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

By A. Severin, J. Woody, Yung‐Tsi Bolon, Bindu Joseph, Brian W. Diers, A. Farmer, G. Muehlbauer, Rex T. Nelson, D. Grant, J. Specht and 5 more. BMC Plant Biology, 2010

680 citations recorded by the source corpus.

BackgroundNext 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.ResultsThe 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.ConclusionsThis 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.

Subfields: Plant Science

View Paper: https://www.semanticscholar.org/paper/7335ec423663d9f13731ba8bfbc7ac21c89069f1

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Citations in the corpus

Achievements and Challenges in Legume Breeding for Pest and Disease Resistance (2015, background): “Chickpea, faba bean, lentil, lupin, pea, peanut, pigeonpea, and soybean transcriptomes have also been reported (Le et al., 2007; Severin et al., 2010; Franssen et al., 2011; Garg et al., 2011; Hiremath et al., 2011; Libault et al., 2011; Duan et al., 2012; Kaur et al., 2012; O’Rourke et al., 2013; S”
Inorganic Nitrogen Uptake and Transport in Beneficial Plant Root-Microbe Interactions (2015, background): “The M. truncatula gene expression atlas (Benedito et al., 2010) and the soybean transcriptomes (Libault et al., 2010; Severin et al., 2010) have shown nodule enhanced expression of a number of members of the NTR(PTR) family.”