to an r (2) = 0.2 for genetic intervals of 120 bp, but extended up to 350 bp with r (2) = 0.1. A general linear model with modification to account for population structure was found the best fitting model for this population and was used for association mapping. Both HaCOI1-1 and HaCOI1-2 were found to be strongly associated with Sclerotinia stalk rot resistance and explained 7.4 % of phenotypic variation in this population. These SNP markers associated with Sclerotinia stalk rot resistance can potentially be applied to the selection of favorable genotypes, which will significantly improve the efficiency of MAS during the development of stalk rot resistant cultivars.

  18. A GRAS-like gene of sunflower (Helianthus annuus L.) alters the gibberellin content and axillary meristem outgrowth in transgenic Arabidopsis plants.

    Fambrini, M; Mariotti, L; Parlanti, S; Salvini, M; Pugliesi, C

    2015-11-01

    The GRAS proteins belong to a plant transcriptional regulator family that function in the regulation of plant growth and development. Despite their important roles, in sunflower only one GRAS gene (HaDella1) with the DELLA domain has been reported. Here, we provide a functional characterisation of a GRAS-like gene from Helianthus annuus (Ha-GRASL) lacking the DELLA motif. The Ha-GRASL gene contains an intronless open reading frame of 1,743 bp encoding 580 amino acids. Conserved motifs in the GRAS domain are detected, including VHIID, PFYRE, SAW and two LHR motifs. Within the VHII motif, the P-H-N-D-Q-L residues are entirely maintained. Phylogenetic analysis reveals that Ha-GRASL belongs to the SCARECROW LIKE4/7 (SCL4/7) subfamily of the GRAS consensus tree. Accumulation of Ha-GRASL mRNA at the adaxial boundaries from P6/P7 leaf primordia suggests a role of Ha-GRASL in the initiation of median and basal axillary meristems (AMs) of sunflower. When Ha-GRASL is over-expressed in Arabidopsis wild-type plants, the number of lateral bolts increases differently from untransformed plants. However, Ha-GRASL slightly affects the lateral suppressor (las-4-) mutation. Therefore, we hypothesise that Ha-GRASL and LAS are not functionally equivalent. The over-expression of Ha-GRASL reduces metabolic flow of gibberellins (GAs) in Arabidopsis and this modification could be relevant in AM development. Phylogenetic analysis includes LAS and SCL4/7 in the same major clade, suggesting a more recent separation of these genes with respect to other GRAS members. We propose that some features of their ancestor, as well as AM initiation and outgrowth, are partially retained in both LAS and SCL4/7. © 2015 German Botanical Society and The Royal Botanical Society of the Netherlands.

  19. The analysis on of the effect of urea, iron sulfate and vermicompost fertilizers on the growth characteristics and yield of sunflower (Helianthus annuus L. The city Darreh Gaz

    mahdiyeh zomorrodi

    2015-12-01

    Full Text Available To study the effect of vermicompost and urea and iron sulfate fertilizers on the growth characteristics and yield of sunflower seed (Helianthus annuus L. an pediment was conducted in Darreh Gaz located in Khorasan Razavi province in 2012. Factorial experiment in a randomized complete block design with three factors and three repetition. In this experiment three levels of urea (50; 150 and 250 kg per hectare as the first factor and two level of vermicompost (7 tons per hectare consumption and non-consumption as the second factor and two iron sulfate (80 kilogram per hectare consumption and non- consumption were considered as the third factor. The results showed that the effect of urea × vermicompost treatment combination on stem height, head diameter, stem dry weight and yield was significantly at one percent probability level. The treatment combination of 250 kg. ha-1 × iron sulfate× vermicompost increased plant height, head diameter, petiole dry weight. Vermicompost × iron sulfate treatment combination on the dry weight’s leaf, petiole, stem and head were the highest significant (p≤0.01. The application of vermicompost × iron sulfate treatment combination resulted in the highest rate of stem diameter, leaf dry weight and stem the highest yield belonged to 250 kg.ha-1 × vermicompost. Iron sulfate use different amounts of urea fertilizer redact yield. The lowest yield of 250 kg.ha-1× iron sulfate was related to treatment combination. So it seems that the combined application of organic vermicompost fertilizer and urea and iron sulfate fertilizers on the growth and yield of sunflower Darreh Gaz can be effective in improving properties.

  20. Irrigation of Castor Bean (Ricinus communis L. and Sunflower (Helianthus annus L. Plant Species with Municipal Wastewater Effluent: Impacts on Soil Properties and Seed Yield

    Vasileios A. Tzanakakis

    2011-11-01

    Full Text Available The effects of plant species (castor bean (Ricinus communis L. versus sunflower (Helianthus annus L. and irrigation regime (freshwater versus secondary treated municipal wastewater on soil properties and on seed and biodiesel yield were studied in a three year pot trial. Plant species were irrigated at rates according to their water requirements with either freshwater or wastewater effluent. Pots irrigated with freshwater received commercial fertilizer, containing N, P, and K, applied at the beginning of each irrigation period. The results obtained in this study showed that irrigation with effluent did not result in significant changes in soil pH, soil organic matter (SOM, total kjeldahl nitrogen (TKN, and dehydrogenase activity, whereas soil available P was found to increase in the upper soil layer. Soil salinity varied slightly throughout the experiment in effluent irrigated pots but no change was detected at the end of the experiment compared to the initial value, suggesting sufficient salt leaching. Pots irrigated with effluent had higher soil salinity, P, and dehydrogenase activity but lower SOM and TKN than freshwater irrigated pots. Sunflower showed greater SOM and TKN values than castor bean suggesting differences between plant species in the microorganisms carrying out C and N mineralization in the soil. Plant species irrigated with freshwater achieved higher seed yield compared to those irrigated with effluent probably reflecting the lower level of soil salinity in freshwater irrigated pots. Castor bean achieved greater seed yield than sunflower. Biodiesel production followed the pattern of seed yield. The findings of this study suggest that wastewater effluent can constitute an important source of irrigation water and nutrients for bioenergy crop cultivations with minor adverse impacts on soil properties and seed yield. Plant species play an important role with regard to the changes in soil properties and to the related factors of

  1. Comparative Genome Analysis and Genome Evolution

    Snel, Berend

    2002-01-01

    This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies.

  2. Genomic Data Commons launches

    The Genomic Data Commons (GDC), a unified data system that promotes sharing of genomic and clinical data between researchers, launched today with a visit from Vice President Joe Biden to the operations center at the University of Chicago.

  3. Rat Genome Database (RGD)

    U.S. Department of Health & Human Services — The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research to collect, consolidate,...

  4. Visualization for genomics: the Microbial Genome Viewer.

    Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

    2004-07-22

    A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

  5. Genomic prediction using subsampling

    Xavier, Alencar; Xu, Shizhong; Muir, William; Rainey, Katy Martin

    2017-01-01

    Background Genome-wide assisted selection is a critical tool for the?genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each rou...

  6. Ebolavirus comparative genomics

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms...

  7. Identification and characterization of contrasting sunflower genotypes to early leaf senescence process combining molecular and physiological studies (Helianthus annuus L.).

    López Gialdi, A I; Moschen, S; Villán, C S; López Fernández, M P; Maldonado, S; Paniego, N; Heinz, R A; Fernandez, P

    2016-09-01

    Leaf senescence is a complex mechanism ruled by multiple genetic and environmental variables that affect crop yields. It is the last stage in leaf development, is characterized by an active decline in photosynthetic rate, nutrients recycling and cell death. The aim of this work was to identify contrasting sunflower inbred lines differing in leaf senescence and to deepen the study of this process in sunflower. Ten sunflower genotypes, previously selected by physiological analysis from 150 inbred genotypes, were evaluated under field conditions through physiological, cytological and molecular analysis. The physiological measurement allowed the identification of two contrasting senescence inbred lines, R453 and B481-6, with an increase in yield in the senescence delayed genotype. These findings were confirmed by cytological and molecular analysis using TUNEL, genomic DNA gel electrophoresis, flow sorting and gene expression analysis by qPCR. These results allowed the selection of the two most promising contrasting genotypes, which enables future studies and the identification of new biomarkers associated to early senescence in sunflower. In addition, they allowed the tuning of cytological techniques for a non-model species and its integration with molecular variables. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  8. The Sequenced Angiosperm Genomes and Genome Databases.

    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.

  9. Molecular cloning, phylogenetic analysis, and expression patterns of LATERAL SUPPRESSOR-LIKE and REGULATOR OF AXILLARY MERISTEM FORMATION-LIKE genes in sunflower (Helianthus annuus L.).

    Fambrini, Marco; Salvini, Mariangela; Pugliesi, Claudio

    2017-03-01

    The wild sunflower (Helianthus annuus) plants develop a highly branched form with numerous small flowering heads. The origin of a no branched sunflower, producing a single large head, has been a key event in the domestication process of this species. The interaction between hormonal factors and several genes organizes the initiation and outgrowth of axillary meristems (AMs). From sunflower, we have isolated two genes putatively involved in this process, LATERAL SUPPRESSOR (LS)-LIKE (Ha-LSL) and REGULATOR OF AXILLARY MERISTEM FORMATION (ROX)-LIKE (Ha-ROXL), encoding for a GRAS and a bHLH transcription factor (TF), respectively. Typical amino acid residues and phylogenetic analyses suggest that Ha-LSL and Ha-ROXL are the orthologs of the branching regulator LS and ROX/LAX1, involved in the growth habit of both dicot and monocot species. qRT-PCR analyses revealed a high accumulation of Ha-LSL transcripts in roots, vegetative shoots, and inflorescence shoots. By contrast, in internodal stems and young leaves, a lower amount of Ha-LSL transcripts was observed. A comparison of transcription patterns between Ha-LSL and Ha-ROXL revealed some analogies but also remarkable differences; in fact, the gene Ha-ROXL displayed a low expression level in all organs analyzed. In situ hybridization (ISH) analysis showed that Ha-ROXL transcription was strongly restricted to a small domain within the boundary zone separating the shoot apical meristem (SAM) and the leaf primordia and in restricted regions of the inflorescence meristem, beforehand the separation of floral bracts from disc flower primordia. These results suggested that Ha-ROXL may be involved to establish a cell niche for the initiation of AMs as well as flower primordia. The accumulation of Ha-LSL transcripts was not restricted to the boundary zones in vegetative and inflorescence shoots, but the mRNA activity was expanded in other cellular domains of primary shoot apical meristem as well as AMs. In addition, Ha

  10. Growth and N2-fixation of dhaincha (Sesbania aculata) and sunflower (Helianthus annuus) in an inter cropping system using natural abundances of 15N and 13C

    Kurdali, F.

    2010-06-01

    A field experiment on dhaincha (Sesbania aculata) and sunflower (Helianthus annuus) plants grown in mono cropping and inter cropping systems was conducted to evaluate seed yield , oil content, dry matter production (DM), land equivalent ratio (LER), N- yield, competition for soil N uptake and N 2 -fixation using 13 C and 15 N natural abundance techniques. Three different combinations of sesbania (ses) and sunflower (sun) were investigated in the inter cropping system (1ses:1sun; 1ses:2sun, and 2ses:1sun, row ratio). The results showed that: From productivity standpoint, the 1ses:1sun surpassed the other treatments in terms of N and DM yields and exhibited a similar distribution of total DM and N uptake in the sesbania and sunflower plant species. The 1ses:2sun was next in order in terms of DM and N uptake showing also a similar distribution of total N in both plant species. On the other hand, the 1ses:2sun gave the greatest seed and oil production and together with 1ses:1sun treatment were satisfactory in terms of LER for DM in both species having almost similar values. However, the former treatment was more appropriate than the latter because of its higher LER value for seed and oil yield of sunflower plants. Nevertheless, 2ses:1sun treatment seemed not to be an appropriate treatment due to the divergence of LER values in both species, where sunflower plants had a low value as compared to sesbania. From ecological standpoint, the best treatment was 1ses:2sun which showed the greatest N 2 -fixation. Sesbania plants fixed almost identical amounts of atmospheric N 2 in both the mono cropping and inter cropping systems although the density of these plants in the latter was only 1/3 that of the former system. Moreover, soil N-uptake in the 1ses:2sun was the lowest among other treatments. These results give an advantage to the 1ses:2sun treatment over other treatments in terms of soil N consumption and N 2 fixation to meet sesbania's N requirements. %Δ 13 C in the

  11. Bioinformatics decoding the genome

    CERN. Geneva; Deutsch, Sam; Michielin, Olivier; Thomas, Arthur; Descombes, Patrick

    2006-01-01

    Extracting the fundamental genomic sequence from the DNA From Genome to Sequence : Biology in the early 21st century has been radically transformed by the availability of the full genome sequences of an ever increasing number of life forms, from bacteria to major crop plants and to humans. The lecture will concentrate on the computational challenges associated with the production, storage and analysis of genome sequence data, with an emphasis on mammalian genomes. The quality and usability of genome sequences is increasingly conditioned by the careful integration of strategies for data collection and computational analysis, from the construction of maps and libraries to the assembly of raw data into sequence contigs and chromosome-sized scaffolds. Once the sequence is assembled, a major challenge is the mapping of biologically relevant information onto this sequence: promoters, introns and exons of protein-encoding genes, regulatory elements, functional RNAs, pseudogenes, transposons, etc. The methodological ...

  12. Genomic research in Eucalyptus.

    Poke, Fiona S; Vaillancourt, René E; Potts, Brad M; Reid, James B

    2005-09-01

    Eucalyptus L'Hérit. is a genus comprised of more than 700 species that is of vital importance ecologically to Australia and to the forestry industry world-wide, being grown in plantations for the production of solid wood products as well as pulp for paper. With the sequencing of the genomes of Arabidopsis thaliana and Oryza sativa and the recent completion of the first tree genome sequence, Populus trichocarpa, attention has turned to the current status of genomic research in Eucalyptus. For several eucalypt species, large segregating families have been established, high-resolution genetic maps constructed and large EST databases generated. Collaborative efforts have been initiated for the integration of diverse genomic projects and will provide the framework for future research including exploiting the sequence of the entire eucalypt genome which is currently being sequenced. This review summarises the current position of genomic research in Eucalyptus and discusses the direction of future research.

  13. Genome packaging in viruses

    Sun, Siyang; Rao, Venigalla B.; Rossmann, Michael G.

    2010-01-01

    Genome packaging is a fundamental process in a viral life cycle. Many viruses assemble preformed capsids into which the genomic material is subsequently packaged. These viruses use a packaging motor protein that is driven by the hydrolysis of ATP to condense the nucleic acids into a confined space. How these motor proteins package viral genomes had been poorly understood until recently, when a few X-ray crystal structures and cryo-electron microscopy structures became available. Here we discu...

  14. Between Two Fern Genomes

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves. PMID:25324969

  15. Causes of genome instability

    Langie, Sabine A S; Koppen, Gudrun; Desaulniers, Daniel

    2015-01-01

    function, chromosome segregation, telomere length). The purpose of this review is to describe the crucial aspects of genome instability, to outline the ways in which environmental chemicals can affect this cancer hallmark and to identify candidate chemicals for further study. The overall aim is to make......Genome instability is a prerequisite for the development of cancer. It occurs when genome maintenance systems fail to safeguard the genome's integrity, whether as a consequence of inherited defects or induced via exposure to environmental agents (chemicals, biological agents and radiation). Thus...

  16. Fungal Genomics Program

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  17. MIPS plant genome information resources.

    Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

    2007-01-01

    The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

  18. Agronomic performance and chemical response of sunflower (Helianthus annuus L. to some organic nitrogen sources and conventional nitrogen fertilizers under sandy soil conditions

    Ramadan, Mohamed Fawzy

    2009-03-01

    Full Text Available Sunflower (Helianthus annuus L. is an option for oilseed production, particularly in dry land areas due to good root system development. In this study, two field experiments were performed in the El-Khattara region (Sharkia Governorate, Egypt during the 2005 season. The objective of this research was to determine the effect of organicnitrogen (ON sources and their combinations as well as to compare the effect of ON and ammonium sulfate (AS as a conventional fertilizer added individually or in combination on growth, yield components, oil percentage and the uptake of some macronutrients by sunflowers grown on sandy soil. The treatments of chicken manure (CM and a mixture of farmyard manure (FYM with CM were superior to the other treatments and gave the highest yield, dry matter yield, NPK uptake by plants at all growth stages along with seed yield at the mature stage. The effect of the different ON on crop yield and its components may follow the order; CM> palma residues (PR> FYM. This was more emphasized when the materials were mixed with AS at a ratio of 3:1 and 1:1. The uptake of nitrogen (N, phosphorus (P and potassium (K by plants was affected by the addition of different N sources and treatments. The highest nutrient content and uptake by straw were obtained when treated with CM followed by PR at all growth stages, while it was PR followed by CM for seeds. Oil recovery was shown to respond to the N supply and the changes in individual fatty acids were not statistically different. However, it seems that the application of organic fertilizers resulted in an increase in total unsaturated fatty acids compared to the control.El girasol (Helianthus annuus es una opción para la producción de semillas oleaginosas, en particular en terrenos arenosos debido al buen desarrollo de sus raíces. En este trabajo, dos estudios de campo fueron realizados en la región de El-Ishattara (Sharkia Governorate, Egypt durante la estación 2005. El efecto de

  19. Computational genomics of hyperthermophiles

    Werken, van de H.J.G.

    2008-01-01

    With the ever increasing number of completely sequenced prokaryotic genomes and the subsequent use of functional genomics tools, e.g. DNA microarray and proteomics, computational data analysis and the integration of microbial and molecular data is inevitable. This thesis describes the computational

  20. Safeguarding genome integrity

    Sørensen, Claus Storgaard; Syljuåsen, Randi G

    2012-01-01

    Mechanisms that preserve genome integrity are highly important during the normal life cycle of human cells. Loss of genome protective mechanisms can lead to the development of diseases such as cancer. Checkpoint kinases function in the cellular surveillance pathways that help cells to cope with D...

  1. Human genome I

    Anon.

    1989-01-01

    An international conference, Human Genome I, was held Oct. 2-4, 1989 in San Diego, Calif. Selected speakers discussed: Current Status of the Genome Project; Technique Innovations; Interesting regions; Applications; and Organization - Different Views of Current and Future Science and Procedures. Posters, consisting of 119 presentations, were displayed during the sessions. 119 were indexed for inclusion to the Energy Data Base

  2. Rumen microbial genomics

    Morrison, M.; Nelson, K.E.

    2005-01-01

    Improving microbial degradation of plant cell wall polysaccharides remains one of the highest priority goals for all livestock enterprises, including the cattle herds and draught animals of developing countries. The North American Consortium for Genomics of Fibrolytic Ruminal Bacteria was created to promote the sequencing and comparative analysis of rumen microbial genomes, offering the potential to fully assess the genetic potential in a functional and comparative fashion. It has been found that the Fibrobacter succinogenes genome encodes many more endoglucanases and cellodextrinases than previously isolated, and several new processive endoglucanases have been identified by genome and proteomic analysis of Ruminococcus albus, in addition to a variety of strategies for its adhesion to fibre. The ramifications of acquiring genome sequence data for rumen microorganisms are profound, including the potential to elucidate and overcome the biochemical, ecological or physiological processes that are rate limiting for ruminal fibre degradation. (author)

  3. Microbial Genomes Multiply

    Doolittle, Russell F.

    2002-01-01

    The publication of the first complete sequence of a bacterial genome in 1995 was a signal event, underscored by the fact that the article has been cited more than 2,100 times during the intervening seven years. It was a marvelous technical achievement, made possible by automatic DNA-sequencing machines. The feat is the more impressive in that complete genome sequencing has now been adopted in many different laboratories around the world. Four years ago in these columns I examined the situation after a dozen microbial genomes had been completed. Now, with upwards of 60 microbial genome sequences determined and twice that many in progress, it seems reasonable to assess just what is being learned. Are new concepts emerging about how cells work? Have there been practical benefits in the fields of medicine and agriculture? Is it feasible to determine the genomic sequence of every bacterial species on Earth? The answers to these questions maybe Yes, Perhaps, and No, respectively.

  4. Musa sebagai Model Genom

    RITA MEGIA

    2005-12-01

    Full Text Available During the meeting in Arlington, USA in 2001, the scientists grouped in PROMUSA agreed with the launching of the Global Musa Genomics Consortium. The Consortium aims to apply genomics technologies to the improvement of this important crop. These genome projects put banana as the third model species after Arabidopsis and rice that will be analyzed and sequenced. Comparing to Arabidopsis and rice, banana genome provides a unique and powerful insight into structural and in functional genomics that could not be found in those two species. This paper discussed these subjects-including the importance of banana as the fourth main food in the world, the evolution and biodiversity of this genetic resource and its parasite.

  5. The genome editing revolution

    Stella, Stefano; Montoya, Guillermo

    2016-01-01

    -Cas system has become the main tool for genome editing in many laboratories. Currently the targeted genome editing technology has been used in many fields and may be a possible approach for human gene therapy. Furthermore, it can also be used to modifying the genomes of model organisms for studying human......In the last 10 years, we have witnessed a blooming of targeted genome editing systems and applications. The area was revolutionized by the discovery and characterization of the transcription activator-like effector proteins, which are easier to engineer to target new DNA sequences than...... sequence). This ribonucleoprotein complex protects bacteria from invading DNAs, and it was adapted to be used in genome editing. The CRISPR ribonucleic acid (RNA) molecule guides to the specific DNA site the Cas9 nuclease to cleave the DNA target. Two years and more than 1000 publications later, the CRISPR...

  6. Phytozome Comparative Plant Genomics Portal

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  7. Response of Sunflower (Helianthus annuus L.) to N-application and Bio fertilization with Assessment of Fertilizer N Recovery by 15N Versus Subtraction Methods

    Abdel-Salam, A. A.; Zahra, W.R.; Soliman, S. M.; Galal, Y.G.M.; Moursy, A.A.; Hekal, M.A.

    2015-01-01

    A factorial field experiment was conducted on sunflower (Helianthus annuus L.) grown on a sand soil (98% sand) supplied the different combinations of 4 N rates of 0, 105, 140 and 175 kg N ha -1 i.e. N 0 , N 1 , N 2 , and N 3 respectively - as (NH 4 ) 2 SO 4 and 4 bio fertilization inoculation (B) of none, Azotobacter chroococcum, Azospirillum brasilense and Bacillus megaterium. i.e. B 0 ,B 1 ,B 2 , and B 3 respectively. Labeled ammonium sulphate with 2% 15 N atom excess was used for 15 N assessment. All plots were supplied with 21 Mg compost +24 kg P +80 kg K ha - '1. Non-treated plants gave 0.534 Mg seeds ha -1 while the treated ones - especially those of N or N + bio fertilizers - gave increases of up to 403% (N 2 B). Main effect response patterns were: N: N 3 >N 2 >N 1 , for B: B 1 ≥B 3 ≥B 2 . Seed oil content in the N 0 B 0 treatment was 222 gkg -1 increased reaching as high as 445 gkg -1 by N 2 B 3 ; with N main effect of N 2 >N 3 >N 1 and B main effect of B 2 >B 3 >B 1 . Seed oil yield was 113 kg ha -1 by N 0 B 0 increased to as high as 1105 kg ha -1 by N 2 B 1 with main effects of N 2 >N 3 >N 1 and B 3 ≥B 2 >B 1 .Uptake of N (in total plant parts of roots + stems + leaves + discs + seeds) increased by N application; averages for non-N were 18.1 kg ha -1 18.5,14.7,17.4 by N 0 B 0 , N 0 B 1 , N 0 B 2 , and N 0 B 3 respectively; increased considerably by up to 667% (N 3 B 3 ) upon N application. Plants recovered a portion of fertilizer N of 19.6 to 40.9% by N 1 B 1 and N 2 B 1 respectively as determined by 15 N technique, but 27.7 to 59.6% respectively as calculated by subtraction of non-N from N treatments. The subtraction estimation considerably exceeded the 15 N determined ones by + 39.5% to as high as + 194.6% indicating a non-real estimation of recovered fertilizer-N in crops. Thus, in studies using non-tracer techniques, estimation of uptake of fertilizer N could be erroneous. The reason in the current study could most certainly be a greater

  8. Genome-derived vaccines.

    De Groot, Anne S; Rappuoli, Rino

    2004-02-01

    Vaccine research entered a new era when the complete genome of a pathogenic bacterium was published in 1995. Since then, more than 97 bacterial pathogens have been sequenced and at least 110 additional projects are now in progress. Genome sequencing has also dramatically accelerated: high-throughput facilities can draft the sequence of an entire microbe (two to four megabases) in 1 to 2 days. Vaccine developers are using microarrays, immunoinformatics, proteomics and high-throughput immunology assays to reduce the truly unmanageable volume of information available in genome databases to a manageable size. Vaccines composed by novel antigens discovered from genome mining are already in clinical trials. Within 5 years we can expect to see a novel class of vaccines composed by genome-predicted, assembled and engineered T- and Bcell epitopes. This article addresses the convergence of three forces--microbial genome sequencing, computational immunology and new vaccine technologies--that are shifting genome mining for vaccines onto the forefront of immunology research.

  9. The Banana Genome Hub

    Droc, Gaëtan; Larivière, Delphine; Guignon, Valentin; Yahiaoui, Nabila; This, Dominique; Garsmeur, Olivier; Dereeper, Alexis; Hamelin, Chantal; Argout, Xavier; Dufayard, Jean-François; Lengelle, Juliette; Baurens, Franc-Christophe; Cenci, Alberto; Pitollat, Bertrand; D’Hont, Angélique; Ruiz, Manuel; Rouard, Mathieu; Bocs, Stéphanie

    2013-01-01

    Banana is one of the world’s favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. Database URL: http://banana-genome.cirad.fr/ PMID:23707967

  10. Genomic instability following irradiation

    Hacker-Klom, U.B.; Goehde, W.

    2001-01-01

    Ionising irradiation may induce genomic instability. The broad spectrum of stress reactions in eukaryontic cells to irradiation complicates the discovery of cellular targets and pathways inducing genomic instability. Irradiation may initiate genomic instability by deletion of genes controlling stability, by induction of genes stimulating instability and/or by activating endogeneous cellular viruses. Alternatively or additionally it is discussed that the initiation of genomic instability may be a consequence of radiation or other agents independently of DNA damage implying non nuclear targets, e.g. signal cascades. As a further mechanism possibly involved our own results may suggest radiation-induced changes in chromatin structure. Once initiated the process of genomic instability probably is perpetuated by endogeneous processes necessary for proliferation. Genomic instability may be a cause or a consequence of the neoplastic phenotype. As a conclusion from the data available up to now a new interpretation of low level radiation effects for radiation protection and in radiotherapy appears useful. The detection of the molecular mechanisms of genomic instability will be important in this context and may contribute to a better understanding of phenomenons occurring at low doses <10 cSv which are not well understood up to now. (orig.)

  11. Traditional medicine and genomics

    Kalpana Joshi

    2010-01-01

    Full Text Available ′Omics′ developments in the form of genomics, proteomics and metabolomics have increased the impetus of traditional medicine research. Studies exploring the genomic, proteomic and metabolomic basis of human constitutional types based on Ayurveda and other systems of oriental medicine are becoming popular. Such studies remain important to developing better understanding of human variations and individual differences. Countries like India, Korea, China and Japan are investing in research on evidence-based traditional medicines and scientific validation of fundamental principles. This review provides an account of studies addressing relationships between traditional medicine and genomics.

  12. Traditional medicine and genomics.

    Joshi, Kalpana; Ghodke, Yogita; Shintre, Pooja

    2010-01-01

    'Omics' developments in the form of genomics, proteomics and metabolomics have increased the impetus of traditional medicine research. Studies exploring the genomic, proteomic and metabolomic basis of human constitutional types based on Ayurveda and other systems of oriental medicine are becoming popular. Such studies remain important to developing better understanding of human variations and individual differences. Countries like India, Korea, China and Japan are investing in research on evidence-based traditional medicines and scientific validation of fundamental principles. This review provides an account of studies addressing relationships between traditional medicine and genomics.

  13. Bacillus subtilis genome diversity.

    Earl, Ashlee M; Losick, Richard; Kolter, Roberto

    2007-02-01

    Microarray-based comparative genomic hybridization (M-CGH) is a powerful method for rapidly identifying regions of genome diversity among closely related organisms. We used M-CGH to examine the genome diversity of 17 strains belonging to the nonpathogenic species Bacillus subtilis. Our M-CGH results indicate that there is considerable genetic heterogeneity among members of this species; nearly one-third of Bsu168-specific genes exhibited variability, as measured by the microarray hybridization intensities. The variable loci include those encoding proteins involved in antibiotic production, cell wall synthesis, sporulation, and germination. The diversity in these genes may reflect this organism's ability to survive in diverse natural settings.

  14. Genomic taxonomy of vibrios

    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

  15. Human Genome Project

    Block, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Cornwall, J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, W. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Fortson, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Joyce, G. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Kimble, H. J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Max, C. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Prince, T. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, P. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Woodin, W. H. [The MITRE Corporation, McLean, VA (US). JASON Program Office

    1998-01-04

    The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

  16. Human Genome Program

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  17. Genomic signal processing

    Shmulevich, Ilya

    2007-01-01

    Genomic signal processing (GSP) can be defined as the analysis, processing, and use of genomic signals to gain biological knowledge, and the translation of that knowledge into systems-based applications that can be used to diagnose and treat genetic diseases. Situated at the crossroads of engineering, biology, mathematics, statistics, and computer science, GSP requires the development of both nonlinear dynamical models that adequately represent genomic regulation, and diagnostic and therapeutic tools based on these models. This book facilitates these developments by providing rigorous mathema

  18. Genomics and fish adaptation

    Agostinho Antunes

    2015-12-01

    Full Text Available The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of varied fish species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

  19. Lophotrochozoan mitochondrial genomes

    Valles, Yvonne; Boore, Jeffrey L.

    2005-10-01

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

  20. Mouse Genome Informatics (MGI)

    U.S. Department of Health & Human Services — MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human...

  1. Genomic definition of species

    Crkvenjakov, R.; Drmanac, R.

    1991-07-01

    The subject of this paper is the definition of species based on the assumption that genome is the fundamental level for the origin and maintenance of biological diversity. For this view to be logically consistent it is necessary to assume the existence and operation of the new law which we call genome law. For this reason the genome law is included in the explanation of species phenomenon presented here even if its precise formulation and elaboration are left for the future. The intellectual underpinnings of this definition can be traced to Goldschmidt. We wish to explore some philosophical aspects of the definition of species in terms of the genome. The point of proposing the definition on these grounds is that any real advance in evolutionary theory has to be correct in both its philosophy and its science.

  2. Structural genomics in endocrinology

    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

  3. Epidemiology & Genomics Research Program

    The Epidemiology and Genomics Research Program, in the National Cancer Institute's Division of Cancer Control and Population Sciences, funds research in human populations to understand the determinants of cancer occurrence and outcomes.

  4. Annotating individual human genomes.

    Torkamani, Ali; Scott-Van Zeeland, Ashley A; Topol, Eric J; Schork, Nicholas J

    2011-10-01

    Advances in DNA sequencing technologies have made it possible to rapidly, accurately and affordably sequence entire individual human genomes. As impressive as this ability seems, however, it will not likely amount to much if one cannot extract meaningful information from individual sequence data. Annotating variations within individual genomes and providing information about their biological or phenotypic impact will thus be crucially important in moving individual sequencing projects forward, especially in the context of the clinical use of sequence information. In this paper we consider the various ways in which one might annotate individual sequence variations and point out limitations in the available methods for doing so. It is arguable that, in the foreseeable future, DNA sequencing of individual genomes will become routine for clinical, research, forensic, and personal purposes. We therefore also consider directions and areas for further research in annotating genomic variants. Copyright © 2011 Elsevier Inc. All rights reserved.

  5. ANNOTATING INDIVIDUAL HUMAN GENOMES*

    Torkamani, Ali; Scott-Van Zeeland, Ashley A.; Topol, Eric J.; Schork, Nicholas J.

    2014-01-01

    Advances in DNA sequencing technologies have made it possible to rapidly, accurately and affordably sequence entire individual human genomes. As impressive as this ability seems, however, it will not likely to amount to much if one cannot extract meaningful information from individual sequence data. Annotating variations within individual genomes and providing information about their biological or phenotypic impact will thus be crucially important in moving individual sequencing projects forward, especially in the context of the clinical use of sequence information. In this paper we consider the various ways in which one might annotate individual sequence variations and point out limitations in the available methods for doing so. It is arguable that, in the foreseeable future, DNA sequencing of individual genomes will become routine for clinical, research, forensic, and personal purposes. We therefore also consider directions and areas for further research in annotating genomic variants. PMID:21839162

  6. Yeast genome sequencing:

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  7. Genetical Genomics for Evolutionary Studies

    Prins, J.C.P.; Smant, G.; Jansen, R.C.

    2012-01-01

    Genetical genomics combines acquired high-throughput genomic data with genetic analysis. In this chapter, we discuss the application of genetical genomics for evolutionary studies, where new high-throughput molecular technologies are combined with mapping quantitative trait loci (QTL) on the genome

  8. The human genome project

    Worton, R.

    1996-01-01

    The Human Genome Project is a massive international research project, costing 3 to 5 billion dollars and expected to take 15 years, which will identify the all the genes in the human genome - i.e. the complete sequence of bases in human DNA. The prize will be the ability to identify genes causing or predisposing to disease, and in some cases the development of gene therapy, but this new knowledge will raise important ethical issues

  9. Decoding the human genome

    CERN. Geneva. Audiovisual Unit; Antonerakis, S E

    2002-01-01

    Decoding the Human genome is a very up-to-date topic, raising several questions besides purely scientific, in view of the two competing teams (public and private), the ethics of using the results, and the fact that the project went apparently faster and easier than expected. The lecture series will address the following chapters: Scientific basis and challenges. Ethical and social aspects of genomics.

  10. Molluscan Evolutionary Genomics

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  11. Human Germline Genome Editing

    Ormond, Kelly E.; Mortlock, Douglas P.; Scholes, Derek T.; Bombard, Yvonne; Brody, Lawrence C.; Faucett, W. Andrew; Garrison, Nanibaa’ A.; Hercher, Laura; Isasi, Rosario; Middleton, Anna; Musunuru, Kiran; Shriner, Daniel; Virani, Alice; Young, Caroline E.

    2017-01-01

    With CRISPR/Cas9 and other genome-editing technologies, successful somatic and germline genome editing are becoming feasible. To respond, an American Society of Human Genetics (ASHG) workgroup developed this position statement, which was approved by the ASHG Board in March 2017. The workgroup included representatives from the UK Association of Genetic Nurses and Counsellors, Canadian Association of Genetic Counsellors, International Genetic Epidemiology Society, and US National Society of Gen...

  12. RadGenomics project

    Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu [National Inst. of Radiological Sciences, Chiba (Japan). Frontier Research Center] [and others

    2002-06-01

    Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)

  13. Comparative Genome Viewer

    Molineris, I.; Sales, G.

    2009-01-01

    The amount of information about genomes, both in the form of complete sequences and annotations, has been exponentially increasing in the last few years. As a result there is the need for tools providing a graphical representation of such information that should be comprehensive and intuitive. Visual representation is especially important in the comparative genomics field since it should provide a combined view of data belonging to different genomes. We believe that existing tools are limited in this respect as they focus on a single genome at a time (conservation histograms) or compress alignment representation to a single dimension. We have therefore developed a web-based tool called Comparative Genome Viewer (Cgv): it integrates a bidimensional representation of alignments between two regions, both at small and big scales, with the richness of annotations present in other genome browsers. We give access to our system through a web-based interface that provides the user with an interactive representation that can be updated in real time using the mouse to move from region to region and to zoom in on interesting details.

  14. Human social genomics.

    Steven W Cole

    2014-08-01

    Full Text Available A growing literature in human social genomics has begun to analyze how everyday life circumstances influence human gene expression. Social-environmental conditions such as urbanity, low socioeconomic status, social isolation, social threat, and low or unstable social status have been found to associate with differential expression of hundreds of gene transcripts in leukocytes and diseased tissues such as metastatic cancers. In leukocytes, diverse types of social adversity evoke a common conserved transcriptional response to adversity (CTRA characterized by increased expression of proinflammatory genes and decreased expression of genes involved in innate antiviral responses and antibody synthesis. Mechanistic analyses have mapped the neural "social signal transduction" pathways that stimulate CTRA gene expression in response to social threat and may contribute to social gradients in health. Research has also begun to analyze the functional genomics of optimal health and thriving. Two emerging opportunities now stand to revolutionize our understanding of the everyday life of the human genome: network genomics analyses examining how systems-level capabilities emerge from groups of individual socially sensitive genomes and near-real-time transcriptional biofeedback to empirically optimize individual well-being in the context of the unique genetic, geographic, historical, developmental, and social contexts that jointly shape the transcriptional realization of our innate human genomic potential for thriving.

  15. RadGenomics project

    Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu

    2002-01-01

    Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)

  16. Ultrafast comparison of personal genomes

    Mauldin, Denise; Hood, Leroy; Robinson, Max; Glusman, Gustavo

    2017-01-01

    We present an ultra-fast method for comparing personal genomes. We transform the standard genome representation (lists of variants relative to a reference) into 'genome fingerprints' that can be readily compared across sequencing technologies and reference versions. Because of their reduced size, computation on the genome fingerprints is fast and requires little memory. This enables scaling up a variety of important genome analyses, including quantifying relatedness, recognizing duplicative s...

  17. Genomics using the Assembly of the Mink Genome

    Guldbrandtsen, Bernt; Cai, Zexi; Sahana, Goutam

    2018-01-01

    The American Mink’s (Neovison vison) genome has recently been sequenced. This opens numerous avenues of research both for studying the basic genetics and physiology of the mink as well as genetic improvement in mink. Using genotyping-by-sequencing (GBS) generated marker data for 2,352 Danish farm...... mink runs of homozygosity (ROH) were detect in mink genomes. Detectable ROH made up on average 1.7% of the genome indicating the presence of at most a moderate level of genomic inbreeding. The fraction of genome regions found in ROH varied. Ten percent of the included regions were never found in ROH....... The ability to detect ROH in the mink genome also demonstrates the general reliability of the new mink genome assembly. Keywords: american mink, run of homozygosity, genome, selection, genomic inbreeding...

  18. Genome size analyses of Pucciniales reveal the largest fungal genomes.

    Tavares, Sílvia; Ramos, Ana Paula; Pires, Ana Sofia; Azinheira, Helena G; Caldeirinha, Patrícia; Link, Tobias; Abranches, Rita; Silva, Maria do Céu; Voegele, Ralf T; Loureiro, João; Talhinhas, Pedro

    2014-01-01

    Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.

  19. Genomes to Proteomes

    Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2009-03-01

    Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

  20. Experimental Induction of Genome Chaos.

    Ye, Christine J; Liu, Guo; Heng, Henry H

    2018-01-01

    Genome chaos, or karyotype chaos, represents a powerful survival strategy for somatic cells under high levels of stress/selection. Since the genome context, not the gene content, encodes the genomic blueprint of the cell, stress-induced rapid and massive reorganization of genome topology functions as a very important mechanism for genome (karyotype) evolution. In recent years, the phenomenon of genome chaos has been confirmed by various sequencing efforts, and many different terms have been coined to describe different subtypes of the chaotic genome including "chromothripsis," "chromoplexy," and "structural mutations." To advance this exciting field, we need an effective experimental system to induce and characterize the karyotype reorganization process. In this chapter, an experimental protocol to induce chaotic genomes is described, following a brief discussion of the mechanism and implication of genome chaos in cancer evolution.

  1. Genome Sequences of Oryza Species

    Kumagai, Masahiko; Tanaka, Tsuyoshi; Ohyanagi, Hajime; Hsing, Yue-Ie C.; Itoh, Takeshi

    2018-01-01

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  2. Genome Sequences of Oryza Species

    Kumagai, Masahiko

    2018-02-14

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  3. Genome position specific priors for genomic prediction

    Brøndum, Rasmus Froberg; Su, Guosheng; Lund, Mogens Sandø

    2012-01-01

    casual mutation is different between the populations but affects the same gene. Proportions of a four-distribution mixture for SNP effects in segments of fixed size along the genome are derived from one population and set as location specific prior proportions of distributions of SNP effects...... for the target population. The model was tested using dairy cattle populations of different breeds: 540 Australian Jersey bulls, 2297 Australian Holstein bulls and 5214 Nordic Holstein bulls. The traits studied were protein-, fat- and milk yield. Genotypic data was Illumina 777K SNPs, real or imputed Results...

  4. Genomics of Compositae crops: reference transcriptome assemblies and evidence of hybridization with wild relatives.

    Hodgins, Kathryn A; Lai, Zhao; Oliveira, Luiz O; Still, David W; Scascitelli, Moira; Barker, Michael S; Kane, Nolan C; Dempewolf, Hannes; Kozik, Alex; Kesseli, Richard V; Burke, John M; Michelmore, Richard W; Rieseberg, Loren H

    2014-01-01

    Although the Compositae harbours only two major food crops, sunflower and lettuce, many other species in this family are utilized by humans and have experienced various levels of domestication. Here, we have used next-generation sequencing technology to develop 15 reference transcriptome assemblies for Compositae crops or their wild relatives. These data allow us to gain insight into the evolutionary and genomic consequences of plant domestication. Specifically, we performed Illumina sequencing of Cichorium endivia, Cichorium intybus, Echinacea angustifolia, Iva annua, Helianthus tuberosus, Dahlia hybrida, Leontodon taraxacoides and Glebionis segetum, as well 454 sequencing of Guizotia scabra, Stevia rebaudiana, Parthenium argentatum and Smallanthus sonchifolius. Illumina reads were assembled using Trinity, and 454 reads were assembled using MIRA and CAP3. We evaluated the coverage of the transcriptomes using BLASTX analysis of a set of ultra-conserved orthologs (UCOs) and recovered most of these genes (88-98%). We found a correlation between contig length and read length for the 454 assemblies, and greater contig lengths for the 454 compared with the Illumina assemblies. This suggests that longer reads can aid in the assembly of more complete transcripts. Finally, we compared the divergence of orthologs at synonymous sites (Ks) between Compositae crops and their wild relatives and found greater divergence when the progenitors were self-incompatible. We also found greater divergence between pairs of taxa that had some evidence of postzygotic isolation. For several more distantly related congeners, such as chicory and endive, we identified a signature of introgression in the distribution of Ks values. © 2013 John Wiley & Sons Ltd.

  5. Genomics of Volvocine Algae

    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

  6. Genomics of Preterm Birth

    Swaggart, Kayleigh A.; Pavlicev, Mihaela; Muglia, Louis J.

    2015-01-01

    The molecular mechanisms controlling human birth timing at term, or resulting in preterm birth, have been the focus of considerable investigation, but limited insights have been gained over the past 50 years. In part, these processes have remained elusive because of divergence in reproductive strategies and physiology shown by model organisms, making extrapolation to humans uncertain. Here, we summarize the evolution of progesterone signaling and variation in pregnancy maintenance and termination. We use this comparative physiology to support the hypothesis that selective pressure on genomic loci involved in the timing of parturition have shaped human birth timing, and that these loci can be identified with comparative genomic strategies. Previous limitations imposed by divergence of mechanisms provide an important new opportunity to elucidate fundamental pathways of parturition control through increasing availability of sequenced genomes and associated reproductive physiology characteristics across diverse organisms. PMID:25646385

  7. Genomics of Salmonella Species

    Canals, Rocio; McClelland, Michael; Santiviago, Carlos A.; Andrews-Polymenis, Helene

    Progress in the study of Salmonella survival, colonization, and virulence has increased rapidly with the advent of complete genome sequencing and higher capacity assays for transcriptomic and proteomic analysis. Although many of these techniques have yet to be used to directly assay Salmonella growth on foods, these assays are currently in use to determine Salmonella factors necessary for growth in animal models including livestock animals and in in vitro conditions that mimic many different environments. As sequencing of the Salmonella genome and microarray analysis have revolutionized genomics and transcriptomics of salmonellae over the last decade, so are new high-throughput sequencing technologies currently accelerating the pace of our studies and allowing us to approach complex problems that were not previously experimentally tractable.

  8. Ebolavirus comparative genomics

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat; Uberbacher, Edward C.; Land, Miriam; Zhang, Qian; Wanchai, Visanu; Chai, Juanjuan; Nielsen, Morten; Trolle, Thomas; Lund, Ole; Buzard, Gregory S.; Pedersen, Thomas D.; Wassenaar, Trudy M.; Ussery, David W.

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes. All filovirus genomes sequenced to date encode proteins with similar functions and gene order, although there is considerable divergence in sequences between the three genera Ebolavirus, Cuevavirus and Marburgvirus within the family Filoviridae. Whereas all ebolavirus genomes are quite similar (multiple sequences of the same strain are often identical), variation is most common in the intergenic regions and within specific areas of the genes encoding the glycoprotein (GP), nucleoprotein (NP) and polymerase (L). We predict regions that could contain epitope-binding sites, which might be good vaccine targets. This information, combined with glycosylation sites and experimentally determined epitopes, can identify the most promising regions for the development of therapeutic strategies. This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). PMID:26175035

  9. Brief Guide to Genomics: DNA, Genes and Genomes

    ... clinic. Most new drugs based on genome-based research are estimated to be at least 10 to 15 years away, though recent genome-driven efforts in lipid-lowering therapy have considerably shortened that interval. According ...

  10. Genomic Prediction in Barley

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D

    2015-01-01

    to next generation. The main goal of this study was to see the potential of using genomic prediction in a commercial Barley breeding program. The data used in this study was from Nordic Seed company which is located in Denmark. Around 350 advanced lines were genotyped with 9K Barely chip from Illumina....... Traits used in this study were grain yield, plant height and heading date. Heading date is number days it takes after 1st June for plant to head. Heritabilities were 0.33, 0.44 and 0.48 for yield, height and heading, respectively for the average of nine plots. The GBLUP model was used for genomic...

  11. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

    Machado, Henrique; Gram, Lone

    2017-01-01

    Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur , amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

  12. phiGENOME: an integrative navigation throughout bacteriophage genomes.

    Stano, Matej; Klucar, Lubos

    2011-11-01

    phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and designed for graphical representation of gene regulations. Bringing 542 complete genome sequences accompanied with their rich annotations and references, makes phiGENOME a unique information resource in the field of phage genomics. Copyright © 2011 Elsevier Inc. All rights reserved.

  13. Illuminating the Druggable Genome (IDG)

    Federal Laboratory Consortium — Results from the Human Genome Project revealed that the human genome contains 20,000 to 25,000 genes. A gene contains (encodes) the information that each cell uses...

  14. National Human Genome Research Institute

    ... Care Genomic Medicine Working Group New Horizons and Research Patient Management Policy and Ethics Issues Quick Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for ...

  15. Genomic prediction using subsampling.

    Xavier, Alencar; Xu, Shizhong; Muir, William; Rainey, Katy Martin

    2017-03-24

    Genome-wide assisted selection is a critical tool for the genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each round of a Markov Chain Monte Carlo. We evaluated the effect of subsampling bootstrap on prediction and computational parameters. Across datasets, we observed an optimal subsampling proportion of observations around 50% with replacement, and around 33% without replacement. Subsampling provided a substantial decrease in computation time, reducing the time to fit the model by half. On average, losses on predictive properties imposed by subsampling were negligible, usually below 1%. For each dataset, an optimal subsampling point that improves prediction properties was observed, but the improvements were also negligible. Combining subsampling with Gibbs sampling is an interesting ensemble algorithm. The investigation indicates that the subsampling bootstrap Markov chain algorithm substantially reduces computational burden associated with model fitting, and it may slightly enhance prediction properties.

  16. The Lotus japonicus genome

    Fabaceae, groundbreaking genetic and genomic research has established a significant body of knowledge on Lotus japonicus, which was adopted as a model species more than 20 years ago. The diverse nature of legumes means that such research has a wide potential and agricultural impact, for example...

  17. Genomic taxonomy of vibrios

    Thompson, Cristiane C.; Vicente, Ana Carolina P.; Souza, Rangel C.

    2009-01-01

    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...

  18. The Genome Atlas Resource

    Azam Qureshi, Matloob; Rotenberg, Eva; Stærfeldt, Hans Henrik

    2010-01-01

    with scripts and algorithms developed in a variety of programming languages at the Centre for Biological Sequence Analysis in order to create a three-tier software application for genome analysis. The results are made available via a web interface developed in Java, PHP and Perl CGI. User...

  19. Genomic Signatures of Reinforcement

    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.

  20. Better chocolate through genomics

    Theobroma cacao, the cacao or chocolate tree, is a tropical understory tree whose seeds are used to make chocolate. And like any important crop, cacao is the subject of much research. On September 15, 2010, scientists publicly released a preliminary sequence of the cacao genome--which contains all o...

  1. Functional genomics of tomato

    2014-10-20

    Oct 20, 2014 ... 1Repository of Tomato Genomics Resources, Department of Plant Sciences, School .... Due to its position at the crossroads of Sanger's sequencing .... replacement for the microarray-based expression profiling. .... during RNA fragmentation step prior to library construction, ...... tomato pollen as a test case.

  2. Genomic Signatures of Reinforcement

    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

  3. The Nostoc punctiforme Genome

    John C. Meeks

    2001-12-31

    Nostoc punctiforme is a filamentous cyanobacterium with extensive phenotypic characteristics and a relatively large genome, approaching 10 Mb. The phenotypic characteristics include a photoautotrophic, diazotrophic mode of growth, but N. punctiforme is also facultatively heterotrophic; its vegetative cells have multiple development alternatives, including terminal differentiation into nitrogen-fixing heterocysts and transient differentiation into spore-like akinetes or motile filaments called hormogonia; and N. punctiforme has broad symbiotic competence with fungi and terrestrial plants, including bryophytes, gymnosperms and an angiosperm. The shotgun-sequencing phase of the N. punctiforme strain ATCC 29133 genome has been completed by the Joint Genome Institute. Annotation of an 8.9 Mb database yielded 7432 open reading frames, 45% of which encode proteins with known or probable known function and 29% of which are unique to N. punctiforme. Comparative analysis of the sequence indicates a genome that is highly plastic and in a state of flux, with numerous insertion sequences and multilocus repeats, as well as genes encoding transposases and DNA modification enzymes. The sequence also reveals the presence of genes encoding putative proteins that collectively define almost all characteristics of cyanobacteria as a group. N. punctiforme has an extensive potential to sense and respond to environmental signals as reflected by the presence of more than 400 genes encoding sensor protein kinases, response regulators and other transcriptional factors. The signal transduction systems and any of the large number of unique genes may play essential roles in the cell differentiation and symbiotic interaction properties of N. punctiforme.

  4. Comparative Genomics of Eukaryotes.

    Noort, V. van

    2007-01-01

    This thesis focuses on developing comparative genomics methods in eukaryotes, with an emphasis on applications for gene function prediction and regulatory element detection. In the past, methods have been developed to predict functional associations between gene pairs in prokaryotes. The challenge

  5. Searching for genomic constraints

    Lio` , P [Cambridge, Univ. (United Kingdom). Genetics Dept.; Ruffo, S [Florence, Univ. (Italy). Fac. di Ingegneria. Dipt. di Energetica ` S. Stecco`

    1998-01-01

    The authors have analyzed general properties of very long DNA sequences belonging to simple and complex organisms, by using different correlation methods. They have distinguished those base compositional rules that concern the entire genome which they call `genomic constraints` from the rules that depend on the `external natural selection` acting on single genes, i. e. protein-centered constraints. They show that G + C content, purine / pyrimidine distributions and biological complexity of the organism are the most important factors which determine base compositional rules and genome complexity. Three main facts are here reported: bacteria with high G + C content have more restrictions on base composition than those with low G + C content; at constant G + C content more complex organisms, ranging from prokaryotes to higher eukaryotes (e.g. human) display an increase of repeats 10-20 nucleotides long, which are also partly responsible for long-range correlations; work selection of length 3 to 10 is stronger in human and in bacteria for two distinct reasons. With respect to previous studies, they have also compared the genomic sequence of the archeon Methanococcus jannaschii with those of bacteria and eukaryotes: it shows sometimes an intermediate statistical behaviour.

  6. Searching for genomic constraints

    Lio', P.; Ruffo, S.

    1998-01-01

    The authors have analyzed general properties of very long DNA sequences belonging to simple and complex organisms, by using different correlation methods. They have distinguished those base compositional rules that concern the entire genome which they call 'genomic constraints' from the rules that depend on the 'external natural selection' acting on single genes, i. e. protein-centered constraints. They show that G + C content, purine / pyrimidine distributions and biological complexity of the organism are the most important factors which determine base compositional rules and genome complexity. Three main facts are here reported: bacteria with high G + C content have more restrictions on base composition than those with low G + C content; at constant G + C content more complex organisms, ranging from prokaryotes to higher eukaryotes (e.g. human) display an increase of repeats 10-20 nucleotides long, which are also partly responsible for long-range correlations; work selection of length 3 to 10 is stronger in human and in bacteria for two distinct reasons. With respect to previous studies, they have also compared the genomic sequence of the archeon Methanococcus jannaschii with those of bacteria and eukaryotes: it shows sometimes an intermediate statistical behaviour

  7. Genomic sequencing in clinical trials

    Mestan, Karen K; Ilkhanoff, Leonard; Mouli, Samdeep; Lin, Simon

    2011-01-01

    Abstract Human genome sequencing is the process by which the exact order of nucleic acid base pairs in the 24 human chromosomes is determined. Since the completion of the Human Genome Project in 2003, genomic sequencing is rapidly becoming a major part of our translational research efforts to understand and improve human health and disease. This article reviews the current and future directions of clinical research with respect to genomic sequencing, a technology that is just beginning to fin...

  8. Statistical Methods in Integrative Genomics

    Richardson, Sylvia; Tseng, George C.; Sun, Wei

    2016-01-01

    Statistical methods in integrative genomics aim to answer important biology questions by jointly analyzing multiple types of genomic data (vertical integration) or aggregating the same type of data across multiple studies (horizontal integration). In this article, we introduce different types of genomic data and data resources, and then review statistical methods of integrative genomics, with emphasis on the motivation and rationale of these methods. We conclude with some summary points and future research directions. PMID:27482531

  9. From plant genomes to phenotypes

    Bolger, Marie; Gundlach, Heidrun; Scholz, Uwe; Mayer, Klaus; Usadel, Björn; Schwacke, Rainer; Schmutzer, Thomas; Chen, Jinbo; Arend, Daniel; Oppermann, Markus; Weise, Stephan; Lange, Matthias; Fiorani, Fabio; Spannagl, Manuel

    2017-01-01

    Recent advances in sequencing technologies have greatly accelerated the rate of plant genome and applied breeding research. Despite this advancing trend, plant genomes continue to present numerous difficulties to the standard tools and pipelines not only for genome assembly but also gene annotation and downstream analysis.Here we give a perspective on tools, resources and services necessary to assemble and analyze plant genomes and link them to plant phenotypes.

  10. Plant growth promotion properties of bacterial strains isolated from the rhizosphere of the Jerusalem artichoke (Helianthus tuberosus L.) adapted to saline-alkaline soils and their effect on wheat growth.

    Liu, Xiaolin; Li, Xiangyue; Li, Yan; Li, Runzhi; Xie, Zhihong

    2017-03-01

    The Jerusalem artichoke (JA; Helianthus tuberosus), known to be tolerant to saline-alkaline soil conditions, has been cultivated for many years in the Yellow River delta, Shandong Province coastal zone, in China. The aim of our study was to isolate nitrogen-fixing bacteria colonizing the rhizosphere of JA and to characterize other plant growth promotion properties. The ultimate goal was to identify isolates that could be used as inoculants benefiting an economic crop, in particular for improving wheat growth production in the Yellow River delta. Bacterial strains were isolated from the rhizosphere soil of JA on the basis of growth on nitrogen-free Ashby medium. Identification and phylogenetic analysis was performed after nucleotide sequencing of 16S rRNA gene. Plant-growth-promoting traits, such as nitrogen fixation activity, phosphate solubilization activity, indole-3-acetic acid production, were determined using conventional methods. Eleven strains were isolated and 6 of them were further examined for their level of salt tolerance and their effect on plant growth promotion. Inoculation of Enterobacter sp. strain N10 on JA and wheat led to significant increases in both root and shoot dry mass and shoot height. Enterobacter sp. strain N10 appeared to be the best plant-growth-promoting rhizobacteria to increase wheat productivity in future field applications.

  11. A Thousand Fly Genomes: An Expanded Drosophila Genome Nexus.

    Lack, Justin B; Lange, Jeremy D; Tang, Alison D; Corbett-Detig, Russell B; Pool, John E

    2016-12-01

    The Drosophila Genome Nexus is a population genomic resource that provides D. melanogaster genomes from multiple sources. To facilitate comparisons across data sets, genomes are aligned using a common reference alignment pipeline which involves two rounds of mapping. Regions of residual heterozygosity, identity-by-descent, and recent population admixture are annotated to enable data filtering based on the user's needs. Here, we present a significant expansion of the Drosophila Genome Nexus, which brings the current data object to a total of 1,121 wild-derived genomes. New additions include 305 previously unpublished genomes from inbred lines representing six population samples in Egypt, Ethiopia, France, and South Africa, along with another 193 genomes added from recently-published data sets. We also provide an aligned D. simulans genome to facilitate divergence comparisons. This improved resource will broaden the range of population genomic questions that can addressed from multi-population allele frequencies and haplotypes in this model species. The larger set of genomes will also enhance the discovery of functionally relevant natural variation that exists within and between populations. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  12. The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics.

    Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F X; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

    2013-02-01

    Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.

  13. Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute's genomic medicine portfolio.

    Manolio, Teri A

    2016-10-01

    Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual's genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of "Genomic Medicine Meetings," under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and difficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI's genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so. Published by Elsevier Ireland Ltd.

  14. Applied Genomics of Foodborne Pathogens

    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....

  15. Chromatin dynamics in genome stability

    Nair, Nidhi; Shoaib, Muhammad; Sørensen, Claus Storgaard

    2017-01-01

    Genomic DNA is compacted into chromatin through packaging with histone and non-histone proteins. Importantly, DNA accessibility is dynamically regulated to ensure genome stability. This is exemplified in the response to DNA damage where chromatin relaxation near genomic lesions serves to promote...... access of relevant enzymes to specific DNA regions for signaling and repair. Furthermore, recent data highlight genome maintenance roles of chromatin through the regulation of endogenous DNA-templated processes including transcription and replication. Here, we review research that shows the importance...... of chromatin structure regulation in maintaining genome integrity by multiple mechanisms including facilitating DNA repair and directly suppressing endogenous DNA damage....

  16. Evolution of small prokaryotic genomes

    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.

  17. Informational laws of genome structures

    Bonnici, Vincenzo; Manca, Vincenzo

    2016-06-01

    In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined.

  18. Toward genome-enabled mycology.

    Hibbett, David S; Stajich, Jason E; Spatafora, Joseph W

    2013-01-01

    Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computational tools in all aspects of fungal biology. Genome-enabled mycology is integrative and often requires teams of researchers with diverse skills in organismal mycology, bioinformatics and molecular biology. This issue of Mycologia presents the first complete fungal genomes in the history of the journal, reflecting the ongoing transformation of mycology into a genome-enabled science. Here, we consider the prospects for genome-enabled mycology and the technical and social challenges that will need to be overcome to grow the database of complete fungal genomes and enable all fungal biologists to make use of the new data.

  19. Genomic research perspectives in Kazakhstan

    Ainur Akilzhanova

    2014-01-01

    Full Text Available Introduction: Technological advancements rapidly propel the field of genome research. Advances in genetics and genomics such as the sequence of the human genome, the human haplotype map, open access databases, cheaper genotyping and chemical genomics, have transformed basic and translational biomedical research. Several projects in the field of genomic and personalized medicine have been conducted at the Center for Life Sciences in Nazarbayev University. The prioritized areas of research include: genomics of multifactorial diseases, cancer genomics, bioinformatics, genetics of infectious diseases and population genomics. At present, DNA-based risk assessment for common complex diseases, application of molecular signatures for cancer diagnosis and prognosis, genome-guided therapy, and dose selection of therapeutic drugs are the important issues in personalized medicine. Results: To further develop genomic and biomedical projects at Center for Life Sciences, the development of bioinformatics research and infrastructure and the establishment of new collaborations in the field are essential. Widespread use of genetic tools will allow the identification of diseases before the onset of clinical symptoms, the individualization of drug treatment, and could induce individual behavioral changes on the basis of calculated disease risk. However, many challenges remain for the successful translation of genomic knowledge and technologies into health advances, such as medicines and diagnostics. It is important to integrate research and education in the fields of genomics, personalized medicine, and bioinformatics, which will be possible with opening of the new Medical Faculty at Nazarbayev University. People in practice and training need to be educated about the key concepts of genomics and engaged so they can effectively apply their knowledge in a matter that will bring the era of genomic medicine to patient care. This requires the development of well

  20. Mycobacteriophage genome database.

    Joseph, Jerrine; Rajendran, Vasanthi; Hassan, Sameer; Kumar, Vanaja

    2011-01-01

    Mycobacteriophage genome database (MGDB) is an exclusive repository of the 64 completely sequenced mycobacteriophages with annotated information. It is a comprehensive compilation of the various gene parameters captured from several databases pooled together to empower mycobacteriophage researchers. The MGDB (Version No.1.0) comprises of 6086 genes from 64 mycobacteriophages classified into 72 families based on ACLAME database. Manual curation was aided by information available from public databases which was enriched further by analysis. Its web interface allows browsing as well as querying the classification. The main objective is to collect and organize the complexity inherent to mycobacteriophage protein classification in a rational way. The other objective is to browse the existing and new genomes and describe their functional annotation. The database is available for free at http://mpgdb.ibioinformatics.org/mpgdb.php.

  1. Precision genome editing

    Steentoft, Catharina; Bennett, Eric P; Schjoldager, Katrine Ter-Borch Gram

    2014-01-01

    Precise and stable gene editing in mammalian cell lines has until recently been hampered by the lack of efficient targeting methods. While different gene silencing strategies have had tremendous impact on many biological fields, they have generally not been applied with wide success in the field...... of glycobiology, primarily due to their low efficiencies, with resultant failure to impose substantial phenotypic consequences upon the final glycosylation products. Here, we review novel nuclease-based precision genome editing techniques enabling efficient and stable gene editing, including gene disruption...... by introducing single or double-stranded breaks at a defined genomic sequence. We here compare and contrast the different techniques and summarize their current applications, highlighting cases from the field of glycobiology as well as pointing to future opportunities. The emerging potential of precision gene...

  2. Alignment of whole genomes.

    Delcher, A L; Kasif, S; Fleischmann, R D; Peterson, J; White, O; Salzberg, S L

    1999-01-01

    A new system for aligning whole genome sequences is described. Using an efficient data structure called a suffix tree, the system is able to rapidly align sequences containing millions of nucleotides. Its use is demonstrated on two strains of Mycoplasma tuberculosis, on two less similar species of Mycoplasma bacteria and on two syntenic sequences from human chromosome 12 and mouse chromosome 6. In each case it found an alignment of the input sequences, using between 30 s and 2 min of computation time. From the system output, information on single nucleotide changes, translocations and homologous genes can easily be extracted. Use of the algorithm should facilitate analysis of syntenic chromosomal regions, strain-to-strain comparisons, evolutionary comparisons and genomic duplications. PMID:10325427

  3. eGenomics: Cataloguing Our Complete Genome Collection III

    Dawn Field

    2007-01-01

    Full Text Available This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS, Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS specification (v1.1, consensus on a variety of features to be added to the Genome Catalogue (GCat, agreement by several researchers to adopt MIGS for imminent genome publications, and an agreement by the EBI and NCBI to input their genome collections into GCat for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates and working towards a single, global list of all public genomes and metagenomes.

  4. Genomics Portals: integrative web-platform for mining genomics data.

    Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario

    2010-01-13

    A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

  5. Genomics Portals: integrative web-platform for mining genomics data

    Ghosh Krishnendu

    2010-01-01

    Full Text Available Abstract Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc, and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

  6. Family genome browser: visualizing genomes with pedigree information.

    Juan, Liran; Liu, Yongzhuang; Wang, Yongtian; Teng, Mingxiang; Zang, Tianyi; Wang, Yadong

    2015-07-15

    Families with inherited diseases are widely used in Mendelian/complex disease studies. Owing to the advances in high-throughput sequencing technologies, family genome sequencing becomes more and more prevalent. Visualizing family genomes can greatly facilitate human genetics studies and personalized medicine. However, due to the complex genetic relationships and high similarities among genomes of consanguineous family members, family genomes are difficult to be visualized in traditional genome visualization framework. How to visualize the family genome variants and their functions with integrated pedigree information remains a critical challenge. We developed the Family Genome Browser (FGB) to provide comprehensive analysis and visualization for family genomes. The FGB can visualize family genomes in both individual level and variant level effectively, through integrating genome data with pedigree information. Family genome analysis, including determination of parental origin of the variants, detection of de novo mutations, identification of potential recombination events and identical-by-decent segments, etc., can be performed flexibly. Diverse annotations for the family genome variants, such as dbSNP memberships, linkage disequilibriums, genes, variant effects, potential phenotypes, etc., are illustrated as well. Moreover, the FGB can automatically search de novo mutations and compound heterozygous variants for a selected individual, and guide investigators to find high-risk genes with flexible navigation options. These features enable users to investigate and understand family genomes intuitively and systematically. The FGB is available at http://mlg.hit.edu.cn/FGB/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  7. Human Germline Genome Editing.

    Ormond, Kelly E; Mortlock, Douglas P; Scholes, Derek T; Bombard, Yvonne; Brody, Lawrence C; Faucett, W Andrew; Garrison, Nanibaa' A; Hercher, Laura; Isasi, Rosario; Middleton, Anna; Musunuru, Kiran; Shriner, Daniel; Virani, Alice; Young, Caroline E

    2017-08-03

    With CRISPR/Cas9 and other genome-editing technologies, successful somatic and germline genome editing are becoming feasible. To respond, an American Society of Human Genetics (ASHG) workgroup developed this position statement, which was approved by the ASHG Board in March 2017. The workgroup included representatives from the UK Association of Genetic Nurses and Counsellors, Canadian Association of Genetic Counsellors, International Genetic Epidemiology Society, and US National Society of Genetic Counselors. These groups, as well as the American Society for Reproductive Medicine, Asia Pacific Society of Human Genetics, British Society for Genetic Medicine, Human Genetics Society of Australasia, Professional Society of Genetic Counselors in Asia, and Southern African Society for Human Genetics, endorsed the final statement. The statement includes the following positions. (1) At this time, given the nature and number of unanswered scientific, ethical, and policy questions, it is inappropriate to perform germline gene editing that culminates in human pregnancy. (2) Currently, there is no reason to prohibit in vitro germline genome editing on human embryos and gametes, with appropriate oversight and consent from donors, to facilitate research on the possible future clinical applications of gene editing. There should be no prohibition on making public funds available to support this research. (3) Future clinical application of human germline genome editing should not proceed unless, at a minimum, there is (a) a compelling medical rationale, (b) an evidence base that supports its clinical use, (c) an ethical justification, and (d) a transparent public process to solicit and incorporate stakeholder input. Copyright © 2017 American Society of Human Genetics. All rights reserved.

  8. Genomic Prediction from Whole Genome Sequence in Livestock: The 1000 Bull Genomes Project

    Hayes, Benjamin J; MacLeod, Iona M; Daetwyler, Hans D

    Advantages of using whole genome sequence data to predict genomic estimated breeding values (GEBV) include better persistence of accuracy of GEBV across generations and more accurate GEBV across breeds. The 1000 Bull Genomes Project provides a database of whole genome sequenced key ancestor bulls....... In a dairy data set, predictions using BayesRC and imputed sequence data from 1000 Bull Genomes were 2% more accurate than with 800k data. We could demonstrate the method identified causal mutations in some cases. Further improvements will come from more accurate imputation of sequence variant genotypes...

  9. Genomic technologies in neonatology

    L. N. Chernova

    2017-01-01

    Full Text Available In recent years, there has been a tremendous trend toward personalized medicine. Advances in the field forced clinicians, including neonatologists, to take a fresh look at prevention, tactics of management and therapy of various diseases. In the center of attention of foreign, and increasingly Russian, researchers and doctors, there are individual genomic data that allow not only to assess the risks of some form of pathology, but also to successfully apply personalized strategies of prediction, prevention and targeted treatment. This article provides a brief review of the latest achievements of genomic technologies in newborns, examines the problems and potential applications of genomics in promoting the concept of personalized medicine in neonatology. The increasing amount of personalized data simply impossible to analyze only by the human mind. In this connection, the need of computers and bioinformatics is obvious. The article reveals the role of translational bioinformatics in the analysis and integration of the results of the accumulated fundamental research into complete clinical decisions. The latest advances in neonatal translational bioinformatics such as clinical decision support systems are considered. It helps to monitor vital parameters of newborns influencing the course of a particular disease, to calculate the increased risks of the development of various pathologies and to select the drugs.

  10. Value-based genomics.

    Gong, Jun; Pan, Kathy; Fakih, Marwan; Pal, Sumanta; Salgia, Ravi

    2018-03-20

    Advancements in next-generation sequencing have greatly enhanced the development of biomarker-driven cancer therapies. The affordability and availability of next-generation sequencers have allowed for the commercialization of next-generation sequencing platforms that have found widespread use for clinical-decision making and research purposes. Despite the greater availability of tumor molecular profiling by next-generation sequencing at our doorsteps, the achievement of value-based care, or improving patient outcomes while reducing overall costs or risks, in the era of precision oncology remains a looming challenge. In this review, we highlight available data through a pre-established and conceptualized framework for evaluating value-based medicine to assess the cost (efficiency), clinical benefit (effectiveness), and toxicity (safety) of genomic profiling in cancer care. We also provide perspectives on future directions of next-generation sequencing from targeted panels to whole-exome or whole-genome sequencing and describe potential strategies needed to attain value-based genomics.

  11. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

    Machado, Henrique; Gram, Lone

    2017-01-01

    was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.......Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand...... the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two...

  12. Genome update: the 1000th genome - a cautionary tale

    Lagesen, Karin; Ussery, David; Wassenaar, Gertrude Maria

    2010-01-01

    conclusions for example about the largest bacterial genome sequenced. Biological diversity is far greater than many have thought. For example, analysis of multiple Escherichia coli genomes has led to an estimate of around 45 000 gene families more genes than are recognized in the human genome. Moreover......There are now more than 1000 sequenced prokaryotic genomes deposited in public databases and available for analysis. Currently, although the sequence databases GenBank, DNA Database of Japan and EMBL are synchronized continually, there are slight differences in content at the genomes level...... for a variety of logistical reasons, including differences in format and loading errors, such as those caused by file transfer protocol interruptions. This means that the 1000th genome will be different in the various databases. Some of the data on the highly accessed web pages are inaccurate, leading to false...

  13. Efficient Breeding by Genomic Mating.

    Akdemir, Deniz; Sánchez, Julio I

    2016-01-01

    Selection in breeding programs can be done by using phenotypes (phenotypic selection), pedigree relationship (breeding value selection) or molecular markers (marker assisted selection or genomic selection). All these methods are based on truncation selection, focusing on the best performance of parents before mating. In this article we proposed an approach to breeding, named genomic mating, which focuses on mating instead of truncation selection. Genomic mating uses information in a similar fashion to genomic selection but includes information on complementation of parents to be mated. Following the efficiency frontier surface, genomic mating uses concepts of estimated breeding values, risk (usefulness) and coefficient of ancestry to optimize mating between parents. We used a genetic algorithm to find solutions to this optimization problem and the results from our simulations comparing genomic selection, phenotypic selection and the mating approach indicate that current approach for breeding complex traits is more favorable than phenotypic and genomic selection. Genomic mating is similar to genomic selection in terms of estimating marker effects, but in genomic mating the genetic information and the estimated marker effects are used to decide which genotypes should be crossed to obtain the next breeding population.

  14. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

    Henrique Machado; Henrique Machado; Lone Gram

    2017-01-01

    Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationship...

  15. High-throughput genotyping-by-sequencing facilitates molecular tagging of a novel rust resistance gene, R 15 , in sunflower (Helianthus annuus L.).

    Ma, G J; Song, Q J; Markell, S G; Qi, L L

    2018-03-21

    A novel rust resistance gene, R 15 , derived from the cultivated sunflower HA-R8 was assigned to linkage group 8 of the sunflower genome using a genotyping-by-sequencing approach. SNP markers closely linked to R 15 were identified, facilitating marker-assisted selection of resistance genes. The rust virulence gene is co-evolving with the resistance gene in sunflower, leading to the emergence of new physiologic pathotypes. This presents a continuous threat to the sunflower crop necessitating the development of resistant sunflower hybrids providing a more efficient, durable, and environmentally friendly host plant resistance. The inbred line HA-R8 carries a gene conferring resistance to all known races of the rust pathogen in North America and can be used as a broad-spectrum resistance resource. Based on phenotypic assessments of 140 F 2 individuals derived from a cross of HA 89 with HA-R8, rust resistance in the population was found to be conferred by a single dominant gene (R 15 ) originating from HA-R8. Genotypic analysis with the currently available SSR markers failed to find any association between rust resistance and any markers. Therefore, we used genotyping-by-sequencing (GBS) analysis to achieve better genomic coverage. The GBS data showed that R 15 was located at the top end of linkage group (LG) 8. Saturation with 71 previously mapped SNP markers selected within this region further showed that it was located in a resistance gene cluster on LG8, and mapped to a 1.0-cM region between three co-segregating SNP makers SFW01920, SFW00128, and SFW05824 as well as the NSA_008457 SNP marker. These closely linked markers will facilitate marker-assisted selection and breeding in sunflower.

  16. Genome Surfing As Driver of Microbial Genomic Diversity.

    Choudoir, Mallory J; Panke-Buisse, Kevin; Andam, Cheryl P; Buckley, Daniel H

    2017-08-01

    Historical changes in population size, such as those caused by demographic range expansions, can produce nonadaptive changes in genomic diversity through mechanisms such as gene surfing. We propose that demographic range expansion of a microbial population capable of horizontal gene exchange can result in genome surfing, a mechanism that can cause widespread increase in the pan-genome frequency of genes acquired by horizontal gene exchange. We explain that patterns of genetic diversity within Streptomyces are consistent with genome surfing, and we describe several predictions for testing this hypothesis both in Streptomyces and in other microorganisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Genome U-Plot: a whole genome visualization.

    Gaitatzes, Athanasios; Johnson, Sarah H; Smadbeck, James B; Vasmatzis, George

    2018-05-15

    The ability to produce and analyze whole genome sequencing (WGS) data from samples with structural variations (SV) generated the need to visualize such abnormalities in simplified plots. Conventional two-dimensional representations of WGS data frequently use either circular or linear layouts. There are several diverse advantages regarding both these representations, but their major disadvantage is that they do not use the two-dimensional space very efficiently. We propose a layout, termed the Genome U-Plot, which spreads the chromosomes on a two-dimensional surface and essentially quadruples the spatial resolution. We present the Genome U-Plot for producing clear and intuitive graphs that allows researchers to generate novel insights and hypotheses by visualizing SVs such as deletions, amplifications, and chromoanagenesis events. The main features of the Genome U-Plot are its layered layout, its high spatial resolution and its improved aesthetic qualities. We compare conventional visualization schemas with the Genome U-Plot using visualization metrics such as number of line crossings and crossing angle resolution measures. Based on our metrics, we improve the readability of the resulting graph by at least 2-fold, making apparent important features and making it easy to identify important genomic changes. A whole genome visualization tool with high spatial resolution and improved aesthetic qualities. An implementation and documentation of the Genome U-Plot is publicly available at https://github.com/gaitat/GenomeUPlot. vasmatzis.george@mayo.edu. Supplementary data are available at Bioinformatics online.

  18. Genomic Data Commons and Genomic Cloud Pilots - Google Hangout

    Join us for a live, moderated discussion about two NCI efforts to expand access to cancer genomics data: the Genomic Data Commons and Genomic Cloud Pilots. NCI subject matters experts will include Louis M. Staudt, M.D., Ph.D., Director Center for Cancer Genomics, Warren Kibbe, Ph.D., Director, NCI Center for Biomedical Informatics and Information Technology, and moderated by Anthony Kerlavage, Ph.D., Chief, Cancer Informatics Branch, Center for Biomedical Informatics and Information Technology. We welcome your questions before and during the Hangout on Twitter using the hashtag #AskNCI.

  19. Ensembl 2002: accommodating comparative genomics.

    Clamp, M; Andrews, D; Barker, D; Bevan, P; Cameron, G; Chen, Y; Clark, L; Cox, T; Cuff, J; Curwen, V; Down, T; Durbin, R; Eyras, E; Gilbert, J; Hammond, M; Hubbard, T; Kasprzyk, A; Keefe, D; Lehvaslaiho, H; Iyer, V; Melsopp, C; Mongin, E; Pettett, R; Potter, S; Rust, A; Schmidt, E; Searle, S; Slater, G; Smith, J; Spooner, W; Stabenau, A; Stalker, J; Stupka, E; Ureta-Vidal, A; Vastrik, I; Birney, E

    2003-01-01

    The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.

  20. The Ensembl genome database project.

    Hubbard, T; Barker, D; Birney, E; Cameron, G; Chen, Y; Clark, L; Cox, T; Cuff, J; Curwen, V; Down, T; Durbin, R; Eyras, E; Gilbert, J; Hammond, M; Huminiecki, L; Kasprzyk, A; Lehvaslaiho, H; Lijnzaad, P; Melsopp, C; Mongin, E; Pettett, R; Pocock, M; Potter, S; Rust, A; Schmidt, E; Searle, S; Slater, G; Smith, J; Spooner, W; Stabenau, A; Stalker, J; Stupka, E; Ureta-Vidal, A; Vastrik, I; Clamp, M

    2002-01-01

    The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.

  1. Comparative Genomics in Homo sapiens.

    Oti, Martin; Sammeth, Michael

    2018-01-01

    Genomes can be compared at different levels of divergence, either between species or within species. Within species genomes can be compared between different subpopulations, such as human subpopulations from different continents. Investigating the genomic differences between different human subpopulations is important when studying complex diseases that are affected by many genetic variants, as the variants involved can differ between populations. The 1000 Genomes Project collected genome-scale variation data for 2504 human individuals from 26 different populations, enabling a systematic comparison of variation between human subpopulations. In this chapter, we present step-by-step a basic protocol for the identification of population-specific variants employing the 1000 Genomes data. These variants are subsequently further investigated for those that affect the proteome or RNA splice sites, to investigate potentially biologically relevant differences between the populations.

  2. Molecular aspects of zygotic embryogenesis in sunflower (Helianthus annuus L.): correlation of positive histone marks with HaWUS expression and putative link HaWUS/HaL1L.

    Salvini, Mariangela; Fambrini, Marco; Giorgetti, Lucia; Pugliesi, Claudio

    2016-01-01

    The link HaWUS/ HaL1L , the opposite transcriptional behavior, and the decrease/increase in positive histone marks bond to both genes suggest an inhibitory effect of WUS on HaL1L in sunflower zygotic embryos. In Arabidopsis, a group of transcription factors implicated in the earliest events of embryogenesis is the WUSCHEL-RELATED HOMEOBOX (WOX) protein family including WUSCHEL (WUS) and other 14 WOX protein, some of which contain a conserved WUS-box domain in addition to the homeodomain. WUS transcripts appear very early in embryogenesis, at the 16-cell embryo stage, but gradually become restricted to the center of the developing shoot apical meristem (SAM) primordium and continues to be expressed in cells of the niche/organizing center of SAM and floral meristems to maintain stem cell population. Moreover, WUS has decisive roles in the embryonic program presumably promoting the vegetative-to-embryonic transition and/or maintaining the identity of the embryonic stem cells. However, data on the direct interaction between WUS and key genes for seed development (as LEC1 and L1L) are not collected. The novelty of this report consists in the characterization of Helianthus annuus WUS (HaWUS) gene and in its analysis regarding the pattern of the methylated lysine 4 (K4) of the Histone H3 and of the acetylated histone H3 during the zygotic embryo development. Also, a parallel investigation was performed for HaL1L gene since two copies of the WUS-binding site (WUSATA), previously identified on HaL1L nucleotide sequence, were able to be bound by the HaWUS recombinant protein suggesting a not described effect of HaWUS on HaL1L transcription.

  3. Impact of wheat straw biochar addition to soil on the sorption, leaching, dissipation of the herbicide (4-chloro-2-methylphenoxy)acetic acid and the growth of sunflower (Helianthus annuus L.).

    Tatarková, Veronika; Hiller, Edgar; Vaculík, Marek

    2013-06-01

    Biochar addition to agricultural soils might increase the sorption of herbicides, and therefore, affect other sorption-related processes such as leaching, dissipation and toxicity for plants. In this study, the impact of wheat straw biochar on the sorption, leaching and dissipation in a soil, and toxicity for sunflower of (4-chloro-2-methylphenoxy)acetic acid (MCPA), a commonly used ionizable herbicide, was investigated. The results showed that MCPA sorption by biochar and biochar-amended soil (1.0wt% biochar) was 82 and 2.53 times higher than that by the non-amended soil, respectively. However, desorption of MCPA from biochar-amended soil was only 1.17 times lower than its desorption in non-amended soil. Biochar addition to soil reduced both MCPA leaching and dissipation. About 35% of the applied MCPA was transported through biochar-amended soil, while up to 56% was recovered in the leachates transported through non-amended soil. The half-life value of MCPA increased from 5.2d in non-amended soil to 21.5 d in biochar-amended soil. Pot experiments with sunflower (Helianthus annuus L.) grown in MCPA-free, but biochar-amended soil showed no positive effect of biochar on the growth of sunflower in comparison to the non-amended soil. However, biochar itself significantly reduced the content of photosynthetic pigments (chlorophyll a, b) in sunflower. There was no significant difference in the phytotoxic effects of MCPA on sunflowers between the biochar-amended soil and the non-amended soil. Furthermore, MCPA had no effect on the photosynthetic pigment contents in sunflower. Copyright © 2013 Elsevier Inc. All rights reserved.

  4. Contaminação por Aspergillus flavus e A. fumigatus em sementes de girassol (Helianthus annuus utilizados na alimentação de psitacídeos

    Alexsandro Machado Conceição

    2010-04-01

    Full Text Available http://dx.doi.org/10.5007/2175-7925.2010v23n2p145 Amplamente difundido na alimentação de psitacídeos em razão do preço baixo, elevada palatabilidade, e por razões culturais, o Helianthus annuus, conhecido como girassol, vem se mostrando importante na clínica aviária em decorrência do excesso de calorias, e da alta incidência na contaminação por alguns fungos, principalmente do gênero Aspergillus, especificamente A. flavus e A. fumigatus. O objetivo deste estudo foi avaliar a contaminação por Aspegillus ssp. em sementes de girassol destinada à alimentação de psitacídeos comercializadas em Aracaju, estado de Sergipe. As análises foram realizadas no Laboratório de Microbiologia, do Hospital Veterinário Dr. Vicente Borreli, na Faculdade Pio Décimo. Avaliaram-se quatro amostras de sementes de girassol, sendo uma comercializada no mercado público municipal, de forma granel e três marcas comerciais, envasadas e de diferentes hipermercados, processadas segundo Forsythe (2002. De acordo com a pesquisa realizada, foi possível observar um elevado desenvolvimento de A. flavus e A. fumigatus nas sementes de girassol. Esta contaminação pode estar relacionada a vários fatores: colheita e fases de secagem, beneficiamento e armazenamento do grão inadequado. Além disso, é importante destacar a necessidade de que haja um melhor armazenamento de grãos, com controle de temperatura e umidade relativa, visando reduzir a possibilidade de contaminação por Aspergillus spp. que causa prejuízos na alimentação de psitacídeos, e de outras espécies animais.

  5. The genome of Arabidopsis thaliana.

    Goodman, H M; Ecker, J R; Dean, C

    1995-01-01

    Arabidopsis thaliana is a small flowering plant that is a member of the family cruciferae. It has many characteristics--diploid genetics, rapid growth cycle, relatively low repetitive DNA content, and small genome size--that recommend it as the model for a plant genome project. The current status of the genetic and physical maps, as well as efforts to sequence the genome, are presented. Examples are given of genes isolated by using map-based cloning. The importance of the Arabidopsis project ...

  6. Advances in editing microalgae genomes

    Daboussi, Fayza

    2017-01-01

    There have been significant advances in microalgal genomics over the last decade. Nevertheless, there are still insufficient tools for the manipulation of microalgae genomes and the development of microalgae as industrial biofactories. Several research groups have recently contributed to progress by demonstrating that particular nucleases can be used for targeted and stable modifications of the genomes of some microalgae species. The nucleases include Meganucleases, Zinc Finger nucleases, TAL...

  7. Genomic selection in plant breeding.

    Newell, Mark A; Jannink, Jean-Luc

    2014-01-01

    Genomic selection (GS) is a method to predict the genetic value of selection candidates based on the genomic estimated breeding value (GEBV) predicted from high-density markers positioned throughout the genome. Unlike marker-assisted selection, the GEBV is based on all markers including both minor and major marker effects. Thus, the GEBV may capture more of the genetic variation for the particular trait under selection.

  8. Genomic Feature Models

    Sørensen, Peter; Edwards, Stefan McKinnon; Rohde, Palle Duun

    -additive genetic mechanisms. These modeling approaches have proven to be highly useful to determine population genetic parameters as well as prediction of genetic risk or value. We present a series of statistical modelling approaches that use prior biological information for evaluating the collective action......Whole-genome sequences and multiple trait phenotypes from large numbers of individuals will soon be available in many populations. Well established statistical modeling approaches enable the genetic analyses of complex trait phenotypes while accounting for a variety of additive and non...... regions and gene ontologies) that provide better model fit and increase predictive ability of the statistical model for this trait....

  9. Genomic dairy cattle breeding

    Mark, Thomas; Sandøe, Peter

    2010-01-01

    the thoughts of breeders and other stakeholders on how to best make use of genomic breeding in the future. Intensive breeding has played a major role in securing dramatic increases in milk yield since the Second World War. Until recently, the main focus in dairy cattle breeding was on production traits...... it less accountable to the concern of private farmers for the welfare of their animals. It is argued that there is a need to mobilise a wide range of stakeholders to monitor developments and maintain pressure on breeding companies so that they are aware of the need to take precautionary measures to avoid...

  10. Organizational heterogeneity of vertebrate genomes.

    Frenkel, Svetlana; Kirzhner, Valery; Korol, Abraham

    2012-01-01

    Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as "texts" using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS) analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers) in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter--GDM) allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.

  11. Organizational heterogeneity of vertebrate genomes.

    Svetlana Frenkel

    Full Text Available Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as "texts" using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter--GDM allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.

  12. Genome engineering in Vibrio cholerae

    Val, Marie-Eve; Skovgaard, Ole; Ducos-Galand, Magaly

    2012-01-01

    Although bacteria with multipartite genomes are prevalent, our knowledge of the mechanisms maintaining their genome is very limited, and much remains to be learned about the structural and functional interrelationships of multiple chromosomes. Owing to its bi-chromosomal genome architecture and its....... This difficulty was surmounted using a unique and powerful strategy based on massive rearrangement of prokaryotic genomes. We developed a site-specific recombination-based engineering tool, which allows targeted, oriented, and reciprocal DNA exchanges. Using this genetic tool, we obtained a panel of V. cholerae...

  13. Genome Writing: Current Progress and Related Applications

    Yueqiang Wang

    2018-02-01

    Full Text Available The ultimate goal of synthetic biology is to build customized cells or organisms to meet specific industrial or medical needs. The most important part of the customized cell is a synthetic genome. Advanced genomic writing technologies are required to build such an artificial genome. Recently, the partially-completed synthetic yeast genome project represents a milestone in this field. In this mini review, we briefly introduce the techniques for de novo genome synthesis and genome editing. Furthermore, we summarize recent research progresses and highlight several applications in the synthetic genome field. Finally, we discuss current challenges and future prospects. Keywords: Synthetic biology, Genome writing, Genome editing, Bioethics, Biosafety

  14. Comparative genomics of Lactobacillus and other LAB

    Wassenaar, Trudy M.; Lukjancenko, Oksana

    2014-01-01

    that of the others, with the two Streptococcus species having the shortest genomes. The widest distribution in genome content was observed for Lactobacillus. The number of tRNA and rRNA gene copies varied considerably, with exceptional high numbers observed for Lb. delbrueckii, while these numbers were relatively......The genomes of 66 LABs, belonging to five different genera, were compared for genome size and gene content. The analyzed genomes included 37 Lactobacillus genomes of 17 species, six Lactococcus lactis genomes, four Leuconostoc genomes of three species, six Streptococcus genomes of two species...

  15. Genome Update: alignment of bacterial chromosomes

    Ussery, David; Jensen, Mette; Poulsen, Tine Rugh

    2004-01-01

    There are four new microbial genomes listed in this month's Genome Update, three belonging to Gram-positive bacteria and one belonging to an archaeon that lives at pH 0; all of these genomes are listed in Table 1⇓. The method of genome comparison this month is that of genome alignment and, as an ...

  16. Insights into structural variations and genome rearrangements in prokaryotic genomes.

    Periwal, Vinita; Scaria, Vinod

    2015-01-01

    Structural variations (SVs) are genomic rearrangements that affect fairly large fragments of DNA. Most of the SVs such as inversions, deletions and translocations have been largely studied in context of genetic diseases in eukaryotes. However, recent studies demonstrate that genome rearrangements can also have profound impact on prokaryotic genomes, leading to altered cell phenotype. In contrast to single-nucleotide variations, SVs provide a much deeper insight into organization of bacterial genomes at a much better resolution. SVs can confer change in gene copy number, creation of new genes, altered gene expression and many other functional consequences. High-throughput technologies have now made it possible to explore SVs at a much refined resolution in bacterial genomes. Through this review, we aim to highlight the importance of the less explored field of SVs in prokaryotic genomes and their impact. We also discuss its potential applicability in the emerging fields of synthetic biology and genome engineering where targeted SVs could serve to create sophisticated and accurate genome editing. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  17. Comparative genomics reveals insights into avian genome evolution and adaptation

    Zhang, Guojie; Li, Cai; Li, Qiye

    2014-01-01

    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, ...

  18. Pre-genomic, genomic and post-genomic study of microbial communities involved in bioenergy.

    Rittmann, Bruce E; Krajmalnik-Brown, Rosa; Halden, Rolf U

    2008-08-01

    Microorganisms can produce renewable energy in large quantities and without damaging the environment or disrupting food supply. The microbial communities must be robust and self-stabilizing, and their essential syntrophies must be managed. Pre-genomic, genomic and post-genomic tools can provide crucial information about the structure and function of these microbial communities. Applying these tools will help accelerate the rate at which microbial bioenergy processes move from intriguing science to real-world practice.

  19. Genomic instability and radiation

    Little, John B [Harvard School of Public Health, Boston, MA 02115 (United States)

    2003-06-01

    Genomic instability is a hallmark of cancer cells, and is thought to be involved in the process of carcinogenesis. Indeed, a number of rare genetic disorders associated with a predisposition to cancer are characterised by genomic instability occurring in somatic cells. Of particular interest is the observation that transmissible instability can be induced in somatic cells from normal individuals by exposure to ionising radiation, leading to a persistent enhancement in the rate at which mutations and chromosomal aberrations arise in the progeny of the irradiated cells after many generations of replication. If such induced instability is involved in radiation carcinogenesis, it would imply that the initial carcinogenic event may not be a rare mutation occurring in a specific gene or set of genes. Rather, radiation may induce a process of instability in many cells in a population, enhancing the rate at which the multiple gene mutations necessary for the development of cancer may arise in a given cell lineage. Furthermore, radiation could act at any stage in the development of cancer by facilitating the accumulation of the remaining genetic events required to produce a fully malignant tumour. The experimental evidence for such induced instability is reviewed. (review)

  20. Genomic instability and radiation

    Little, John B

    2003-01-01

    Genomic instability is a hallmark of cancer cells, and is thought to be involved in the process of carcinogenesis. Indeed, a number of rare genetic disorders associated with a predisposition to cancer are characterised by genomic instability occurring in somatic cells. Of particular interest is the observation that transmissible instability can be induced in somatic cells from normal individuals by exposure to ionising radiation, leading to a persistent enhancement in the rate at which mutations and chromosomal aberrations arise in the progeny of the irradiated cells after many generations of replication. If such induced instability is involved in radiation carcinogenesis, it would imply that the initial carcinogenic event may not be a rare mutation occurring in a specific gene or set of genes. Rather, radiation may induce a process of instability in many cells in a population, enhancing the rate at which the multiple gene mutations necessary for the development of cancer may arise in a given cell lineage. Furthermore, radiation could act at any stage in the development of cancer by facilitating the accumulation of the remaining genetic events required to produce a fully malignant tumour. The experimental evidence for such induced instability is reviewed. (review)

  1. Theory of microbial genome evolution

    Koonin, Eugene

    Bacteria and archaea have small genomes tightly packed with protein-coding genes. This compactness is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size. By fitting the genome size distributions in multiple groups of prokaryotes to predictions of mathematical models of population evolution, we show that only models in which acquisition of additional genes is, on average, slightly beneficial yield a good fit to genomic data. Thus, the number of genes in prokaryotic genomes seems to reflect the equilibrium between the benefit of additional genes that diminishes as the genome grows and deletion bias. New genes acquired by microbial genomes, on average, appear to be adaptive. Evolution of bacterial and archaeal genomes involves extensive horizontal gene transfer and gene loss. Many microbes have open pangenomes, where each newly sequenced genome contains more than 10% `ORFans', genes without detectable homologues in other species. A simple, steady-state evolutionary model reveals two sharply distinct classes of microbial genes, one of which (ORFans) is characterized by effectively instantaneous gene replacement, whereas the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of at least a billion distinct genes in the prokaryotic genomic universe.

  2. Genomic selection: genome-wide prediction in plant improvement.

    Desta, Zeratsion Abera; Ortiz, Rodomiro

    2014-09-01

    Association analysis is used to measure relations between markers and quantitative trait loci (QTL). Their estimation ignores genes with small effects that trigger underpinning quantitative traits. By contrast, genome-wide selection estimates marker effects across the whole genome on the target population based on a prediction model developed in the training population (TP). Whole-genome prediction models estimate all marker effects in all loci and capture small QTL effects. Here, we review several genomic selection (GS) models with respect to both the prediction accuracy and genetic gain from selection. Phenotypic selection or marker-assisted breeding protocols can be replaced by selection, based on whole-genome predictions in which phenotyping updates the model to build up the prediction accuracy. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Parasite Genome Projects and the Trypanosoma cruzi Genome Initiative

    Wim Degrave

    1997-11-01

    Full Text Available Since the start of the human genome project, a great number of genome projects on other "model" organism have been initiated, some of them already completed. Several initiatives have also been started on parasite genomes, mainly through support from WHO/TDR, involving North-South and South-South collaborations, and great hopes are vested in that these initiatives will lead to new tools for disease control and prevention, as well as to the establishment of genomic research technology in developing countries. The Trypanosoma cruzi genome project, using the clone CL-Brener as starting point, has made considerable progress through the concerted action of more than 20 laboratories, most of them in the South. A brief overview of the current state of the project is given

  4. A Taste of Algal Genomes from the Joint Genome Institute

    Kuo, Alan; Grigoriev, Igor

    2012-06-17

    Algae play profound roles in aquatic food chains and the carbon cycle, can impose health and economic costs through toxic blooms, provide models for the study of symbiosis, photosynthesis, and eukaryotic evolution, and are candidate sources for bio-fuels; all of these research areas are part of the mission of DOE's Joint Genome Institute (JGI). To date JGI has sequenced, assembled, annotated, and released to the public the genomes of 18 species and strains of algae, sampling almost all of the major clades of photosynthetic eukaryotes. With more algal genomes currently undergoing analysis, JGI continues its commitment to driving forward basic and applied algal science. Among these ongoing projects are the pan-genome of the dominant coccolithophore Emiliania huxleyi, the interrelationships between the 4 genomes in the nucleomorph-containing Bigelowiella natans and Guillardia theta, and the search for symbiosis genes of lichens.

  5. OryzaGenome: Genome Diversity Database of Wild Oryza Species

    Ohyanagi, Hajime

    2015-11-18

    The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a textbased browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tabdelimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/ scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through http://viewer.shigen.info/oryzagenome/.

  6. Cocoa/Cotton Comparative Genomics

    With genome sequence from two members of the Malvaceae family recently made available, we are exploring syntenic relationships, gene content, and evolutionary trajectories between the cacao and cotton genomes. An assembly of cacao (Theobroma cacao) using Illumina and 454 sequence technology yielded ...

  7. Genomic selection in dairy cattle

    Roos, de A.P.W.

    2011-01-01

    The objectives of this Ph.D. thesis were (1) to optimise genomic selection in dairy cattle with respect to the accuracy of predicting total genetic merit and (2) to optimise a dairy cattle breeding program using genomic selection. The study was performed using a combination of real data sets and

  8. Cloud computing for comparative genomics

    Pivovarov Rimma

    2010-05-01

    Full Text Available Abstract Background Large comparative genomics studies and tools are becoming increasingly more compute-expensive as the number of available genome sequences continues to rise. The capacity and cost of local computing infrastructures are likely to become prohibitive with the increase, especially as the breadth of questions continues to rise. Alternative computing architectures, in particular cloud computing environments, may help alleviate this increasing pressure and enable fast, large-scale, and cost-effective comparative genomics strategies going forward. To test this, we redesigned a typical comparative genomics algorithm, the reciprocal smallest distance algorithm (RSD, to run within Amazon's Elastic Computing Cloud (EC2. We then employed the RSD-cloud for ortholog calculations across a wide selection of fully sequenced genomes. Results We ran more than 300,000 RSD-cloud processes within the EC2. These jobs were farmed simultaneously to 100 high capacity compute nodes using the Amazon Web Service Elastic Map Reduce and included a wide mix of large and small genomes. The total computation time took just under 70 hours and cost a total of $6,302 USD. Conclusions The effort to transform existing comparative genomics algorithms from local compute infrastructures is not trivial. However, the speed and flexibility of cloud computing environments provides a substantial boost with manageable cost. The procedure designed to transform the RSD algorithm into a cloud-ready application is readily adaptable to similar comparative genomics problems.

  9. Cloud computing for comparative genomics.

    Wall, Dennis P; Kudtarkar, Parul; Fusaro, Vincent A; Pivovarov, Rimma; Patil, Prasad; Tonellato, Peter J

    2010-05-18

    Large comparative genomics studies and tools are becoming increasingly more compute-expensive as the number of available genome sequences continues to rise. The capacity and cost of local computing infrastructures are likely to become prohibitive with the increase, especially as the breadth of questions continues to rise. Alternative computing architectures, in particular cloud computing environments, may help alleviate this increasing pressure and enable fast, large-scale, and cost-effective comparative genomics strategies going forward. To test this, we redesigned a typical comparative genomics algorithm, the reciprocal smallest distance algorithm (RSD), to run within Amazon's Elastic Computing Cloud (EC2). We then employed the RSD-cloud for ortholog calculations across a wide selection of fully sequenced genomes. We ran more than 300,000 RSD-cloud processes within the EC2. These jobs were farmed simultaneously to 100 high capacity compute nodes using the Amazon Web Service Elastic Map Reduce and included a wide mix of large and small genomes. The total computation time took just under 70 hours and cost a total of $6,302 USD. The effort to transform existing comparative genomics algorithms from local compute infrastructures is not trivial. However, the speed and flexibility of cloud computing environments provides a substantial boost with manageable cost. The procedure designed to transform the RSD algorithm into a cloud-ready application is readily adaptable to similar comparative genomics problems.

  10. The promise of insect genomics

    Grimmelikhuijzen, Cornelis J P; Cazzamali, Giuseppe; Williamson, Michael

    2007-01-01

    Insects are the largest animal group in the world and are ecologically and economically extremely important. This importance of insects is reflected by the existence of currently 24 insect genome projects. Our perspective discusses the state-of-the-art of these genome projects and the impacts...

  11. Bioinformatics of genomic association mapping

    Vaez Barzani, Ahmad

    2015-01-01

    In this thesis we present an overview of bioinformatics-based approaches for genomic association mapping, with emphasis on human quantitative traits and their contribution to complex diseases. We aim to provide a comprehensive walk-through of the classic steps of genomic association mapping

  12. Allele coding in genomic evaluation

    Standen, Ismo; Christensen, Ole Fredslund

    2011-01-01

    Genomic data are used in animal breeding to assist genetic evaluation. Several models to estimate genomic breeding values have been studied. In general, two approaches have been used. One approach estimates the marker effects first and then, genomic breeding values are obtained by summing marker...... effects. In the second approach, genomic breeding values are estimated directly using an equivalent model with a genomic relationship matrix. Allele coding is the method chosen to assign values to the regression coefficients in the statistical model. A common allele coding is zero for the homozygous...... genotype of the first allele, one for the heterozygote, and two for the homozygous genotype for the other allele. Another common allele coding changes these regression coefficients by subtracting a value from each marker such that the mean of regression coefficients is zero within each marker. We call...

  13. Pathophysiology of MDS: genomic aberrations.

    Ichikawa, Motoshi

    2016-01-01

    Myelodysplastic syndromes (MDS) are characterized by clonal proliferation of hematopoietic stem/progenitor cells and their apoptosis, and show a propensity to progress to acute myelogenous leukemia (AML). Although MDS are recognized as neoplastic diseases caused by genomic aberrations of hematopoietic cells, the details of the genetic abnormalities underlying disease development have not as yet been fully elucidated due to difficulties in analyzing chromosomal abnormalities. Recent advances in comprehensive analyses of disease genomes including whole-genome sequencing technologies have revealed the genomic abnormalities in MDS. Surprisingly, gene mutations were found in approximately 80-90% of cases with MDS, and the novel mutations discovered with these technologies included previously unknown, MDS-specific, mutations such as those of the genes in the RNA-splicing machinery. It is anticipated that these recent studies will shed new light on the pathophysiology of MDS due to genomic aberrations.

  14. Chemical biology on the genome.

    Balasubramanian, Shankar

    2014-08-15

    In this article I discuss studies towards understanding the structure and function of DNA in the context of genomes from the perspective of a chemist. The first area I describe concerns the studies that led to the invention and subsequent development of a method for sequencing DNA on a genome scale at high speed and low cost, now known as Solexa/Illumina sequencing. The second theme will feature the four-stranded DNA structure known as a G-quadruplex with a focus on its fundamental properties, its presence in cellular genomic DNA and the prospects for targeting such a structure in cels with small molecules. The final topic for discussion is naturally occurring chemically modified DNA bases with an emphasis on chemistry for decoding (or sequencing) such modifications in genomic DNA. The genome is a fruitful topic to be further elucidated by the creation and application of chemical approaches. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. IMA Genome-F 5G

    Wingfield, Brenda D.; Barnes, Irene; Wilhelm de Beer, Z.; De Vos, Lieschen; Duong, Tuan A.; Kanzi, Aquillah M.; Naidoo, Kershney; Nguyen, Hai D.T.; Santana, Quentin C.; Sayari, Mohammad; Seifert, Keith A.; Steenkamp, Emma T.; Trollip, Conrad; van der Merwe, Nicolaas A.; van der Nest, Magriet A.

    2015-01-01

    The genomes of Ceratocystis eucalypticola, Chrysoporthe cubensis, Chrysoporthe deuterocubensis, Davidsoniella virescens, Fusarium temperatum, Graphilbum fragrans, Penicillium nordicum and Thielaviopsis musarum are presented in this genome announcement. These seven genomes are from plant pathogens and otherwise economically important fungal species. The genome sizes range from 28 Mb in the case of T. musarum to 45 Mb for Fusarium temperatum. These genomes include the first reports of genomes f...

  16. [Preface for genome editing special issue].

    Gu, Feng; Gao, Caixia

    2017-10-25

    Genome editing technology, as an innovative biotechnology, has been widely used for editing the genome from model organisms, animals, plants and microbes. CRISPR/Cas9-based genome editing technology shows its great value and potential in the dissection of functional genomics, improved breeding and genetic disease treatment. In the present special issue, the principle and application of genome editing techniques has been summarized. The advantages and disadvantages of the current genome editing technology and future prospects would also be highlighted.

  17. Privacy in the Genomic Era.

    Naveed, Muhammad; Ayday, Erman; Clayton, Ellen W; Fellay, Jacques; Gunter, Carl A; Hubaux, Jean-Pierre; Malin, Bradley A; Wang, Xiaofeng

    2015-09-01

    Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical services. While the benefits of the genomics revolution are trumpeted by the biomedical community, the increased availability of such data has major implications for personal privacy; notably because the genome has certain essential features, which include (but are not limited to) (i) an association with traits and certain diseases, (ii) identification capability (e.g., forensics), and (iii) revelation of family relationships. Moreover, direct-to-consumer DNA testing increases the likelihood that genome data will be made available in less regulated environments, such as the Internet and for-profit companies. The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy. While the computer scientists have addressed data privacy for various data types, there has been less attention dedicated to genomic data. Thus, the goal of this paper is to provide a systematization of knowledge for the computer science community. In doing so, we address some of the (sometimes erroneous) beliefs of this field and we report on a survey we conducted about genome data privacy with biomedical specialists. Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these attacks from the perspective of medicine and public policy. This paper concludes with an enumeration of the challenges for genome data privacy and presents a framework to systematize the analysis of threats and the design of countermeasures as the field moves forward.

  18. Privacy in the Genomic Era

    NAVEED, MUHAMMAD; AYDAY, ERMAN; CLAYTON, ELLEN W.; FELLAY, JACQUES; GUNTER, CARL A.; HUBAUX, JEAN-PIERRE; MALIN, BRADLEY A.; WANG, XIAOFENG

    2015-01-01

    Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical services. While the benefits of the genomics revolution are trumpeted by the biomedical community, the increased availability of such data has major implications for personal privacy; notably because the genome has certain essential features, which include (but are not limited to) (i) an association with traits and certain diseases, (ii) identification capability (e.g., forensics), and (iii) revelation of family relationships. Moreover, direct-to-consumer DNA testing increases the likelihood that genome data will be made available in less regulated environments, such as the Internet and for-profit companies. The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy. While the computer scientists have addressed data privacy for various data types, there has been less attention dedicated to genomic data. Thus, the goal of this paper is to provide a systematization of knowledge for the computer science community. In doing so, we address some of the (sometimes erroneous) beliefs of this field and we report on a survey we conducted about genome data privacy with biomedical specialists. Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these attacks from the perspective of medicine and public policy. This paper concludes with an enumeration of the challenges for genome data privacy and presents a framework to systematize the analysis of threats and the design of countermeasures as the field moves forward. PMID:26640318

  19. Genetic control of water use efficiency and leaf carbon isotope discrimination in sunflower (Helianthus annuus L.) subjected to two drought scenarios.

    Adiredjo, Afifuddin Latif; Navaud, Olivier; Muños, Stephane; Langlade, Nicolas B; Lamaze, Thierry; Grieu, Philippe

    2014-01-01

    High water use efficiency (WUE) can be achieved by coordination of biomass accumulation and water consumption. WUE is physiologically and genetically linked to carbon isotope discrimination (CID) in leaves of plants. A population of 148 recombinant inbred lines (RILs) of sunflower derived from a cross between XRQ and PSC8 lines was studied to identify quantitative trait loci (QTL) controlling WUE and CID, and to compare QTL associated with these traits in different drought scenarios. We conducted greenhouse experiments in 2011 and 2012 by using 100 balances which provided a daily measurement of water transpired, and we determined WUE, CID, biomass and cumulative water transpired by plants. Wide phenotypic variability, significant genotypic effects, and significant negative correlations between WUE and CID were observed in both experiments. A total of nine QTL controlling WUE and eight controlling CID were identified across the two experiments. A QTL for phenotypic response controlling WUE and CID was also significantly identified. The QTL for WUE were specific to the drought scenarios, whereas the QTL for CID were independent of the drought scenarios and could be found in all the experiments. Our results showed that the stable genomic regions controlling CID were located on the linkage groups 06 and 13 (LG06 and LG13). Three QTL for CID were co-localized with the QTL for WUE, biomass and cumulative water transpired. We found that CID and WUE are highly correlated and have common genetic control. Interestingly, the genetic control of these traits showed an interaction with the environment (between the two drought scenarios and control conditions). Our results open a way for breeding higher WUE by using CID and marker-assisted approaches and therefore help to maintain the stability of sunflower crop production.

  20. The genomes and comparative genomics of Lactobacillus delbrueckii phages.

    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.

  1. Genomics technologies to study structural variations in the grapevine genome

    Cardone Maria Francesca

    2016-01-01

    Full Text Available Grapevine is one of the most important crop plants in the world. Recently there was great expansion of genomics resources about grapevine genome, thus providing increasing efforts for molecular breeding. Current cultivars display a great level of inter-specific differentiation that needs to be investigated to reach a comprehensive understanding of the genetic basis of phenotypic differences, and to find responsible genes selected by cross breeding programs. While there have been significant advances in resolving the pattern and nature of single nucleotide polymorphisms (SNPs on plant genomes, few data are available on copy number variation (CNV. Furthermore association between structural variations and phenotypes has been described in only a few cases. We combined high throughput biotechnologies and bioinformatics tools, to reveal the first inter-varietal atlas of structural variation (SV for the grapevine genome. We sequenced and compared four table grape cultivars with the Pinot noir inbred line PN40024 genome as the reference. We detected roughly 8% of the grapevine genome affected by genomic variations. Taken into account phenotypic differences existing among the studied varieties we performed comparison of SVs among them and the reference and next we performed an in-depth analysis of gene content of polymorphic regions. This allowed us to identify genes showing differences in copy number as putative functional candidates for important traits in grapevine cultivation.

  2. Marine Bacterial Genomics

    Machado, Henrique

    For decades, terrestrial microorganisms have been used as sources of countless enzymes and chemical compounds that have been produced by pharmaceutical and biotech companies and used by mankind. There is a need for new chemical compounds, including antibiotics,new enzymatic activities and new...... microorganisms to be used as cell factories for production. Therefore exploitation of new microbial niches and use of different strategies is an opportunity to boost discoveries. Even though scientists have started to explore several habitats other than the terrestrial ones, the marine environment stands out...... as a hitherto under-explored niche. This thesis work uses high-throughput sequencing technologies on a collection of marine bacteria established during the Galathea 3 expedition, with the purpose of unraveling new biodiversity and new bioactivities. Several tools were used for genomic analysis in order...

  3. The South Asian genome.

    John C Chambers

    Full Text Available The genetic sequence variation of people from the Indian subcontinent who comprise one-quarter of the world's population, is not well described. We carried out whole genome sequencing of 168 South Asians, along with whole-exome sequencing of 147 South Asians to provide deeper characterisation of coding regions. We identify 12,962,155 autosomal sequence variants, including 2,946,861 new SNPs and 312,738 novel indels. This catalogue of SNPs and indels amongst South Asians provides the first comprehensive map of genetic variation in this major human population, and reveals evidence for selective pressures on genes involved in skin biology, metabolism, infection and immunity. Our results will accelerate the search for the genetic variants underlying susceptibility to disorders such as type-2 diabetes and cardiovascular disease which are highly prevalent amongst South Asians.

  4. Comparative RNA genomics

    Backofen, Rolf; Gorodkin, Jan; Hofacker, Ivo L.

    2018-01-01

    Over the last two decades it has become clear that RNA is much more than just a boring intermediate in protein expression. Ancient RNAs still appear in the core information metabolism and comprise a surprisingly large component in bacterial gene regulation. A common theme with these types of mostly...... small RNAs is their reliance of conserved secondary structures. Large scale sequencing projects, on the other hand, have profoundly changed our understanding of eukaryotic genomes. Pervasively transcribed, they give rise to a plethora of large and evolutionarily extremely flexible noncoding RNAs...... that exert a vastly diverse array of molecule functions. In this chapter we provide a—necessarily incomplete—overview of the current state of comparative analysis of noncoding RNAs, emphasizing computational approaches as a means to gain a global picture of the modern RNA world....

  5. Materials Genome Initiative

    Vickers, John

    2015-01-01

    The Materials Genome Initiative (MGI) project element is a cross-Center effort that is focused on the integration of computational tools to simulate manufacturing processes and materials behavior. These computational simulations will be utilized to gain understanding of processes and materials behavior to accelerate process development and certification to more efficiently integrate new materials in existing NASA projects and to lead to the design of new materials for improved performance. This NASA effort looks to collaborate with efforts at other government agencies and universities working under the national MGI. MGI plans to develop integrated computational/experimental/ processing methodologies for accelerating discovery and insertion of materials to satisfy NASA's unique mission demands. The challenges include validated design tools that incorporate materials properties, processes, and design requirements; and materials process control to rapidly mature emerging manufacturing methods and develop certified manufacturing processes

  6. Inheritance of the yeast mitochondrial genome

    Piskur, Jure

    1994-01-01

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

  7. Plantagora: modeling whole genome sequencing and assembly of plant genomes.

    Roger Barthelson

    Full Text Available BACKGROUND: Genomics studies are being revolutionized by the next generation sequencing technologies, which have made whole genome sequencing much more accessible to the average researcher. Whole genome sequencing with the new technologies is a developing art that, despite the large volumes of data that can be produced, may still fail to provide a clear and thorough map of a genome. The Plantagora project was conceived to address specifically the gap between having the technical tools for genome sequencing and knowing precisely the best way to use them. METHODOLOGY/PRINCIPAL FINDINGS: For Plantagora, a platform was created for generating simulated reads from several different plant genomes of different sizes. The resulting read files mimicked either 454 or Illumina reads, with varying paired end spacing. Thousands of datasets of reads were created, most derived from our primary model genome, rice chromosome one. All reads were assembled with different software assemblers, including Newbler, Abyss, and SOAPdenovo, and the resulting assemblies were evaluated by an extensive battery of metrics chosen for these studies. The metrics included both statistics of the assembly sequences and fidelity-related measures derived by alignment of the assemblies to the original genome source for the reads. The results were presented in a website, which includes a data graphing tool, all created to help the user compare rapidly the feasibility and effectiveness of different sequencing and assembly strategies prior to testing an approach in the lab. Some of our own conclusions regarding the different strategies were also recorded on the website. CONCLUSIONS/SIGNIFICANCE: Plantagora provides a substantial body of information for comparing different approaches to sequencing a plant genome, and some conclusions regarding some of the specific approaches. Plantagora also provides a platform of metrics and tools for studying the process of sequencing and assembly

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

    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.

  9. 1000 Bull Genomes - Toward genomic Selectionf from whole genome sequence Data in Dairy and Beef Cattle

    Hayes, B.; Daetwyler, H.D.; Fries, R.; Guldbrandtsen, B.; Mogens Sando Lund, M.; Didier A. Boichard, D.A.; Stothard, P.; Veerkamp, R.F.; Hulsegge, B.; Rocha, D.; Tassell, C.; Mullaart, E.; Gredler, B.; Druet, T.; Bagnato, A.; Goddard, M.E.; Chamberlain, H.L.

    2013-01-01

    Genomic prediction of breeding values is now used as the basis for selection of dairy cattle, and in some cases beef cattle, in a number of countries. When genomic prediction was introduced most of the information was to thought to be derived from linkage disequilibrium between markers and causative

  10. Comparing Mycobacterium tuberculosis genomes using genome topology networks.

    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

  11. A universal genomic coordinate translator for comparative genomics.

    Zamani, Neda; Sundström, Görel; Meadows, Jennifer R S; Höppner, Marc P; Dainat, Jacques; Lantz, Henrik; Haas, Brian J; Grabherr, Manfred G

    2014-06-30

    Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences. However, a comprehensive analysis of duplication events and their contributions to evolution would require all-to-all genome alignments, which increases at N2 with the number of available genomes, N. Here, we introduce Kraken, software that omits the all-to-all requirement by recursively traversing a graph of pairwise alignments and dynamically re-computing orthology. Kraken scales linearly with the number of targeted genomes, N, which allows for including large numbers of genomes in analyses. We first evaluated the method on the set of 12 Drosophila genomes, finding that orthologous correspondence computed indirectly through a graph of multiple synteny maps comes at minimal cost in terms of sensitivity, but reduces overall computational runtime by an order of magnitude. We then used the method on three well-annotated mammalian genomes, human, mouse, and rat, and show that up to 93% of protein coding transcripts have unambiguous pairwise orthologous relationships across the genomes. On a nucleotide level, 70 to 83% of exons match exactly at both splice junctions, and up to 97% on at least one junction. We last applied Kraken to an RNA-sequencing dataset from multiple vertebrates and diverse tissues, where we confirmed that brain-specific gene family members, i.e. one-to-many or many-to-many homologs, are more highly correlated across species than single-copy (i.e. one-to-one homologous) genes. Not limited to protein coding genes, Kraken also identifies thousands of newly identified transcribed loci, likely non-coding RNAs that are consistently transcribed in human, chimpanzee and gorilla, and maintain significant correlation of expression levels across

  12. The Perennial Ryegrass GenomeZipper – Targeted Use of Genome Resources for Comparative Grass Genomics

    Pfeiffer, Matthias; Martis, Mihaela; Asp, Torben

    2013-01-01

    (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold......Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass...... to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous...

  13. Components of Adenovirus Genome Packaging

    Ahi, Yadvinder S.; Mittal, Suresh K.

    2016-01-01

    Adenoviruses (AdVs) are icosahedral viruses with double-stranded DNA (dsDNA) genomes. Genome packaging in AdV is thought to be similar to that seen in dsDNA containing icosahedral bacteriophages and herpesviruses. Specific recognition of the AdV genome is mediated by a packaging domain located close to the left end of the viral genome and is mediated by the viral packaging machinery. Our understanding of the role of various components of the viral packaging machinery in AdV genome packaging has greatly advanced in recent years. Characterization of empty capsids assembled in the absence of one or more components involved in packaging, identification of the unique vertex, and demonstration of the role of IVa2, the putative packaging ATPase, in genome packaging have provided compelling evidence that AdVs follow a sequential assembly pathway. This review provides a detailed discussion on the functions of the various viral and cellular factors involved in AdV genome packaging. We conclude by briefly discussing the roles of the empty capsids, assembly intermediates, scaffolding proteins, portal vertex and DNA encapsidating enzymes in AdV assembly and packaging. PMID:27721809

  14. The genome of Eucalyptus grandis

    Myburg, Alexander A.; Grattapaglia, Dario; Tuskan, Gerald A.; Hellsten, Uffe; Hayes, Richard D.; Grimwood, Jane; Jenkins, Jerry; Lindquist, Erika; Tice, Hope; Bauer, Diane; Goodstein, David M.; Dubchak, Inna; Poliakov, Alexandre; Mizrachi, Eshchar; Kullan, Anand R. K.; Hussey, Steven G.; Pinard, Desre; van der Merwe, Karen; Singh, Pooja; van Jaarsveld, Ida; Silva-Junior, Orzenil B.; Togawa, Roberto C.; Pappas, Marilia R.; Faria, Danielle A.; Sansaloni, Carolina P.; Petroli, Cesar D.; Yang, Xiaohan; Ranjan, Priya; Tschaplinski, Timothy J.; Ye, Chu-Yu; Li, Ting; Sterck, Lieven; Vanneste, Kevin; Murat, Florent; Soler, Marçal; Clemente, Hélène San; Saidi, Naijib; Cassan-Wang, Hua; Dunand, Christophe; Hefer, Charles A.; Bornberg-Bauer, Erich; Kersting, Anna R.; Vining, Kelly; Amarasinghe, Vindhya; Ranik, Martin; Naithani, Sushma; Elser, Justin; Boyd, Alexander E.; Liston, Aaron; Spatafora, Joseph W.; Dharmwardhana, Palitha; Raja, Rajani; Sullivan, Christopher; Romanel, Elisson; Alves-Ferreira, Marcio; Külheim, Carsten; Foley, William; Carocha, Victor; Paiva, Jorge; Kudrna, David; Brommonschenkel, Sergio H.; Pasquali, Giancarlo; Byrne, Margaret; Rigault, Philippe; Tibbits, Josquin; Spokevicius, Antanas; Jones, Rebecca C.; Steane, Dorothy A.; Vaillancourt, René E.; Potts, Brad M.; Joubert, Fourie; Barry, Kerrie; Pappas, Georgios J.; Strauss, Steven H.; Jaiswal, Pankaj; Grima-Pettenati, Jacqueline; Salse, Jérôme; Van de Peer, Yves; Rokhsar, Daniel S.; Schmutz, Jeremy

    2014-06-11

    Eucalypts are the world s most widely planted hardwood trees. Their broad adaptability, rich species diversity, fast growth and superior multipurpose wood, have made them a global renewable resource of fiber and energy that mitigates human pressures on natural forests. We sequenced and assembled >94% of the 640 Mbp genome of Eucalyptus grandis into its 11 chromosomes. A set of 36,376 protein coding genes were predicted revealing that 34% occur in tandem duplications, the largest proportion found thus far in any plant genome. Eucalypts also show the highest diversity of genes for plant specialized metabolism that act as chemical defence against biotic agents and provide unique pharmaceutical oils. Resequencing of a set of inbred tree genomes revealed regions of strongly conserved heterozygosity, likely hotspots of inbreeding depression. The resequenced genome of the sister species E. globulus underscored the high inter-specific genome colinearity despite substantial genome size variation in the genus. The genome of E. grandis is the first reference for the early diverging Rosid order Myrtales and is placed here basal to the Eurosids. This resource expands knowledge on the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.

  15. [Genome editing of industrial microorganism].

    Zhu, Linjiang; Li, Qi

    2015-03-01

    Genome editing is defined as highly-effective and precise modification of cellular genome in a large scale. In recent years, such genome-editing methods have been rapidly developed in the field of industrial strain improvement. The quickly-updating methods thoroughly change the old mode of inefficient genetic modification, which is "one modification, one selection marker, and one target site". Highly-effective modification mode in genome editing have been developed including simultaneous modification of multiplex genes, highly-effective insertion, replacement, and deletion of target genes in the genome scale, cut-paste of a large DNA fragment. These new tools for microbial genome editing will certainly be applied widely, and increase the efficiency of industrial strain improvement, and promote the revolution of traditional fermentation industry and rapid development of novel industrial biotechnology like production of biofuel and biomaterial. The technological principle of these genome-editing methods and their applications were summarized in this review, which can benefit engineering and construction of industrial microorganism.

  16. Genome size variation in the genus Avena.

    Yan, Honghai; Martin, Sara L; Bekele, Wubishet A; Latta, Robert G; Diederichsen, Axel; Peng, Yuanying; Tinker, Nicholas A

    2016-03-01

    Genome size is an indicator of evolutionary distance and a metric for genome characterization. Here, we report accurate estimates of genome size in 99 accessions from 26 species of Avena. We demonstrate that the average genome size of C genome diploid species (2C = 10.26 pg) is 15% larger than that of A genome species (2C = 8.95 pg), and that this difference likely accounts for a progression of size among tetraploid species, where AB genome configuration had similar genome sizes (average 2C = 25.74 pg). Genome size was mostly consistent within species and in general agreement with current information about evolutionary distance among species. Results also suggest that most of the polyploid species in Avena have experienced genome downsizing in relation to their diploid progenitors. Genome size measurements could provide additional quality control for species identification in germplasm collections, especially in cases where diploid and polyploid species have similar morphology.

  17. Relocation of a rust resistance gene R 2 and its marker-assisted gene pyramiding in confection sunflower (Helianthus annuus L.).

    Qi, L L; Ma, G J; Long, Y M; Hulke, B S; Gong, L; Markell, S G

    2015-03-01

    The rust resistance gene R 2 was reassigned to linkage group 14 of the sunflower genome. DNA markers linked to R 2 were identified and used for marker-assisted gene pyramiding in a confection type genetic background. Due to the frequent evolution of new pathogen races, sunflower rust is a recurring threat to sunflower production worldwide. The inbred line Morden Cross 29 (MC29) carries the rust resistance gene, R 2 , conferring resistance to numerous races of rust fungus in the US, Canada, and Australia, and can be used as a broad-spectrum resistance resource. Based on phenotypic assessments and SSR marker analyses on the 117 F2 individuals derived from a cross of HA 89 with MC29 (USDA), R 2 was mapped to linkage group (LG) 14 of the sunflower, and not to the previously reported location on LG9. The closest SSR marker HT567 was located at 4.3 cM distal to R 2 . Furthermore, 36 selected SNP markers from LG14 were used to saturate the R 2 region. Two SNP markers, NSA_002316 and SFW01272, flanked R 2 at a genetic distance of 2.8 and 1.8 cM, respectively. Of the three closely linked markers, SFW00211 amplified an allele specific for the presence of R 2 in a marker validation set of 46 breeding lines, and SFW01272 was also shown to be diagnostic for R 2 . These newly developed markers, together with the previously identified markers linked to the gene R 13a , were used to screen 524 F2 individuals from a cross of a confection R 2 line and HA-R6 carrying R 13a . Eleven homozygous double-resistant F2 plants with the gene combination of R 2 and R 13a were obtained. This double-resistant line will be extremely useful in confection sunflower, where few rust R genes are available, risking evolution of new virulence phenotypes and further disease epidemics.

  18. OryzaGenome: Genome Diversity Database of Wild Oryza Species

    Ohyanagi, Hajime; Ebata, Toshinobu; Huang, Xuehui; Gong, Hao; Fujita, Masahiro; Mochizuki, Takako; Toyoda, Atsushi; Fujiyama, Asao; Kaminuma, Eli; Nakamura, Yasukazu; Feng, Qi; Wang, Zi Xuan; Han, Bin; Kurata, Nori

    2015-01-01

    . Portable VCF (variant call format) file or tabdelimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/ scaffolds/contigs and genome-wide variation information for almost all

  19. Genome Modeling System: A Knowledge Management Platform for Genomics.

    Malachi Griffith

    2015-07-01

    Full Text Available In this work, we present the Genome Modeling System (GMS, an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395 and matched lymphoblastoid line (HCC1395BL. These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at https://github.com/genome/gms.

  20. Comparative genomics reveals insights into avian genome evolution and adaptation

    Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M.; Lee, Chul; Storz, Jay F.; Antunes, Agostinho; Greenwold, Matthew J.; Meredith, Robert W.; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R.; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T.; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V.; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S.; Gatesy, John; Hoffmann, Federico G.; Opazo, Juan C.; Håstad, Olle; Sawyer, Roger H.; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W.; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F.; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A.; Green, Richard E.; O’Brien, Stephen J.; Griffin, Darren; Johnson, Warren E.; Haussler, David; Ryder, Oliver A.; Willerslev, Eske; Graves, Gary R.; Alström, Per; Fjeldså, Jon; Mindell, David P.; Edwards, Scott V.; Braun, Edward L.; Rahbek, Carsten; Burt, David W.; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D.; Gilbert, M. Thomas P.; Wang, Jun

    2015-01-01

    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. PMID:25504712

  1. The bonobo genome compared with the chimpanzee and human genomes

    Prüfer, Kay; Munch, Kasper; Hellmann, Ines; Akagi, Keiko; Miller, Jason R.; Walenz, Brian; Koren, Sergey; Sutton, Granger; Kodira, Chinnappa; Winer, Roger; Knight, James R.; Mullikin, James C.; Meader, Stephen J.; Ponting, Chris P.; Lunter, Gerton; Higashino, Saneyuki; Hobolth, Asger; Dutheil, Julien; Karakoç, Emre; Alkan, Can; Sajjadian, Saba; Catacchio, Claudia Rita; Ventura, Mario; Marques-Bonet, Tomas; Eichler, Evan E.; André, Claudine; Atencia, Rebeca; Mugisha, Lawrence; Junhold, Jörg; Patterson, Nick; Siebauer, Michael; Good, Jeffrey M.; Fischer, Anne; Ptak, Susan E.; Lachmann, Michael; Symer, David E.; Mailund, Thomas; Schierup, Mikkel H.; Andrés, Aida M.; Kelso, Janet; Pääbo, Svante

    2012-01-01

    Two African apes are the closest living relatives of humans: the chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus). Although they are similar in many respects, bonobos and chimpanzees differ strikingly in key social and sexual behaviours1–4, and for some of these traits they show more similarity with humans than with each other. Here we report the sequencing and assembly of the bonobo genome to study its evolutionary relationship with the chimpanzee and human genomes. We find that more than three per cent of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. These regions allow various aspects of the ancestry of the two ape species to be reconstructed. In addition, many of the regions that overlap genes may eventually help us understand the genetic basis of phenotypes that humans share with one of the two apes to the exclusion of the other. PMID:22722832

  2. Capturing prokaryotic dark matter genomes.

    Gasc, Cyrielle; Ribière, Céline; Parisot, Nicolas; Beugnot, Réjane; Defois, Clémence; Petit-Biderre, Corinne; Boucher, Delphine; Peyretaillade, Eric; Peyret, Pierre

    2015-12-01

    Prokaryotes are the most diverse and abundant cellular life forms on Earth. Most of them, identified by indirect molecular approaches, belong to microbial dark matter. The advent of metagenomic and single-cell genomic approaches has highlighted the metabolic capabilities of numerous members of this dark matter through genome reconstruction. Thus, linking functions back to the species has revolutionized our understanding of how ecosystem function is sustained by the microbial world. This review will present discoveries acquired through the illumination of prokaryotic dark matter genomes by these innovative approaches. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  3. Human genome. 1993 Program report

    1994-03-01

    The purpose of this report is to update the Human Genome 1991-92 Program Report and provide new information on the DOE genome program to researchers, program managers, other government agencies, and the interested public. This FY 1993 supplement includes abstracts of 60 new or renewed projects and listings of 112 continuing and 28 completed projects. These two reports, taken together, present the most complete published view of the DOE Human Genome Program through FY 1993. Research is progressing rapidly toward 15-year goals of mapping and sequencing the DNA of each of the 24 different human chromosomes.

  4. Implementing Genome-Driven Oncology

    Hyman, David M.; Taylor, Barry S.; Baselga, José

    2017-01-01

    Early successes in identifying and targeting individual oncogenic drivers, together with the increasing feasibility of sequencing tumor genomes, have brought forth the promise of genome-driven oncology care. As we expand the breadth and depth of genomic analyses, the biological and clinical complexity of its implementation will be unparalleled. Challenges include target credentialing and validation, implementing drug combinations, clinical trial designs, targeting tumor heterogeneity, and deploying technologies beyond DNA sequencing, among others. We review how contemporary approaches are tackling these challenges and will ultimately serve as an engine for biological discovery and increase our insight into cancer and its treatment. PMID:28187282

  5. Deep whole-genome sequencing of 90 Han Chinese genomes.

    Lan, Tianming; Lin, Haoxiang; Zhu, Wenjuan; Laurent, Tellier Christian Asker Melchior; Yang, Mengcheng; Liu, Xin; Wang, Jun; Wang, Jian; Yang, Huanming; Xu, Xun; Guo, Xiaosen

    2017-09-01

    Next-generation sequencing provides a high-resolution insight into human genetic information. However, the focus of previous studies has primarily been on low-coverage data due to the high cost of sequencing. Although the 1000 Genomes Project and the Haplotype Reference Consortium have both provided powerful reference panels for imputation, low-frequency and novel variants remain difficult to discover and call with accuracy on the basis of low-coverage data. Deep sequencing provides an optimal solution for the problem of these low-frequency and novel variants. Although whole-exome sequencing is also a viable choice for exome regions, it cannot account for noncoding regions, sometimes resulting in the absence of important, causal variants. For Han Chinese populations, the majority of variants have been discovered based upon low-coverage data from the 1000 Genomes Project. However, high-coverage, whole-genome sequencing data are limited for any population, and a large amount of low-frequency, population-specific variants remain uncharacterized. We have performed whole-genome sequencing at a high depth (∼×80) of 90 unrelated individuals of Chinese ancestry, collected from the 1000 Genomes Project samples, including 45 Northern Han Chinese and 45 Southern Han Chinese samples. Eighty-three of these 90 have been sequenced by the 1000 Genomes Project. We have identified 12 568 804 single nucleotide polymorphisms, 2 074 210 short InDels, and 26 142 structural variations from these 90 samples. Compared to the Han Chinese data from the 1000 Genomes Project, we have found 7 000 629 novel variants with low frequency (defined as minor allele frequency genome. Compared to the 1000 Genomes Project, these Han Chinese deep sequencing data enhance the characterization of a large number of low-frequency, novel variants. This will be a valuable resource for promoting Chinese genetics research and medical development. Additionally, it will provide a valuable supplement to the 1000

  6. Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome

    CRISPR/Cas9 has been recently demonstrated as an effective and popular genome editing tool for modifying genomes of human, animals, microorganisms, and plants. Success of such genome editing is highly dependent on the availability of suitable target sites in the genomes to be edited. Many specific t...

  7. Genomics and the human genome project: implications for psychiatry

    Kelsoe, J R

    2004-01-01

    In the past decade the Human Genome Project has made extraordinary strides in understanding of fundamental human genetics. The complete human genetic sequence has been determined, and the chromosomal location of almost all human genes identified. Presently, a large international consortium, the HapMap Project, is working to identify a large portion of genetic variation in different human populations and the structure and relationship of these variants to each other. The Human Genome Project h...

  8. Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

    Kuo, Alan; Grigoriev, Igor

    2009-04-17

    Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.

  9. Genome projects and the functional-genomic era.

    Sauer, Sascha; Konthur, Zoltán; Lehrach, Hans

    2005-12-01

    The problems we face today in public health as a result of the -- fortunately -- increasing age of people and the requirements of developing countries create an urgent need for new and innovative approaches in medicine and in agronomics. Genomic and functional genomic approaches have a great potential to at least partially solve these problems in the future. Important progress has been made by procedures to decode genomic information of humans, but also of other key organisms. The basic comprehension of genomic information (and its transfer) should now give us the possibility to pursue the next important step in life science eventually leading to a basic understanding of biological information flow; the elucidation of the function of all genes and correlative products encoded in the genome, as well as the discovery of their interactions in a molecular context and the response to environmental factors. As a result of the sequencing projects, we are now able to ask important questions about sequence variation and can start to comprehensively study the function of expressed genes on different levels such as RNA, protein or the cell in a systematic context including underlying networks. In this article we review and comment on current trends in large-scale systematic biological research. A particular emphasis is put on technology developments that can provide means to accomplish the tasks of future lines of functional genomics.

  10. The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly

    J. W. Clouse

    2016-03-01

    Full Text Available Amaranth ( L. is an emerging pseudocereal native to the New World that has garnered increased attention in recent years because of its nutritional quality, in particular its seed protein and more specifically its high levels of the essential amino acid lysine. It belongs to the Amaranthaceae family, is an ancient paleopolyploid that shows disomic inheritance (2 = 32, and has an estimated genome size of 466 Mb. Here we present a high-quality draft genome sequence of the grain amaranth. The genome assembly consisted of 377 Mb in 3518 scaffolds with an N of 371 kb. Repetitive element analysis predicted that 48% of the genome is comprised of repeat sequences, of which -like elements were the most commonly classified retrotransposon. A de novo transcriptome consisting of 66,370 contigs was assembled from eight different amaranth tissue and abiotic stress libraries. Annotation of the genome identified 23,059 protein-coding genes. Seven grain amaranths (, , and and their putative progenitor ( were resequenced. A single nucleotide polymorphism (SNP phylogeny supported the classification of as the progenitor species of the grain amaranths. Lastly, we generated a de novo physical map for using the BioNano Genomics’ Genome Mapping platform. The physical map spanned 340 Mb and a hybrid assembly using the BioNano physical maps nearly doubled the N of the assembly to 697 kb. Moreover, we analyzed synteny between amaranth and sugar beet ( L. and estimated, using analysis, the age of the most recent polyploidization event in amaranth.

  11. Whole genome sequencing and bioinformatics analysis of two Egyptian genomes.

    ElHefnawi, Mahmoud; Jeon, Sungwon; Bhak, Youngjune; ElFiky, Asmaa; Horaiz, Ahmed; Jun, JeHoon; Kim, Hyunho; Bhak, Jong

    2018-05-15

    We report two Egyptian male genomes (EGP1 and EGP2) sequenced at ~ 30× sequencing depths. EGP1 had 4.7 million variants, where 198,877 were novel variants while EGP2 had 209,109 novel variants out of 4.8 million variants. The mitochondrial haplogroup of the two individuals were identified to be H7b1 and L2a1c, respectively. We also identified the Y haplogroup of EGP1 (R1b) and EGP2 (J1a2a1a2 > P58 > FGC11). EGP1 had a mutation in the NADH gene of the mitochondrial genome ND4 (m.11778 G > A) that causes Leber's hereditary optic neuropathy. Some SNPs shared by the two genomes were associated with an increased level of cholesterol and triglycerides, probably related with Egyptians obesity. Comparison of these genomes with African and Western-Asian genomes can provide insights on Egyptian ancestry and genetic history. This resource can be used to further understand genomic diversity and functional classification of variants as well as human migration and evolution across Africa and Western-Asia. Copyright © 2017. Published by Elsevier B.V.

  12. Comparative genomic hybridization.

    Pinkel, Daniel; Albertson, Donna G

    2005-01-01

    Altering DNA copy number is one of the many ways that gene expression and function may be modified. Some variations are found among normal individuals ( 14, 35, 103 ), others occur in the course of normal processes in some species ( 33 ), and still others participate in causing various disease states. For example, many defects in human development are due to gains and losses of chromosomes and chromosomal segments that occur prior to or shortly after fertilization, whereas DNA dosage alterations that occur in somatic cells are frequent contributors to cancer. Detecting these aberrations, and interpreting them within the context of broader knowledge, facilitates identification of critical genes and pathways involved in biological processes and diseases, and provides clinically relevant information. Over the past several years array comparative genomic hybridization (array CGH) has demonstrated its value for analyzing DNA copy number variations. In this review we discuss the state of the art of array CGH and its applications in medical genetics and cancer, emphasizing general concepts rather than specific results.

  13. Functional Genomics Group. Program Description

    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...

  14. Genomic Resources for Cancer Epidemiology

    This page provides links to research resources, complied by the Epidemiology and Genomics Research Program, that may be of interest to genetic epidemiologists conducting cancer research, but is not exhaustive.

  15. Fungal genomics beyond Saccharomyces cerevisiae?

    Hofmann, Gerald; Mcintyre, Mhairi; Nielsen, Jens

    2003-01-01

    Fungi are used extensively in both fundamental research and industrial applications. Saccharomyces cerevisiae has been the model organism for fungal research for many years, particularly in functional genomics. However, considering the diversity within the fungal kingdom, it is obvious...

  16. Genome engineering in human cells.

    Song, Minjung; Kim, Young-Hoon; Kim, Jin-Soo; Kim, Hyongbum

    2014-01-01

    Genome editing in human cells is of great value in research, medicine, and biotechnology. Programmable nucleases including zinc-finger nucleases, transcription activator-like effector nucleases, and RNA-guided engineered nucleases recognize a specific target sequence and make a double-strand break at that site, which can result in gene disruption, gene insertion, gene correction, or chromosomal rearrangements. The target sequence complexities of these programmable nucleases are higher than 3.2 mega base pairs, the size of the haploid human genome. Here, we briefly introduce the structure of the human genome and the characteristics of each programmable nuclease, and review their applications in human cells including pluripotent stem cells. In addition, we discuss various delivery methods for nucleases, programmable nickases, and enrichment of gene-edited human cells, all of which facilitate efficient and precise genome editing in human cells.

  17. [Advances in microbial genome reduction and modification].

    Wang, Jianli; Wang, Xiaoyuan

    2013-08-01

    Microbial genome reduction and modification are important strategies for constructing cellular chassis used for synthetic biology. This article summarized the essential genes and the methods to identify them in microorganisms, compared various strategies for microbial genome reduction, and analyzed the characteristics of some microorganisms with the minimized genome. This review shows the important role of genome reduction in constructing cellular chassis.

  18. 2004 Structural, Function and Evolutionary Genomics

    Douglas L. Brutlag Nancy Ryan Gray

    2005-03-23

    This Gordon conference will cover the areas of structural, functional and evolutionary genomics. It will take a systematic approach to genomics, examining the evolution of proteins, protein functional sites, protein-protein interactions, regulatory networks, and metabolic networks. Emphasis will be placed on what we can learn from comparative genomics and entire genomes and proteomes.

  19. Draft Genome Sequence of Lactobacillus rhamnosus 2166.

    Karlyshev, Andrey V.; Melnikov, Vyacheslav G.; Kosarev, Igor V.; Abramov, Vyacheslav M.

    2014-01-01

    In this report, we present a draft sequence of the genome of Lactobacillus rhamnosus strain 2166, a potential novel probiotic. Genome annotation and read mapping onto a reference genome of L. rhamnosus strain GG allowed for the identification of the differences and similarities in the genomic contents and gene arrangements of these strains.

  20. Genomic instability and radiation effects

    Christian Streffer

    2007-01-01

    Complete text of publication follows. Cancer, genetic mutations and developmental abnormalities are apparently associated with an increased genomic instability. Such phenomena have been frequently shown in human cancer cells in vitro and in situ. It is also well-known that individuals with a genetic predisposition for cancer proneness, such as ataxia telangiectesia, Fanconi anaemia etc. demonstrate a general high genomic instability e.g. in peripheral lymphocytes before a cancer has developed. Analogous data have been found in mice which develop a specific congenital malformation which has a genetic background. Under these aspects it is of high interest that ionising radiation can increase the genomic instability of mammalian cells after exposures in vitro an in vivo. This phenomenon is expressed 20 to 40 cell cycles after the exposure e.g. by de novo chromosomal aberrations. Such effects have been observed with high and low LET radiation, high LET radiation is more efficient. With low LET radiation a good dose response is observed in the dose range 0.2 to 2.0 Gy, Recently it has been reported that senescence and genomic instability was induced in human fibroblasts after 1 mGy carbon ions (1 in 18 cells are hit), apparently bystander effects also occurred under these conditions. The instability has been shown with DNA damage, chromosomal aberrations, gene mutation and cell death. It is also transferred to the next generation of mice with respect to gene mutations, chromosomal aberrations and congenital malformations. Several mechanisms have been discussed. The involvement of telomeres has gained interest. Genomic instability seems to be induced by a general lesion to the whole genome. The transmission of one chromosome from an irradiated cell to an non-irradiated cell leads to genomic instability in the untreated cells. Genomic instability increases mutation rates in the affected cells in general. As radiation late effects (cancer, gene mutations and congenital

  1. Genomic diversity of Lactobacillus salivarius

    Raftis, Emma J.

    2015-01-01

    Lactobacillus salivarius is unusual among the lactobacilli due to its multireplicon genome architecture. The circular megaplasmids harboured by L. salivarius strains encode strain-specific traits for intestinal survival and probiotic activity. L. salivarius strains are increasingly being exploited for their probiotic properties in humans and animals. In terms of probiotic strain selection, it is important to have an understanding of the level of genomic diversity present in this species. Comp...

  2. Population Genomics of Paramecium Species.

    Johri, Parul; Krenek, Sascha; Marinov, Georgi K; Doak, Thomas G; Berendonk, Thomas U; Lynch, Michael

    2017-05-01

    Population-genomic analyses are essential to understanding factors shaping genomic variation and lineage-specific sequence constraints. The dearth of such analyses for unicellular eukaryotes prompted us to assess genomic variation in Paramecium, one of the most well-studied ciliate genera. The Paramecium aurelia complex consists of ∼15 morphologically indistinguishable species that diverged subsequent to two rounds of whole-genome duplications (WGDs, as long as 320 MYA) and possess extremely streamlined genomes. We examine patterns of both nuclear and mitochondrial polymorphism, by sequencing whole genomes of 10-13 worldwide isolates of each of three species belonging to the P. aurelia complex: P. tetraurelia, P. biaurelia, P. sexaurelia, as well as two outgroup species that do not share the WGDs: P. caudatum and P. multimicronucleatum. An apparent absence of global geographic population structure suggests continuous or recent dispersal of Paramecium over long distances. Intergenic regions are highly constrained relative to coding sequences, especially in P. caudatum and P. multimicronucleatum that have shorter intergenic distances. Sequence diversity and divergence are reduced up to ∼100-150 bp both upstream and downstream of genes, suggesting strong constraints imposed by the presence of densely packed regulatory modules. In addition, comparison of sequence variation at non-synonymous and synonymous sites suggests similar recent selective pressures on paralogs within and orthologs across the deeply diverging species. This study presents the first genome-wide population-genomic analysis in ciliates and provides a valuable resource for future studies in evolutionary and functional genetics in Paramecium. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  3. Reconstructing ancient genomes and epigenomes

    Orlando, Ludovic Antoine Alexandre; Gilbert, M. Thomas P.; Willerslev, Eske

    2015-01-01

    DNA studies have now progressed to whole-genome sequencing for an increasing number of ancient individuals and extinct species, as well as to epigenomic characterization. Such advances have enabled the sequencing of specimens of up to 1 million years old, which, owing to their extensive DNA damage...... and contamination, were previously not amenable to genetic analyses. In this Review, we discuss these varied technical challenges and solutions for sequencing ancient genomes and epigenomes....

  4. GOBASE: an organelle genome database

    O?Brien, Emmet A.; Zhang, Yue; Wang, Eric; Marie, Veronique; Badejoko, Wole; Lang, B. Franz; Burger, Gertraud

    2008-01-01

    The organelle genome database GOBASE, now in its 21st release (June 2008), contains all published mitochondrion-encoded sequences (?913 000) and chloroplast-encoded sequences (?250 000) from a wide range of eukaryotic taxa. For all sequences, information on related genes, exons, introns, gene products and taxonomy is available, as well as selected genome maps and RNA secondary structures. Recent major enhancements to database functionality include: (i) addition of an interface for RNA editing...

  5. The fishes of Genome 10K

    Bernardi, Giacomo

    2012-09-01

    The Genome 10K project aims to sequence the genomes of 10,000 vertebrates, representing approximately one genome for each vertebrate genus. Since fishes (cartilaginous fishes, ray-finned fishes and lobe-finned fishes) represent more than 50% of extant vertebrates, it is planned to target 4,000 fish genomes. At present, nearly 60 fish genomes are being sequenced at various public funded labs, and under a Genome 10K and BGI pilot project. An additional 100 fishes have been identified for sequencing in the next phase of Genome 10K project. © 2012 Elsevier B.V.

  6. The integrated microbial genome resource of analysis.

    Checcucci, Alice; Mengoni, Alessio

    2015-01-01

    Integrated Microbial Genomes and Metagenomes (IMG) is a biocomputational system that allows to provide information and support for annotation and comparative analysis of microbial genomes and metagenomes. IMG has been developed by the US Department of Energy (DOE)-Joint Genome Institute (JGI). IMG platform contains both draft and complete genomes, sequenced by Joint Genome Institute and other public and available genomes. Genomes of strains belonging to Archaea, Bacteria, and Eukarya domains are present as well as those of viruses and plasmids. Here, we provide some essential features of IMG system and case study for pangenome analysis.

  7. The fishes of Genome 10K

    Bernardi, Giacomo; Wiley, Edward O.; Mansour, Hicham; Miller, Michael R.; Ortí , Guillermo; Haussler, David H.; O'Brien, Stephen J O; Ryder, Oliver A.; Venkatesh, Byrappa

    2012-01-01

    The Genome 10K project aims to sequence the genomes of 10,000 vertebrates, representing approximately one genome for each vertebrate genus. Since fishes (cartilaginous fishes, ray-finned fishes and lobe-finned fishes) represent more than 50% of extant vertebrates, it is planned to target 4,000 fish genomes. At present, nearly 60 fish genomes are being sequenced at various public funded labs, and under a Genome 10K and BGI pilot project. An additional 100 fishes have been identified for sequencing in the next phase of Genome 10K project. © 2012 Elsevier B.V.

  8. The dynamic genome of Hydra

    Chapman, Jarrod A.; Kirkness, Ewen F.; Simakov, Oleg; Hampson, Steven E.; Mitros, Therese; Weinmaier, Therese; Rattei, Thomas; Balasubramanian, Prakash G.; Borman, Jon; Busam, Dana; Disbennett, Kathryn; Pfannkoch, Cynthia; Sumin, Nadezhda; Sutton, Granger G.; Viswanathan, Lakshmi Devi; Walenz, Brian; Goodstein, David M.; Hellsten, Uffe; Kawashima, Takeshi; Prochnik, Simon E.; Putnam, Nicholas H.; Shu, Shengquiang; Blumberg, Bruce; Dana, Catherine E.; Gee, Lydia; Kibler, Dennis F.; Law, Lee; Lindgens, Dirk; Martinez, Daniel E.; Peng, Jisong; Wigge, Philip A.; Bertulat, Bianca; Guder, Corina; Nakamura, Yukio; Ozbek, Suat; Watanabe, Hiroshi; Khalturin, Konstantin; Hemmrich, Georg; Franke, André; Augustin, René; Fraune, Sebastian; Hayakawa, Eisuke; Hayakawa, Shiho; Hirose, Mamiko; Hwang, Jung Shan; Ikeo, Kazuho; Nishimiya-Fujisawa, Chiemi; Ogura, Atshushi; Takahashi, Toshio; Steinmetz, Patrick R. H.; Zhang, Xiaoming; Aufschnaiter, Roland; Eder, Marie-Kristin; Gorny, Anne-Kathrin; Salvenmoser, Willi; Heimberg, Alysha M.; Wheeler, Benjamin M.; Peterson, Kevin J.; Böttger, Angelika; Tischler, Patrick; Wolf, Alexander; Gojobori, Takashi; Remington, Karin A.; Strausberg, Robert L.; Venter, J. Craig; Technau, Ulrich; Hobmayer, Bert; Bosch, Thomas C. G.; Holstein, Thomas W.; Fujisawa, Toshitaka; Bode, Hans R.; David, Charles N.; Rokhsar, Daniel S.; Steele, Robert E.

    2015-01-01

    The freshwater cnidarian Hydra was first described in 17021 and has been the object of study for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery of asexual reproduction of an animal by budding, the first description of regeneration in an animal, and successful transplantation of tissue between animals2. Today, Hydra is an important model for studies of axial patterning3, stem cell biology4 and regeneration5. Here we report the genome of Hydra magnipapillata and compare it to the genomes of the anthozoan Nematostella vectensis6 and other animals. The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle. We also report the sequence of the genome of a novel bacterium stably associated with H. magnipapillata. Comparisons of the Hydra genome to the genomes of other animals shed light on the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, the Spemann–Mangold organizer, pluripotency genes and the neuromuscular junction. PMID:20228792

  9. Universal pacemaker of genome evolution.

    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.

  10. A Genome-Wide Landscape of Retrocopies in Primate Genomes.

    Navarro, Fábio C P; Galante, Pedro A F

    2015-07-29

    Gene duplication is a key factor contributing to phenotype diversity across and within species. Although the availability of complete genomes has led to the extensive study of genomic duplications, the dynamics and variability of gene duplications mediated by retrotransposition are not well understood. Here, we predict mRNA retrotransposition and use comparative genomics to investigate their origin and variability across primates. Analyzing seven anthropoid primate genomes, we found a similar number of mRNA retrotranspositions (∼7,500 retrocopies) in Catarrhini (Old Word Monkeys, including humans), but a surprising large number of retrocopies (∼10,000) in Platyrrhini (New World Monkeys), which may be a by-product of higher long interspersed nuclear element 1 activity in these genomes. By inferring retrocopy orthology, we dated most of the primate retrocopy origins, and estimated a decrease in the fixation rate in recent primate history, implying a smaller number of species-specific retrocopies. Moreover, using RNA-Seq data, we identified approximately 3,600 expressed retrocopies. As expected, most of these retrocopies are located near or within known genes, present tissue-specific and even species-specific expression patterns, and no expression correlation to their parental genes. Taken together, our results provide further evidence that mRNA retrotransposition is an active mechanism in primate evolution and suggest that retrocopies may not only introduce great genetic variability between lineages but also create a large reservoir of potentially functional new genomic loci in primate genomes. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  11. HGVA: the Human Genome Variation Archive

    Lopez, Javier; Coll, Jacobo; Haimel, Matthias; Kandasamy, Swaathi; Tarraga, Joaquin; Furio-Tari, Pedro; Bari, Wasim; Bleda, Marta; Rueda, Antonio; Gr?f, Stefan; Rendon, Augusto; Dopazo, Joaquin; Medina, Ignacio

    2017-01-01

    Abstract High-profile genomic variation projects like the 1000 Genomes project or the Exome Aggregation Consortium, are generating a wealth of human genomic variation knowledge which can be used as an essential reference for identifying disease-causing genotypes. However, accessing these data, contrasting the various studies and integrating those data in downstream analyses remains cumbersome. The Human Genome Variation Archive (HGVA) tackles these challenges and facilitates access to genomic...

  12. The Genomic Code: Genome Evolution and Potential Applications

    Bernardi, Giorgio

    2016-01-25

    The genome of metazoans is organized according to a genomic code which comprises three laws: 1) Compositional correlations hold between contiguous coding and non-coding sequences, as well as among the three codon positions of protein-coding genes; these correlations are the consequence of the fact that the genomes under consideration consist of fairly homogeneous, long (≥200Kb) sequences, the isochores; 2) Although isochores are defined on the basis of purely compositional properties, GC levels of isochores are correlated with all tested structural and functional properties of the genome; 3) GC levels of isochores are correlated with chromosome architecture from interphase to metaphase; in the case of interphase the correlation concerns isochores and the three-dimensional “topological associated domains” (TADs); in the case of mitotic chromosomes, the correlation concerns isochores and chromosomal bands. Finally, the genomic code is the fourth and last pillar of molecular biology, the first three pillars being 1) the double helix structure of DNA; 2) the regulation of gene expression in prokaryotes; and 3) the genetic code.

  13. Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome

    Sharp, Andrew J.; Hansen, Sierra; Selzer, Rebecca R.; Cheng, Ze; Regan, Regina; Hurst, Jane A.; Stewart, Helen; Price, Sue M.; Blair, Edward; Hennekam, Raoul C.; Fitzpatrick, Carrie A.; Segraves, Rick; Richmond, Todd A.; Guiver, Cheryl; Albertson, Donna G.; Pinkel, Daniel; Eis, Peggy S.; Schwartz, Stuart; Knight, Samantha J. L.; Eichler, Evan E.

    2006-01-01

    Genomic disorders are characterized by the presence of flanking segmental duplications that predispose these regions to recurrent rearrangement. Based on the duplication architecture of the genome, we investigated 130 regions that we hypothesized as candidates for previously undescribed genomic

  14. Supplementary Material for: Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates

    Black, PA; Vos, M. de; Louw, GE; Merwe, RG van der; Dippenaar, A.; Streicher, EM; Abdallah, AM; Sampson, SL; Victor, TC; Dolby, T.; Simpson, JA; Helden, PD van; Warren, RM; Pain, Arnab

    2015-01-01

    Abstract Background Whole genome sequencing has revolutionised the interrogation of mycobacterial genomes. Recent studies have reported conflicting findings on the genomic stability of Mycobacterium tuberculosis during the evolution of drug

  15. Réponse de deux variétés de tournesol (Helianthus sp. à la fertilisation à base de fiente de poule sur un Hapli-Humic Ferralsol du Yongka Western Highlands Research Garden Park (YWHRGP Nkwen-Bamenda, Cameroun, Afrique centrale

    Yerima, BPK.

    2014-01-01

    Full Text Available Response of Two Sunflower (Helianthus sp. Varieties to Poultry Manure Fertilization on a Hapli-Humic Ferralsol at the Yongka Western Highlands Research Garden-Park (YWHRGP Nkwen-Bamenda, Cameroon, Central Africa. An experiment on a Hapli-Humic Ferralsol was conducted at the YWHRGP, Nkwen-Bamenda, to evaluate the response of two sunflower varieties (Helianthus sp. to five levels of poultry manure (0; 1.2; 2.8; 4.2 and 5.6 Tons/ha. Italian White and African Giant varieties were used. The experiment was laid out in a randomized complete block design with three and six replications for African Giant and Italian White varieties, respectively. Poultry manure was analyzed and growth, development and yield parameters were collected. The acid soil (pH≤5.5 showed nutrient deficiencies. The poultry manure (pH=7.8 is rich in essential nutrients and had a significant effect on sunflower growth parameters. The 4.2 Tons/ha manure level maximised growth and yield parameters of the African Giant variety. For the Italian White variety, 5.6 Tons/ha manure level gave a head weight yield (0.74 Tons/ha lower than that of the African Giant (1.33 Tons/ha. Significant differences were also observed between the two varieties. However, the African Giant variety appears to be more adapted for seed production, while the Italian White variety appears to be best indicated for use as an ornamental plant or to produce cut flowers.

  16. Human Genome Education Program

    Richard Myers; Lane Conn

    2000-05-01

    The funds from the DOE Human Genome Program, for the project period 2/1/96 through 1/31/98, have provided major support for the curriculum development and field testing efforts for two high school level instructional units: Unit 1, ''Exploring Genetic Conditions: Genes, Culture and Choices''; and Unit 2, ''DNA Snapshots: Peaking at Your DNA''. In the original proposal, they requested DOE support for the partial salary and benefits of a Field Test Coordinator position to: (1) complete the field testing and revision of two high school curriculum units, and (2) initiate the education of teachers using these units. During the project period of this two-year DOE grant, a part-time Field-Test Coordinator was hired (Ms. Geraldine Horsma) and significant progress has been made in both of the original proposal objectives. Field testing for Unit 1 has occurred in over 12 schools (local and non-local sites with diverse student populations). Field testing for Unit 2 has occurred in over 15 schools (local and non-local sites) and will continue in 12-15 schools during the 96-97 school year. For both curricula, field-test sites and site teachers were selected for their interest in genetics education and in hands-on science education. Many of the site teachers had no previous experience with HGEP or the unit under development. Both of these first-year biology curriculum units, which contain genetics, biotechnology, societal, ethical and cultural issues related to HGP, are being implemented in many local and non-local schools (SF Bay Area, Southern California, Nebraska, Hawaii, and Texas) and in programs for teachers. These units will reach over 10,000 students in the SF Bay Area and continues to receive support from local corporate and private philanthropic organizations. Although HGEP unit development is nearing completion for both units, data is still being gathered and analyzed on unit effectiveness and student learning. The final field

  17. Allele coding in genomic evaluation

    Christensen Ole F

    2011-06-01

    Full Text Available Abstract Background Genomic data are used in animal breeding to assist genetic evaluation. Several models to estimate genomic breeding values have been studied. In general, two approaches have been used. One approach estimates the marker effects first and then, genomic breeding values are obtained by summing marker effects. In the second approach, genomic breeding values are estimated directly using an equivalent model with a genomic relationship matrix. Allele coding is the method chosen to assign values to the regression coefficients in the statistical model. A common allele coding is zero for the homozygous genotype of the first allele, one for the heterozygote, and two for the homozygous genotype for the other allele. Another common allele coding changes these regression coefficients by subtracting a value from each marker such that the mean of regression coefficients is zero within each marker. We call this centered allele coding. This study considered effects of different allele coding methods on inference. Both marker-based and equivalent models were considered, and restricted maximum likelihood and Bayesian methods were used in inference. Results Theoretical derivations showed that parameter estimates and estimated marker effects in marker-based models are the same irrespective of the allele coding, provided that the model has a fixed general mean. For the equivalent models, the same results hold, even though different allele coding methods lead to different genomic relationship matrices. Calculated genomic breeding values are independent of allele coding when the estimate of the general mean is included into the values. Reliabilities of estimated genomic breeding values calculated using elements of the inverse of the coefficient matrix depend on the allele coding because different allele coding methods imply different models. Finally, allele coding affects the mixing of Markov chain Monte Carlo algorithms, with the centered coding being

  18. Genomic selection in maritime pine.

    Isik, Fikret; Bartholomé, Jérôme; Farjat, Alfredo; Chancerel, Emilie; Raffin, Annie; Sanchez, Leopoldo; Plomion, Christophe; Bouffier, Laurent

    2016-01-01

    A two-generation maritime pine (Pinus pinaster Ait.) breeding population (n=661) was genotyped using 2500 SNP markers. The extent of linkage disequilibrium and utility of genomic selection for growth and stem straightness improvement were investigated. The overall intra-chromosomal linkage disequilibrium was r(2)=0.01. Linkage disequilibrium corrected for genomic relationships derived from markers was smaller (rV(2)=0.006). Genomic BLUP, Bayesian ridge regression and Bayesian LASSO regression statistical models were used to obtain genomic estimated breeding values. Two validation methods (random sampling 50% of the population and 10% of the progeny generation as validation sets) were used with 100 replications. The average predictive ability across statistical models and validation methods was about 0.49 for stem sweep, and 0.47 and 0.43 for total height and tree diameter, respectively. The sensitivity analysis suggested that prior densities (variance explained by markers) had little or no discernible effect on posterior means (residual variance) in Bayesian prediction models. Sampling from the progeny generation for model validation increased the predictive ability of markers for tree diameter and stem sweep but not for total height. The results are promising despite low linkage disequilibrium and low marker coverage of the genome (∼1.39 markers/cM). Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  19. The genome of Prunus mume.

    Zhang, Qixiang; Chen, Wenbin; Sun, Lidan; Zhao, Fangying; Huang, Bangqing; Yang, Weiru; Tao, Ye; Wang, Jia; Yuan, Zhiqiong; Fan, Guangyi; Xing, Zhen; Han, Changlei; Pan, Huitang; Zhong, Xiao; Shi, Wenfang; Liang, Xinming; Du, Dongliang; Sun, Fengming; Xu, Zongda; Hao, Ruijie; Lv, Tian; Lv, Yingmin; Zheng, Zequn; Sun, Ming; Luo, Le; Cai, Ming; Gao, Yike; Wang, Junyi; Yin, Ye; Xu, Xun; Cheng, Tangren; Wang, Jun

    2012-01-01

    Prunus mume (mei), which was domesticated in China more than 3,000 years ago as ornamental plant and fruit, is one of the first genomes among Prunus subfamilies of Rosaceae been sequenced. Here, we assemble a 280M genome by combining 101-fold next-generation sequencing and optical mapping data. We further anchor 83.9% of scaffolds to eight chromosomes with genetic map constructed by restriction-site-associated DNA sequencing. Combining P. mume genome with available data, we succeed in reconstructing nine ancestral chromosomes of Rosaceae family, as well as depicting chromosome fusion, fission and duplication history in three major subfamilies. We sequence the transcriptome of various tissues and perform genome-wide analysis to reveal the characteristics of P. mume, including its regulation of early blooming in endodormancy, immune response against bacterial infection and biosynthesis of flower scent. The P. mume genome sequence adds to our understanding of Rosaceae evolution and provides important data for improvement of fruit trees.

  20. The genome of Chenopodium quinoa

    Jarvis, David Erwin; Ho, Yung Shwen; Lightfoot, Damien; Schmö ckel, Sandra M.; Li, Bo; Borm, Theo J. A.; Ohyanagi, Hajime; Mineta, Katsuhiko; Michell, Craig; Saber, Noha; Kharbatia, Najeh M.; Rupper, Ryan R.; Sharp, Aaron R.; Dally, Nadine; Boughton, Berin A.; Woo, Yong; Gao, Ge; Schijlen, Elio G. W. M.; Guo, Xiujie; Momin, Afaque Ahmad Imtiyaz; Negrã o, Só nia; Al-Babili, Salim; Gehring, Christoph A; Roessner, Ute; Jung, Christian; Murphy, Kevin; Arold, Stefan T.; Gojobori, Takashi; Linden, C. Gerard van der; Loo, Eibertus N. van; Jellen, Eric N.; Maughan, Peter J.; Tester, Mark A.

    2017-01-01

    Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.

  1. The genome of Chenopodium quinoa

    Jarvis, David Erwin

    2017-02-08

    Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.

  2. The genome of Chenopodium quinoa.

    Jarvis, David E; Ho, Yung Shwen; Lightfoot, Damien J; Schmöckel, Sandra M; Li, Bo; Borm, Theo J A; Ohyanagi, Hajime; Mineta, Katsuhiko; Michell, Craig T; Saber, Noha; Kharbatia, Najeh M; Rupper, Ryan R; Sharp, Aaron R; Dally, Nadine; Boughton, Berin A; Woo, Yong H; Gao, Ge; Schijlen, Elio G W M; Guo, Xiujie; Momin, Afaque A; Negrão, Sónia; Al-Babili, Salim; Gehring, Christoph; Roessner, Ute; Jung, Christian; Murphy, Kevin; Arold, Stefan T; Gojobori, Takashi; Linden, C Gerard van der; van Loo, Eibertus N; Jellen, Eric N; Maughan, Peter J; Tester, Mark

    2017-02-16

    Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.

  3. Genomics of Arctic cod

    Wilson, Robert E.; Sage, George K.; Sonsthagen, Sarah A.; Gravley, Megan C.; Menning, Damian; Talbot, Sandra L.

    2017-01-01

    The Arctic cod (Boreogadus saida) is an abundant marine fish that plays a vital role in the marine food web. To better understand the population genetic structure and the role of natural selection acting on the maternally-inherited mitochondrial genome (mitogenome), a molecule often associated with adaptations to temperature, we analyzed genetic data collected from 11 biparentally-inherited nuclear microsatellite DNA loci and nucleotide sequence data from from the mitochondrial DNA (mtDNA) cytochrome b (cytb) gene and, for a subset of individuals, the entire mitogenome. In addition, due to potential of species misidentification with morphologically similar Polar cod (Arctogadus glacialis), we used ddRAD-Seq data to determine the level of divergence between species and identify species-specific markers. Based on the findings presented here, Arctic cod across the Pacific Arctic (Bering, Chukchi, and Beaufort Seas) comprise a single panmictic population with high genetic diversity compared to other gadids. High genetic diversity was indicated across all 13 protein-coding genes in the mitogenome. In addition, we found moderate levels of genetic diversity in the nuclear microsatellite loci, with highest diversity found in the Chukchi Sea. Our analyses of markers from both marker classes (nuclear microsatellite fragment data and mtDNA cytb sequence data) failed to uncover a signal of microgeographic genetic structure within Arctic cod across the three regions, within the Alaskan Beaufort Sea, or between near-shore or offshore habitats. Further, data from a subset of mitogenomes revealed no genetic differentiation between Bering, Chukchi, and Beaufort seas populations for Arctic cod, Saffron cod (Eleginus gracilis), or Walleye pollock (Gadus chalcogrammus). However, we uncovered significant differences in the distribution of microsatellite alleles between the southern Chukchi and central and eastern Beaufort Sea samples of Arctic cod. Finally, using ddRAD-Seq data, we

  4. The Pediatric Cancer Genome Project

    Downing, James R; Wilson, Richard K; Zhang, Jinghui; Mardis, Elaine R; Pui, Ching-Hon; Ding, Li; Ley, Timothy J; Evans, William E

    2013-01-01

    The St. Jude Children’s Research Hospital–Washington University Pediatric Cancer Genome Project (PCGP) is participating in the international effort to identify somatic mutations that drive cancer. These cancer genome sequencing efforts will not only yield an unparalleled view of the altered signaling pathways in cancer but should also identify new targets against which novel therapeutics can be developed. Although these projects are still deep in the phase of generating primary DNA sequence data, important results are emerging and valuable community resources are being generated that should catalyze future cancer research. We describe here the rationale for conducting the PCGP, present some of the early results of this project and discuss the major lessons learned and how these will affect the application of genomic sequencing in the clinic. PMID:22641210

  5. Integrating genomics into evolutionary medicine.

    Rodríguez, Juan Antonio; Marigorta, Urko M; Navarro, Arcadi

    2014-12-01

    The application of the principles of evolutionary biology into medicine was suggested long ago and is already providing insight into the ultimate causes of disease. However, a full systematic integration of medical genomics and evolutionary medicine is still missing. Here, we briefly review some cases where the combination of the two fields has proven profitable and highlight two of the main issues hindering the development of evolutionary genomic medicine as a mature field, namely the dissociation between fitness and health and the still considerable difficulties in predicting phenotypes from genotypes. We use publicly available data to illustrate both problems and conclude that new approaches are needed for evolutionary genomic medicine to overcome these obstacles. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. Enhancer Identification through Comparative Genomics

    Visel, Axel; Bristow, James; Pennacchio, Len A.

    2006-10-01

    With the availability of genomic sequence from numerousvertebrates, a paradigm shift has occurred in the identification ofdistant-acting gene regulatory elements. In contrast to traditionalgene-centric studies in which investigators randomly scanned genomicfragments that flank genes of interest in functional assays, the modernapproach begins electronically with publicly available comparativesequence datasets that provide investigators with prioritized lists ofputative functional sequences based on their evolutionary conservation.However, although a large number of tools and resources are nowavailable, application of comparative genomic approaches remains far fromtrivial. In particular, it requires users to dynamically consider thespecies and methods for comparison depending on the specific biologicalquestion under investigation. While there is currently no single generalrule to this end, it is clear that when applied appropriately,comparative genomic approaches exponentially increase our power ingenerating biological hypotheses for subsequent experimentaltesting.

  7. Genomics of Escherichia and Shigella

    Perna, Nicole T.

    The laboratory workhorse Escherichia coli K-12 is among the most intensively studied living organisms on earth, and this single strain serves as the model system behind much of our understanding of prokaryotic molecular biology. Dense genome sequencing and recent insightful comparative analyses are making the species E. coli, as a whole, an emerging system for studying prokaryotic population genetics and the relationship between system-scale, or genome-scale, molecular evolution and complex traits like host range and pathogenic potential. Genomic perspective has revealed a coherent but dynamic species united by intraspecific gene flow via homologous lateral or horizontal transfer and differentiated by content flux mediated by acquisition of DNA segments from interspecies transfers.

  8. Genomic composition factors affect codon usage in porcine genome ...

    ... be explored for designing degenerate primers, necessitate selecting appropriate hosts expression systems to manipulate the expression of target genes in vivo or in vitro and improve the accuracy of gene prediction from genomic sequences thus maximizing the effectiveness of genetic manipulations in synthetic biology.

  9. Multiplexed precision genome editing with trackable genomic barcodes in yeast.

    Roy, Kevin R; Smith, Justin D; Vonesch, Sibylle C; Lin, Gen; Tu, Chelsea Szu; Lederer, Alex R; Chu, Angela; Suresh, Sundari; Nguyen, Michelle; Horecka, Joe; Tripathi, Ashutosh; Burnett, Wallace T; Morgan, Maddison A; Schulz, Julia; Orsley, Kevin M; Wei, Wu; Aiyar, Raeka S; Davis, Ronald W; Bankaitis, Vytas A; Haber, James E; Salit, Marc L; St Onge, Robert P; Steinmetz, Lars M

    2018-07-01

    Our understanding of how genotype controls phenotype is limited by the scale at which we can precisely alter the genome and assess the phenotypic consequences of each perturbation. Here we describe a CRISPR-Cas9-based method for multiplexed accurate genome editing with short, trackable, integrated cellular barcodes (MAGESTIC) in Saccharomyces cerevisiae. MAGESTIC uses array-synthesized guide-donor oligos for plasmid-based high-throughput editing and features genomic barcode integration to prevent plasmid barcode loss and to enable robust phenotyping. We demonstrate that editing efficiency can be increased more than fivefold by recruiting donor DNA to the site of breaks using the LexA-Fkh1p fusion protein. We performed saturation editing of the essential gene SEC14 and identified amino acids critical for chemical inhibition of lipid signaling. We also constructed thousands of natural genetic variants, characterized guide mismatch tolerance at the genome scale, and ascertained that cryptic Pol III termination elements substantially reduce guide efficacy. MAGESTIC will be broadly useful to uncover the genetic basis of phenotypes in yeast.

  10. Genomic composition factors affect codon usage in porcine genome

    j.khobondo

    2015-01-28

    Jan 28, 2015 ... The mutational bias hypothesis predicted that genes in the GC-rich regions of the genome ... observed codon divided by its expected frequency at equilibrium. An RSCU value close to 1 indicates lack of bias, ..... study our results points to preferred usage of both C or G and A or T at the synonyms sites as ...

  11. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

    Bowler, Ch.; Allen, A. E.; Badger, J. H.; Grimwood, J.; Jabbari, K.; Kuo, A.; Maheswari, U.; Martens, C.; Maumus, F.; Otillar, R. P.; Rayko, E.; Salamov, A.; Vandepoele, K.; Beszteri, B.; Gruber, A.; Heijde, M.; Katinka, M.; Mock, T.; Valentin, K.; Verret, F.; Berges, J. A.; Brownlee, C.; Cadoret, J.-P.; Chiovitti, A.; Choi, Ch. J.; Coesel, S.; De Martino, A.; Detter, J. Ch.; Durkin, C.; Falciatore, A.; Fournet, J.; Haruta, M.; Huysman, M. J. J.; Jenkins, B. D.; Jiroutová, Kateřina; Jorgensen, R. E.; Joubert, Y.; Kaplan, A.; Kröger, N.; Kroth, P. G.; La Roche, J.; Lindquist, E.; Lommer, M.; Martin–Jézéquel, V.; Lopez, P. J.; Lucas, S.; Mangogna, M.; McGinnis, K.; Medlin, L. K.; Montsant, A.; Oudot–Le Secq, M.-P.; Napoli, C.; Oborník, Miroslav; Schnitzler Parker, M.; Petit, J.-L.; Porcel, B. M.; Poulsen, N.; Robison, M.; Rychlewski, L.; Rynearson, T. A.; Schmutz, J.; Shapiro, H.; Siaut, M.; Stanley, M.; Sussman, M. R.; Taylor, A. R.; Vardi, A.; von Dassow, P.; Vyverman, W.; Willis, A.; Wyrwicz, L. S.; Rokhsar, D. S.; Weissenbach, J.; Armbrust, E. V.; Green, B. R.; Van de Peer, Y.; Grigoriev, I. V.

    2008-01-01

    Roč. 456, 13-11-2008 (2008), s. 239-244 ISSN 0028-0836 Institutional research plan: CEZ:AV0Z60220518 Keywords : Phaeodactylum * genome * evolution * diatom Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 31.434, year: 2008

  12. Genome Size Dynamics and Evolution in Monocots

    Ilia J. Leitch

    2010-01-01

    Full Text Available Monocot genomic diversity includes striking variation at many levels. This paper compares various genomic characters (e.g., range of chromosome numbers and ploidy levels, occurrence of endopolyploidy, GC content, chromosome packaging and organization, genome size between monocots and the remaining angiosperms to discern just how distinctive monocot genomes are. One of the most notable features of monocots is their wide range and diversity of genome sizes, including the species with the largest genome so far reported in plants. This genomic character is analysed in greater detail, within a phylogenetic context. By surveying available genome size and chromosome data it is apparent that different monocot orders follow distinctive modes of genome size and chromosome evolution. Further insights into genome size-evolution and dynamics were obtained using statistical modelling approaches to reconstruct the ancestral genome size at key nodes across the monocot phylogenetic tree. Such approaches reveal that while the ancestral genome size of all monocots was small (1C=1.9 pg, there have been several major increases and decreases during monocot evolution. In addition, notable increases in the rates of genome size-evolution were found in Asparagales and Poales compared with other monocot lineages.

  13. The Perennial Ryegrass GenomeZipper: Targeted Use of Genome Resources for Comparative Grass Genomics1[C][W

    Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F.X.; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

    2013-01-01

    Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species. PMID:23184232

  14. Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute’s genomic medicine portfolio

    Manolio, Teri A.

    2016-01-01

    Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual’s genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of “Genomic Medicine Meetings,” under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and diffficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI’s genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so. PMID:27612677

  15. The Chlamydomonas genome project: a decade on

    Blaby, Ian K.; Blaby-Haas, Crysten; Tourasse, Nicolas; Hom, Erik F. Y.; Lopez, David; Aksoy, Munevver; Grossman, Arthur; Umen, James; Dutcher, Susan; Porter, Mary; King, Stephen; Witman, George; Stanke, Mario; Harris, Elizabeth H.; Goodstein, David; Grimwood, Jane; Schmutz, Jeremy; Vallon, Olivier; Merchant, Sabeeha S.; Prochnik, Simon

    2014-01-01

    The green alga Chlamydomonas reinhardtii is a popular unicellular organism for studying photosynthesis, cilia biogenesis and micronutrient homeostasis. Ten years since its genome project was initiated, an iterative process of improvements to the genome and gene predictions has propelled this organism to the forefront of the “omics” era. Housed at Phytozome, the Joint Genome Institute’s (JGI) plant genomics portal, the most up-to-date genomic data include a genome arranged on chromosomes and high-quality gene models with alternative splice forms supported by an abundance of RNA-Seq data. Here, we present the past, present and future of Chlamydomonas genomics. Specifically, we detail progress on genome assembly and gene model refinement, discuss resources for gene annotations, functional predictions and locus ID mapping between versions and, importantly, outline a standardized framework for naming genes. PMID:24950814

  16. Big Data Analysis of Human Genome Variations

    Gojobori, Takashi

    2016-01-01

    Since the human genome draft sequence was in public for the first time in 2000, genomic analyses have been intensively extended to the population level. The following three international projects are good examples for large-scale studies of human

  17. V-GAP: Viral genome assembly pipeline

    Nakamura, Yoji

    2015-10-22

    Next-generation sequencing technologies have allowed the rapid determination of the complete genomes of many organisms. Although shotgun sequences from large genome organisms are still difficult to reconstruct perfect contigs each of which represents a full chromosome, those from small genomes have been assembled successfully into a very small number of contigs. In this study, we show that shotgun reads from phage genomes can be reconstructed into a single contig by controlling the number of read sequences used in de novo assembly. We have developed a pipeline to assemble small viral genomes with good reliability using a resampling method from shotgun data. This pipeline, named V-GAP (Viral Genome Assembly Pipeline), will contribute to the rapid genome typing of viruses, which are highly divergent, and thus will meet the increasing need for viral genome comparisons in metagenomic studies.

  18. All about the Human Genome Project (HGP)

    ... Care Genomic Medicine Working Group New Horizons and Research Patient Management Policy and Ethics Issues Quick Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for ...

  19. Hapsembler: An Assembler for Highly Polymorphic Genomes

    Donmez, Nilgun; Brudno, Michael

    As whole genome sequencing has become a routine biological experiment, algorithms for assembly of whole genome shotgun data has become a topic of extensive research, with a plethora of off-the-shelf methods that can reconstruct the genomes of many organisms. Simultaneously, several recently sequenced genomes exhibit very high polymorphism rates. For these organisms genome assembly remains a challenge as most assemblers are unable to handle highly divergent haplotypes in a single individual. In this paper we describe Hapsembler, an assembler for highly polymorphic genomes, which makes use of paired reads. Our experiments show that Hapsembler produces accurate and contiguous assemblies of highly polymorphic genomes, while performing on par with the leading tools on haploid genomes. Hapsembler is available for download at http://compbio.cs.toronto.edu/hapsembler.

  20. Collaborative Genomics Study Advances Precision Oncology

    A collaborative study conducted by two Office of Cancer Genomics (OCG) initiatives highlights the importance of integrating structural and functional genomics programs to improve cancer therapies, and more specifically, contribute to precision oncology treatments for children.

  1. Unsupervised statistical identification of genomic islands using ...

    Vibrio species. These investigations lead to observations that are of evolutionary ... Identification of genomic islands in prokaryotic genomes has received considerable attention in the literature due to .... For instance, selective pres- sures as a ...

  2. V-GAP: Viral genome assembly pipeline

    Nakamura, Yoji; Yasuike, Motoshige; Nishiki, Issei; Iwasaki, Yuki; Fujiwara, Atushi; Kawato, Yasuhiko; Nakai, Toshihiro; Nagai, Satoshi; Kobayashi, Takanori; Gojobori, Takashi; Ototake, Mitsuru

    2015-01-01

    Next-generation sequencing technologies have allowed the rapid determination of the complete genomes of many organisms. Although shotgun sequences from large genome organisms are still difficult to reconstruct perfect contigs each of which represents a full chromosome, those from small genomes have been assembled successfully into a very small number of contigs. In this study, we show that shotgun reads from phage genomes can be reconstructed into a single contig by controlling the number of read sequences used in de novo assembly. We have developed a pipeline to assemble small viral genomes with good reliability using a resampling method from shotgun data. This pipeline, named V-GAP (Viral Genome Assembly Pipeline), will contribute to the rapid genome typing of viruses, which are highly divergent, and thus will meet the increasing need for viral genome comparisons in metagenomic studies.

  3. The 1000 bull genome project

    To meet growing global demands for high value protein from milk and meat, rates of genetic gain in domestic cattle must be accelerated. At the same time, animal health and welfare must be considered. The 1000 bull genomes project supports these goals by providing annotated sequence variants and ge...

  4. Computational genomics of specialized metabolism

    Medema, Marnix H.

    2018-01-01

    Microbial and plant specialized metabolites, also known as natural products, are key mediators of microbe-microbe and host-microbe interactions and constitute a rich resource for drug development. In the past decade, genome mining has emerged as a prominent strategy for natural product discovery.

  5. Genomic Heritability: What Is It?

    de los Campos, Gustavo; Sorensen, Daniel; Gianola, Daniel

    2015-01-01

    Whole-genome regression methods are being increasingly used for the analysis and prediction of complex traits and diseases. In human genetics, these methods are commonly used for inferences about genetic parameters, such as the amount of genetic variance among individuals or the proportion of phe...

  6. Targeted sequencing of plant genomes

    Mark D. Huynh

    2014-01-01

    Next-generation sequencing (NGS) has revolutionized the field of genetics by providing a means for fast and relatively affordable sequencing. With the advancement of NGS, wholegenome sequencing (WGS) has become more commonplace. However, sequencing an entire genome is still not cost effective or even beneficial in all cases. In studies that do not require a whole-...

  7. Fungal genome resources at NCBI

    Robbertse, B.; Tatusova, T.

    2011-01-01

    The National Center for Biotechnology Information (NCBI) is well known for the nucleotide sequence archive, GenBank and sequence analysis tool BLAST. However, NCBI integrates many types of biomolecular data from variety of sources and makes it available to the scientific community as interactive web resources as well as organized releases of bulk data. These tools are available to explore and compare fungal genomes. Searching all databases with Fungi [organism] at http://www.ncbi.nlm.nih.gov/ is the quickest way to find resources of interest with fungal entries. Some tools though are resources specific and can be indirectly accessed from a particular database in the Entrez system. These include graphical viewers and comparative analysis tools such as TaxPlot, TaxMap and UniGene DDD (found via UniGene Homepage). Gene and BioProject pages also serve as portals to external data such as community annotation websites, BioGrid and UniProt. There are many different ways of accessing genomic data at NCBI. Depending on the focus and goal of research projects or the level of interest, a user would select a particular route for accessing genomic databases and resources. This review article describes methods of accessing fungal genome data and provides examples that illustrate the use of analysis tools. PMID:22737589

  8. Genomic methods take the plunge

    Cammen, Kristina M.; Andrews, Kimberly R.; Carroll, Emma L.

    2016-01-01

    The dramatic increase in the application of genomic techniques to non-model organisms (NMOs) over the past decade has yielded numerous valuable contributions to evolutionary biology and ecology, many of which would not have been possible with traditional genetic markers. We review this recent...

  9. Ecological Genomics of Marine Picocyanobacteria†

    Scanlan, D. J.; Ostrowski, M.; Mazard, S.; Dufresne, A.; Garczarek, L.; Hess, W. R.; Post, A. F.; Hagemann, M.; Paulsen, I.; Partensky, F.

    2009-01-01

    Summary: Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus numerically dominate the picophytoplankton of the world ocean, making a key contribution to global primary production. Prochlorococcus was isolated around 20 years ago and is probably the most abundant photosynthetic organism on Earth. The genus comprises specific ecotypes which are phylogenetically distinct and differ markedly in their photophysiology, allowing growth over a broad range of light and nutrient conditions within the 45°N to 40°S latitudinal belt that they occupy. Synechococcus and Prochlorococcus are closely related, together forming a discrete picophytoplankton clade, but are distinguishable by their possession of dissimilar light-harvesting apparatuses and differences in cell size and elemental composition. Synechococcus strains have a ubiquitous oceanic distribution compared to that of Prochlorococcus strains and are characterized by phylogenetically discrete lineages with a wide range of pigmentation. In this review, we put our current knowledge of marine picocyanobacterial genomics into an environmental context and present previously unpublished genomic information arising from extensive genomic comparisons in order to provide insights into the adaptations of these marine microbes to their environment and how they are reflected at the genomic level. PMID:19487728

  10. Genomic applications in forensic medicine

    Børsting, Claus; Morling, Niels

    2016-01-01

    Since the 1980s, advances in DNA technology have revolutionized the scope and practice of forensic medicine. From the days of restriction fragment length polymorphisms (RFLPs) to short tandem repeats (STRs), the current focus is on the next generation genome sequencing. It has been almost a decad...

  11. Human Genome Research: Decoding DNA

    dropdown arrow Site Map A-Z Index Menu Synopsis Human Genome Research: Decoding DNA Resources with of the DNA double helix during April 2003. James D. Watson, Francis Crick, and Maurice Wilkins were company Celera announced the completion of a "working draft" reference DNA sequence of the human

  12. The genome of Chenopodium quinoa

    Jarvis, D.E.; Shwen Ho, Yung; Lightfoot, Damien J.; Schmöckel, Sandra M.; Li, Bo; Borm, T.J.A.; Ohyanagi, Hajime; Mineta, Katsuhiko; Mitchell, Craig T.; Saber, Noha; Kharbatia, Najeh M.; Rupper, Ryan R.; Sharp, Aaron R.; Dally, Nadine; Boughton, Berin A.; Woo, Yong H.; Gao, Ge; Schijlen, E.G.W.M.; Guo, Xiujie; Momin, Afaque A.; Negräo, Sónia; Al-Babili, Salim; Gehring, Christoph; Roessner, Ute; Jung, Christian; Murphy, Kevin; Arold, Stefan T.; Gojobori, Takashi; Linden, van der C.G.; Loo, van E.N.; Jellen, Eric N.; Maughan, Peter J.; Tester, Mark

    2017-01-01

    Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for

  13. Genome position and gene amplification

    Jirsová, Pavla; Snijders, A.M.; Kwek, S.; Roydasgupta, R.; Fridlyand, J.; Tokuyasu, T.; Pinkel, D.; Albertson, D. G.

    2007-01-01

    Roč. 8, č. 6 (2007), r120 ISSN 1474-760X Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : gene amplification * array comparative genomic hybridization * oncogene Subject RIV: BO - Biophysics Impact factor: 6.589, year: 2007

  14. India, Genomic diversity & Disease susceptibility

    Table of contents. India, Genomic diversity & Disease susceptibility · India, a paradise for Genetic Studies · Involved in earlier stages of Immune response protecting us from Diseases, Responsible for kidney and other transplant rejections Inherited from our parents · PowerPoint Presentation · Slide 5 · Slide 6 · Slide 7.

  15. GENOMIC FEATURES OF COTESIA PLUTELLAE POLYDNAVIRUS

    LIUCai-ling; ZHUXiang-xiong; FuWen-jun; ZHAOMu-jun

    2003-01-01

    Polydnavirus was purified from the calyx fluid of Cotesia plutellae ovary. The genomic features of C. plutellae polydnavirus (CpPDV) were investigated. The viral genome consists of at least 12 different segments and the aggregate genome size is a lower estimate of 80kbp. By partial digestion of CpPDV DNA with BamHI and subsequent ligation with BamHI-cut plasmid Bluescript, a representative library of CpPDV genome was obtained.

  16. Reconciling Utility with Privacy in Genomics

    Humbert, Mathias; Ayday, Erman; Hubaux, Jean-Pierre; Telenti, Amalio

    2014-01-01

    Direct-to-consumer genetic testing makes it possible for everyone to learn their genome sequences. In order to contribute to medical research, a growing number of people publish their genomic data on the Web, sometimes under their real identities. However, this is at odds not only with their own privacy but also with the privacy of their relatives. The genomes of relatives being highly correlated, some family members might be opposed to revealing any of the family's genomic data. In this pape...

  17. Genome chaos: survival strategy during crisis.

    Liu, Guo; Stevens, Joshua B; Horne, Steven D; Abdallah, Batoul Y; Ye, Karen J; Bremer, Steven W; Ye, Christine J; Chen, David J; Heng, Henry H

    2014-01-01

    Genome chaos, a process of complex, rapid genome re-organization, results in the formation of chaotic genomes, which is followed by the potential to establish stable genomes. It was initially detected through cytogenetic analyses, and recently confirmed by whole-genome sequencing efforts which identified multiple subtypes including "chromothripsis", "chromoplexy", "chromoanasynthesis", and "chromoanagenesis". Although genome chaos occurs commonly in tumors, both the mechanism and detailed aspects of the process are unknown due to the inability of observing its evolution over time in clinical samples. Here, an experimental system to monitor the evolutionary process of genome chaos was developed to elucidate its mechanisms. Genome chaos occurs following exposure to chemotherapeutics with different mechanisms, which act collectively as stressors. Characterization of the karyotype and its dynamic changes prior to, during, and after induction of genome chaos demonstrates that chromosome fragmentation (C-Frag) occurs just prior to chaotic genome formation. Chaotic genomes seem to form by random rejoining of chromosomal fragments, in part through non-homologous end joining (NHEJ). Stress induced genome chaos results in increased karyotypic heterogeneity. Such increased evolutionary potential is demonstrated by the identification of increased transcriptome dynamics associated with high levels of karyotypic variance. In contrast to impacting on a limited number of cancer genes, re-organized genomes lead to new system dynamics essential for cancer evolution. Genome chaos acts as a mechanism of rapid, adaptive, genome-based evolution that plays an essential role in promoting rapid macroevolution of new genome-defined systems during crisis, which may explain some unwanted consequences of cancer treatment.

  18. Genomics-assisted breeding in fruit trees

    Iwata, Hiroyoshi; Minamikawa, Mai F.; Kajiya-Kanegae, Hiromi; Ishimori, Motoyuki; Hayashi, Takeshi

    2016-01-01

    Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the pl...

  19. insights from the genome of Melitaea cinxia

    Ahola, Virpi; Wahlberg, Niklas; Frilander, Mikko J.

    2017-01-01

    The first lepidopteran genome (Bombyx mori) was published in 2004. Ten years later the genome of Melitaea cinxia came out as the third butterfly genome published, and the first eukaryotic genome sequenced in Finland. Owing to Ilkka Hanski, the M. cinxia system in the angstrom land Islands has become a famous model for metapopulation biology. More than 20 years of research on this system provides a strong ecological basis upon which a genetic framework could be built. Genetic knowledge is an e...

  20. GRAbB : Selective Assembly of Genomic Regions, a New Niche for Genomic Research

    Brankovics, Balázs; Zhang, Hao; van Diepeningen, Anne D; van der Lee, Theo A J; Waalwijk, Cees; de Hoog, G Sybren

    GRAbB (Genomic Region Assembly by Baiting) is a new program that is dedicated to assemble specific genomic regions from NGS data. This approach is especially useful when dealing with multi copy regions, such as mitochondrial genome and the rDNA repeat region, parts of the genome that are often

  1. Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

    Wolf Yuri I; Novichkov Pavel S; Sorokin Alexander V; Makarova Kira S; Koonin Eugene V

    2007-01-01

    Abstract Background An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs). Rapid accumulation of genome sequences creates opportunities for refining COGs ...

  2. Accounting for discovery bias in genomic EPD

    Genomics has contributed substantially to genetic improvement of beef cattle. The implementation is through computation of genomically enhanced expected progeny differences (GE-EPD), which are predictions of genetic merit of individual animals based on genomic information, pedigree, and data on the ...

  3. The UCSC Genome Browser Database: update 2006

    Hinrichs, A S; Karolchik, D; Baertsch, R

    2006-01-01

    The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, ...

  4. The UCSC genome browser database: update 2007

    Kuhn, R M; Karolchik, D; Zweig, A S

    2006-01-01

    The University of California, Santa Cruz Genome Browser Database contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up t...

  5. Impact of genomics on microbial food safety

    Abee, T.; Schaik, van W.; Siezen, R.J.

    2004-01-01

    Genome sequences are now available for many of the microbes that cause food-borne diseases. The information contained in pathogen genome sequences, together with the development of themed and whole-genome DNA microarrays and improved proteomics techniques, might provide tools for the rapid detection

  6. Genomic individuality and its biological implications.

    Zhao, J

    1996-06-01

    It is a widely accepted fundamental concept that all somatic genomes of a human individual are identical to each other. The theoretical basis of this concept is that all of these somatic genomes are the descendants of the genome of a single fertilized cell as well as the simple replicated products of asexual reproduction, thus not forming any new recombined genomes. The question here is whether such a concept might only represent one side of somatic genome biology and, even worse, whether it has perhaps already led to a very prevalent misconception that within the organism body, there exists no variability among individual somatic genomes. A hypothesis, called genomic individuality, is proposed, simply saying that every individual somatic genome, perhaps with rare exceptions, has its own unique or individual 'genetic identity' or 'fingerprint', which is characterized by its distinctive sequences or patterns of deoxyribonucleic acid molecules, or both. Thus, no two somatic genomes can be identical to each other in every or all aspects, and consequently, there must be a great deal of genomic variation present within the body of any multicellular organism. The concept or hypothesis of genomic individuality would not only provide a more complete understanding of genome biology, but also suggest a new insight into the studies of the biology of cells and organisms.

  7. Leaner and meaner genomes in Escherichia coli

    Ussery, David

    2006-01-01

    A 'better' Escherichia coli K-12 genome has recently been engineered in which about 15% of the genome has been removed by planned deletions. Comparison with related bacterial genomes that have undergone a natural reduction in size suggests that there is plenty of scope for yet more deletions....

  8. Comparative Genomics of Carp Herpesviruses

    Kurobe, Tomofumi; Gatherer, Derek; Cunningham, Charles; Korf, Ian; Fukuda, Hideo; Hedrick, Ronald P.; Waltzek, Thomas B.

    2013-01-01

    Three alloherpesviruses are known to cause disease in cyprinid fish: cyprinid herpesviruses 1 and 3 (CyHV1 and CyHV3) in common carp and koi and cyprinid herpesvirus 2 (CyHV2) in goldfish. We have determined the genome sequences of CyHV1 and CyHV2 and compared them with the published CyHV3 sequence. The CyHV1 and CyHV2 genomes are 291,144 and 290,304 bp, respectively, in size, and thus the CyHV3 genome, at 295,146 bp, remains the largest recorded among the herpesviruses. Each of the three genomes consists of a unique region flanked at each terminus by a sizeable direct repeat. The CyHV1, CyHV2, and CyHV3 genomes are predicted to contain 137, 150, and 155 unique, functional protein-coding genes, respectively, of which six, four, and eight, respectively, are duplicated in the terminal repeat. The three viruses share 120 orthologous genes in a largely colinear arrangement, of which up to 55 are also conserved in the other member of the genus Cyprinivirus, anguillid herpesvirus 1. Twelve genes are conserved convincingly in all sequenced alloherpesviruses, and two others are conserved marginally. The reference CyHV3 strain has been reported to contain five fragmented genes that are presumably nonfunctional. The CyHV2 strain has two fragmented genes, and the CyHV1 strain has none. CyHV1, CyHV2, and CyHV3 have five, six, and five families of paralogous genes, respectively. One family unique to CyHV1 is related to cellular JUNB, which encodes a transcription factor involved in oncogenesis. To our knowledge, this is the first time that JUNB-related sequences have been reported in a herpesvirus. PMID:23269803

  9. Genome Variation Map: a data repository of genome variations in BIG Data Center

    Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang

    2017-01-01

    Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research a...

  10. (Helianthus annuus L.) on physiology of wheat

    STORAGESEVER

    2009-08-04

    Aug 4, 2009 ... African Journal of Biotechnology Vol. 8 (15), pp. 3555-3559, 4 ... physiology of wheat seedlings including protein, proline, sugars, DNA, peroxidase, superoxide dismutase and .... (1956) as modified by Johnson et al. (1966).

  11. Emulsion properties of sunflower (Helianthus annuus) proteins

    Gonzalez-Perez, S.; Koningsveld, van G.A.; Vereijken, J.M.; Merck, K.B.; Gruppen, H.; Voragen, A.G.J.

    2005-01-01

    Emulsions were made with sunflower protein isolate (SI), helianthinin, and sunflower albumins (SFAs). Emulsion formation and stabilization were studied as a function of pH and ionic strength and after heat treatment of the proteins. The emulsions were characterized with respect to average droplet

  12. Discovering regulatory motifs in the Plasmodium genome using comparative genomics

    Wu, Jie; Sieglaff, Douglas H.; Gervin, Joshua; Xie, Xiaohui S.

    2008-01-01

    Motivation: Understanding gene regulation in Plasmodium, the causative agent of malaria, is an important step in deciphering its complex life cycle as well as leading to possible new targets for therapeutic applications. Very little is known about gene regulation in Plasmodium, and in particular, few regulatory elements have been identified. Such discovery has been significantly hampered by the high A-T content of some of the genomes of Plasmodium species, as well as the challenge in associat...

  13. Prospects for Genomic Research in Forestry

    K. V. Krutovsky

    2014-08-01

    Full Text Available Conifers are keystone species of boreal forests. Their whole genome sequencing, assembly and annotation will allow us to understand the evolution of the complex ancient giant conifer genomes that are 4 times larger in larch and 7–9 times larger in pines than the human genome. Genomic studies will allow also to obtain important whole genome sequence data and develop highly polymorphic and informative genetic markers, such as microsatellites and single nucleotide polymorphisms (SNPs that can be efficiently used in timber origin identification, for genetic variation monitoring, to study local and climate change adaptation and in tree improvement and conservation programs.

  14. Value of a newly sequenced bacterial genome

    Barbosa, Eudes; Aburjaile, Flavia F; Ramos, Rommel Tj

    2014-01-01

    and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the "scientific value" of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses...... heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting...

  15. Software for computing and annotating genomic ranges.

    Michael Lawrence

    Full Text Available We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.

  16. Resolution effects in reconstructing ancestral genomes.

    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.

  17. The ecoresponsive genome of Daphnia pulex

    Colbourne, John K.; Pfrender, Michael E.; Gilbert, Donald; Thomas, W. Kelley; Tucker, Abraham; Oakley, Todd H.; Tokishita, Shinichi; Aerts, Andrea; Arnold, Georg J.; Basu, Malay Kumar; Bauer, Darren J.; Caceres, Carla E.; Carmel, Liran; Casola, Claudio; Choi, Jeong-Hyeon; Detter, John C.; Dong, Qunfeng; Dusheyko, Serge; Eads, Brian D.; Frohlich, Thomas; Geiler-Samerotte, Kerry A.; Gerlach, Daniel; Hatcher, Phil; Jogdeo, Sanjuro; Krijgsveld, Jeroen; Kriventseva, Evgenia V; Kültz, Dietmar; Laforsch, Christian; Lindquist, Erika; Lopez, Jacqueline; Manak, Robert; Muller, Jean; Pangilinan, Jasmyn; Patwardhan, Rupali P.; Pitluck, Samuel; Pritham, Ellen J.; Rechtsteiner, Andreas; Rho, Mina; Rogozin, Igor B.; Sakarya, Onur; Salamov, Asaf; Schaack, Sarah; Shapiro, Harris; Shiga, Yasuhiro; Skalitzky, Courtney; Smith, Zachary; Souvorov, Alexander; Sung, Way; Tang, Zuojian; Tsuchiya, Dai; Tu, Hank; Vos, Harmjan; Wang, Mei; Wolf, Yuri I.; Yamagata, Hideo; Yamada, Takuji; Ye, Yuzhen; Shaw, Joseph R.; Andrews, Justen; Crease, Teresa J.; Tang, Haixu; Lucas, Susan M.; Robertson, Hugh M.; Bork, Peer; Koonin, Eugene V.; Zdobnov, Evgeny M.; Grigoriev, Igor V.; Lynch, Michael; Boore, Jeffrey L.

    2011-02-04

    This document provides supporting material related to the sequencing of the ecoresponsive genome of Daphnia pulex. This material includes information on materials and methods and supporting text, as well as supplemental figures, tables, and references. The coverage of materials and methods addresses genome sequence, assembly, and mapping to chromosomes, gene inventory, attributes of a compact genome, the origin and preservation of Daphnia pulex genes, implications of Daphnia's genome structure, evolutionary diversification of duplicated genes, functional significance of expanded gene families, and ecoresponsive genes. Supporting text covers chromosome studies, gene homology among Daphnia genomes, micro-RNA and transposable elements and the 46 Daphnia pulex opsins. 36 figures, 50 tables, 183 references.

  18. Software for computing and annotating genomic ranges.

    Lawrence, Michael; Huber, Wolfgang; Pagès, Hervé; Aboyoun, Patrick; Carlson, Marc; Gentleman, Robert; Morgan, Martin T; Carey, Vincent J

    2013-01-01

    We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.

  19. Genomic alterations detected by comparative genomic hybridization in ovarian endometriomas

    L.C. Veiga-Castelli

    2010-08-01

    Full Text Available Endometriosis is a complex and multifactorial disease. Chromosomal imbalance screening in endometriotic tissue can be used to detect hot-spot regions in the search for a possible genetic marker for endometriosis. The objective of the present study was to detect chromosomal imbalances by comparative genomic hybridization (CGH in ectopic tissue samples from ovarian endometriomas and eutopic tissue from the same patients. We evaluated 10 ovarian endometriotic tissues and 10 eutopic endometrial tissues by metaphase CGH. CGH was prepared with normal and test DNA enzymatically digested, ligated to adaptors and amplified by PCR. A second PCR was performed for DNA labeling. Equal amounts of both normal and test-labeled DNA were hybridized in human normal metaphases. The Isis FISH Imaging System V 5.0 software was used for chromosome analysis. In both eutopic and ectopic groups, 4/10 samples presented chromosomal alterations, mainly chromosomal gains. CGH identified 11q12.3-q13.1, 17p11.1-p12, 17q25.3-qter, and 19p as critical regions. Genomic imbalances in 11q, 17p, 17q, and 19p were detected in normal eutopic and/or ectopic endometrium from women with ovarian endometriosis. These regions contain genes such as POLR2G, MXRA7 and UBA52 involved in biological processes that may lead to the establishment and maintenance of endometriotic implants. This genomic imbalance may affect genes in which dysregulation impacts both eutopic and ectopic endometrium.

  20. Fungal Genomics for Energy and Environment

    Grigoriev, Igor V.

    2013-03-11

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Sequencing Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 200 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.