RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome

dc.contributor.author Severin, Andrew
dc.contributor.author Woody, Jenna
dc.contributor.author Severin, Andrew
dc.contributor.author Bolon, Yung-Tsi
dc.contributor.author Joseph, Bindu
dc.contributor.author Diers, Brian
dc.contributor.author Farmer, Andrew
dc.contributor.author Muehlbauer, Gary
dc.contributor.author Nelson, Rex
dc.contributor.author Grant, David
dc.contributor.author Specht, James
dc.contributor.author Graham, Michelle
dc.contributor.author Cannon, Steven
dc.contributor.author May, Gregory
dc.contributor.author Vance, Carroll
dc.contributor.author Shoemaker, Randy
dc.contributor.department Agronomy
dc.date 2018-02-17T17:14:54.000
dc.date.accessioned 2020-06-29T23:07:12Z
dc.date.available 2020-06-29T23:07:12Z
dc.date.copyright Fri Jan 01 00:00:00 UTC 2010
dc.date.issued 2010-08-05
dc.description.abstract <p><strong>Background</strong> <br />Next generation sequencing is transforming our understanding of transcriptomes. It can determine the expression level of transcripts with a dynamic range of over six orders of magnitude from multiple tissues, developmental stages or conditions. Patterns of gene expression provide insight into functions of genes with unknown annotation.</p> <p><strong>Results</strong> <br />The RNA Seq-Atlas presented here provides a record of high-resolution gene expression in a set of fourteen diverse tissues. Hierarchical clustering of transcriptional profiles for these tissues suggests three clades with similar profiles: aerial, underground and seed tissues. We also investigate the relationship between gene structure and gene expression and find a correlation between gene length and expression. Additionally, we find dramatic tissue-specific gene expression of both the most highly-expressed genes and the genes specific to legumes in seed development and nodule tissues. Analysis of the gene expression profiles of over 2,000 genes with preferential gene expression in seed suggests there are more than 177 genes with functional roles that are involved in the economically important seed filling process. Finally, the Seq-atlas also provides a means of evaluating existing gene model annotations for the Glycine max genome.</p> <p><strong>Conclusions</strong> <br />This RNA-Seq atlas extends the analyses of previous gene expression atlases performed using Affymetrix GeneChip technology and provides an example of new methods to accommodate the increase in transcriptome data obtained from next generation sequencing. Data contained within this RNA-Seq atlas of Glycine max can be explored at http://www.soybase.org/soyseq.</p>
dc.description.comments <p>This article is from <em>BMC Plant Biology</em> 10 (2010): 160, doi:<a href="http://dx.doi.org/10.1186/1471-2229-10-160" target="_blank">10.1186/1471-2229-10-160</a>. Posted with permission.</p>
dc.format.mimetype application/pdf
dc.identifier archive/lib.dr.iastate.edu/agron_pubs/98/
dc.identifier.articleid 1098
dc.identifier.contextkey 8599069
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath agron_pubs/98
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/5072
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/agron_pubs/98/2010_Severin_RNASeqAtlas.pdf|||Sat Jan 15 02:37:49 UTC 2022
dc.source.uri 10.1186/1471-2229-10-160
dc.subject.disciplines Agronomy and Crop Sciences
dc.subject.disciplines Bioinformatics
dc.subject.disciplines Genomics
dc.subject.disciplines Plant Breeding and Genetics
dc.title RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome
dc.type article
dc.type.genre article
dspace.entity.type Publication
relation.isAuthorOfPublication 87268d62-4b33-4949-a936-2d6d1ff1cfe2
relation.isOrgUnitOfPublication fdd5c06c-bdbe-469c-a38e-51e664fece7a
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