134 research outputs found
Chromosome-scale assembly of wild barley accession “OUH602”
No full textBarley (Hordeum vulgare) was domesticated from its wild ancestral form ca. 10,000 years ago in the Fertile Crescent and is widely cultivated throughout the world, except for in tropical areas. The genome size of both cultivated barley and its conspecific wild ancestor is approximately 5 Gb. High-quality chromosome-level assemblies of 19 cultivated and one wild barley genotype were recently established by pan-genome analysis. Here, we release another equivalent short-read assembly of the wild barley accession “OUH602.” A series of genetic and genomic resources were developed for this genotype in prior studies. Our assembly contains more than 4.4 Gb of sequence, with a scaffold N50 value of over 10 Mb. The haplotype shows high collinearity with the most recently updated barley reference genome, “Morex” V3, with some inversions. Gene projections based on “Morex” gene models revealed 46,807 protein-coding sequences and 43,375 protein-coding genes. Alignments to publicly available sequences of bacterial artificial chromosome (BAC) clones of “OUH602” confirm the high accuracy of the assembly. Since more loci of interest have been identified in “OUH602,” the release of this assembly, with detailed genomic information, should accelerate gene identification and the utilization of this key wild barley accession
Chromosome-scale assembly of barley cv. 'Haruna Nijo' as a resource for barley genetics
No full textCultivated barley (Hordeum vulgare ssp. vulgare) is used for food, animal feed, and alcoholic beverages and is widely grown in temperate regions. Both barley and its wild progenitor (H. vulgare ssp. spontaneum) have large 5.1-Gb genomes. High-quality chromosome-scale assemblies for several representative barley genotypes, both wild and domesticated, have been constructed recently to populate the nascent barley pan-genome infrastructure. Here, we release a chromosome-scale assembly of the Japanese elite malting barley cultivar 'Haruna Nijo' using a similar methodology as in the barley pan-genome project. The 4.28-Gb assembly had a scaffold N50 size of 18.9 Mb. The assembly showed high collinearity with the barley reference genome 'Morex' cultivar, with some inversions. The pseudomolecule assembly was characterized using transcript evidence of gene projection derived from the reference genome and de novo gene annotation achieved using published full-length cDNA sequences and RNA-Seq data for 'Haruna Nijo'. We found good concordance between our whole-genome assembly and the publicly available BAC clone sequence of 'Haruna Nijo'. Interesting phenotypes have since been identified in Haruna Nijo; its genome sequence assembly will facilitate the identification of the underlying genes
Multiple wheat genomes reveal global variation in modern breeding
No full textAbstract Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat ( Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome 1 , and the lack of genome-assembly data for multiple wheat lines 2,3 . Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses 4,5 . We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm1 6 , a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars
The mosaic oat genome gives insights into a uniquely healthy cereal crop
No full textAbstract Cultivated oat ( Avena sativa L.) is an allohexaploid (AACCDD, 2 n = 6 x = 42) thought to have been domesticated more than 3,000 years ago while growing as a weed in wheat, emmer and barley fields in Anatolia 1,2 . Oat has a low carbon footprint, substantial health benefits and the potential to replace animal-based food products. However, the lack of a fully annotated reference genome has hampered efforts to deconvolute its complex evolutionary history and functional gene dynamics. Here we present a high-quality reference genome of A . sativa and close relatives of its diploid ( Avena longiglumis , AA, 2 n = 14) and tetraploid ( Avena insularis , CCDD, 2 n = 4 x = 28) progenitors. We reveal the mosaic structure of the oat genome, trace large-scale genomic reorganizations in the polyploidization history of oat and illustrate a breeding barrier associated with the genome architecture of oat. We showcase detailed analyses of gene families implicated in human health and nutrition, which adds to the evidence supporting oat safety in gluten-free diets, and we perform mapping-by-sequencing of an agronomic trait related to water-use efficiency. This resource for the Avena genus will help to leverage knowledge from other cereal genomes, improve understanding of basic oat biology and accelerate genomics-assisted breeding and reanalysis of quantitative trait studies
In vitro evaluation of carbon and oxygen ion irradiation in hepatocellular carcinoma cell lines
No full textThe reduction of bromate in drinking water by activated carbon
No full textThe reduction of bromate at trace concentrations in drinking water has been studied. Both granular activated carbon and powdered activated carbon have been used to reduce bromate. Solution characteristics which influenced the reduction of bromate during this study include solution pH, initial bromate concentration, ionic strength of the solution, the presence of organic compounds, the dissolved oxygen content of the solution, and the type of activated carbon used.An existing model, originally developed to describe the reduction of free chlorine by granular activated carbon, has been used to describe bromate reduction by activated carbon. Both finite batch tests and packed bed column studies were conducted to test and verify the model predictions. The model generally describes bromate reduction well in distilled water. Tests conducted in natural water samples demonstrated the limitations of the model in describing the competitive effects of natural organic matter.Powdered activated carbon (PAC) was applied in an alternative process: the Haberer process. Bromate was reduced well by powdered carbon in the supported bed configuration. Natural organic matter also had an effect on bromate reduction in the Haberer process. Calculated capacities for bromate reduction by powdered activated carbon in the Haberer process were greater than previously reported PAC capacities.Made available in DSpace on 2011-05-07T13:22:40Z (GMT). No. of bitstreams: 2
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Barley: From Brittle to Stable Harvest
No full textSelection and domestication of plants with genes that prevent grains from shattering in cereals was essential for human civilization’s transition to agriculture-based societies. In this issue, Pourkheirandish et al. show that domestication of barley required evolution of a molecular system distinct from other grains, such as rice and maize, and reveal that present-day cultivars derive from two ancient domestication centers
Discovery of <it>cis</it>-elements between <it>sorghum </it>and rice using co-expression and evolutionary conservation
No full textAbstract Background The spatiotemporal regulation of gene expression largely depends on the presence and absence of cis-regulatory sites in the promoter. In the economically highly important grass family, our knowledge of transcription factor binding sites and transcriptional networks is still very limited. With the completion of the sorghum genome and the available rice genome sequence, comparative promoter analyses now allow genome-scale detection of conserved cis-elements. Results In this study, we identified thousands of phylogenetic footprints conserved between orthologous rice and sorghum upstream regions that are supported by co-expression information derived from three different rice expression data sets. In a complementary approach, cis-motifs were discovered by their highly conserved co-occurrence in syntenic promoter pairs. Sequence conservation and matches to known plant motifs support our findings. Expression similarities of gene pairs positively correlate with the number of motifs that are shared by gene pairs and corroborate the importance of similar promoter architectures for concerted regulation. This strongly suggests that these motifs function in the regulation of transcript levels in rice and, presumably also in sorghum. Conclusion Our work provides the first large-scale collection of cis-elements for rice and sorghum and can serve as a paradigm for cis-element analysis through comparative genomics in grasses in general.</p
A high resolution genome-wide scan for significant selective sweeps: an application to pooled sequence data in laying chickens
No full textIn most studies aimed at localizing footprints of past selection, outliers at tails of the empirical distribution of a given test statistic are assumed to reflect locus-specific selective forces. Significance cutoffs are subjectively determined, rather than being related to a clear set of hypotheses. Here, we define an empirical p-value for the summary statistic by means of a permutation method that uses the observed SNP structure in the real data. To illustrate the methodology, we applied our approach to a panel of 2.9 million autosomal SNPs identified from re-sequencing a pool of 15 individuals from a brown egg layer line. We scanned the genome for local reductions in heterozygosity, suggestive of selective sweeps. We also employed a modified sliding window approach that accounts for gaps in the sequence and increases scanning resolution by moving the overlapping windows by steps of one SNP only, and suggest to call this a "creeping window" strategy. The approach confirmed selective sweeps in the region of previously described candidate genes, i.e. TSHR, PRL, PRLHR, INSR, LEPR, IGF1, and NRAMP1 when used as positive controls. The genome scan revealed 82 distinct regions with strong evidence of selection (genome-wide p-valu
Genome sequencing and analysis of the model grass Brachypodium distachyon
No full textKirjoittajalista kokonaisuudessaan: Principal investigators John P. Vogel, David F. Garvin, Todd C. Mockler, Jeremy Schmutz, Dan Rokhsar, Michael W. Bevan; DNA sequencing and assembly Kerrie Barry, Susan Lucas, Miranda Harmon-Smith, Kathleen Lail, Hope Tice, Jeremy Schmutz (Leader), Jane Grimwood, Neil McKenzie, Michael W. Bevan; Pseudomolecule assembly and BACend sequencing NaxinHuo, Yong Q.Gu,GerardR. Lazo, OlinD.Anderson, John P. Vogel (Leader), Frank M. You,Ming-Cheng Luo, Jan Dvorak, Jonathan Wright, Melanie Febrer, Michael W. Bevan, Dominika Idziak, Robert Hasterok, David F. Garvin; Transcriptome sequencing and analysis Erika Lindquist, Mei Wang, Samuel E. Fox, Henry D. Priest, Sergei A. Filichkin, Scott A. Givan, Douglas W. Bryant, JeffH.Chang, ToddC.Mockler (Leader), HaiyanWu, Wei Wu, An-Ping Hsia, Patrick S. Schnable, Anantharaman Kalyanaraman, Brad Barbazuk, Todd P.Michael, Samuel P.Hazen, JenniferN. Bragg, Debbie Laudencia-Chingcuanco, John P. Vogel, David F. Garvin, Yiqun Weng, Neil McKenzie, Michael W. Bevan; Gene analysis and annotation Georg Haberer, Manuel Spannagl, Klaus Mayer (Leader), Thomas Rattei, ThereseMitros, Dan Rokhsar, Sang-Jik Lee, Jocelyn K. C. Rose, Lukas A. Mueller, Thomas L. York; Repeats analysis Thomas Wicker (Leader), Jan P. Buchmann, Jaakko Tanskanen, Alan H. Schulman (Leader), Heidrun Gundlach, Jonathan Wright, Michael Bevan, Antonio Costa de Oliveira, Luciano da C. Maia, William Belknap, Yong Q. Gu, Ning Jiang, Jinsheng Lai, Liucun Zhu, JianxinMa, Cheng Sun, Ellen Pritham; Comparative genomics Jerome Salse (Leader), Florent Murat, Michael Abrouk, Georg Haberer, Manuel Spannagl, Klaus Mayer, Remy Bruggmann, Joachim Messing, Frank M. You, Ming-Cheng Luo, Jan Dvorak; Small RNA analysis Noah Fahlgren, Samuel E. Fox, Christopher M. Sullivan, Todd C. Mockler, James C. Carrington, Elisabeth J. Chapman, Greg D.May, Jixian Zhai, Matthias Ganssmann, Sai Guna Ranjan Gurazada, Marcelo German, Blake C. Meyers, Pamela J. Green (Leader); Manual annotation and gene family analysis Jennifer N. Bragg, Ludmila Tyler, Jiajie Wu, Yong Q. Gu, Gerard R. Lazo, Debbie Laudencia-Chingcuanco, James Thomson, John P. Vogel (Leader), Samuel P. Hazen, Shan Chen, Henrik V. Scheller, JesperHarholt, Peter Ulvskov, Samuel E. Fox, Sergei A. Filichkin, Noah Fahlgren, Jeffrey A. Kimbrel, Jeff H. Chang, Christopher M. Sullivan, Elisabeth J. Chapman, James C. Carrington, Todd C. Mockler, Laura E. Bartley, Peijian Cao, Ki-Hong Jung, Manoj K Sharma, Miguel Vega-Sanchez, Pamela Ronald, Christopher D.Dardick, StefanieDe Bodt,Wim Verelst, Dirk Inze, Maren Heese, Arp Schnittger, Xiaohan Yang, Udaya C. Kalluri, GeraldA. Tuskan, ZhihuaHua, Richard D. Vierstra, David F. Garvin, Yu Cui, Shuhong Ouyang, Qixin Sun, Zhiyong Liu, Alper Yilmaz, Erich Grotewold, Richard Sibout, Kian Hematy, Gregory Mouille, Herman Hofte, Todd Michael, JeŽrome Pelloux, Devin O Connor, James Schnable, Scott Rowe, Frank Harmon, Cynthia L. Cass, John C. Sedbrook, Mary E. Byrne, SeanWalsh, Janet Higgins, Michael Bevan, PinghuaLi, ThomasBrutnell, TurgayUnver,Hikmet Budak, Harry Belcram, Mathieu Charles, Boulos Chalhoub, Ivan Baxterv2010okBE
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