title: RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Agronomy, Iowa State University, Ames, IA 50011, USA. severin@iastate.edu
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Severin
authors.forename: Jenna L
authors.initials: JL
authors.lastname: Woody
authors.forename: Yung-Tsi
authors.initials: YT
authors.lastname: Bolon
authors.forename: Bindu
authors.initials: B
authors.lastname: Joseph
authors.forename: Brian W
authors.initials: BW
authors.lastname: Diers
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Farmer
authors.forename: Gary J
authors.initials: GJ
authors.lastname: Muehlbauer
authors.forename: Rex T
authors.initials: RT
authors.lastname: Nelson
authors.forename: David
authors.initials: D
authors.lastname: Grant
authors.forename: James E
authors.initials: JE
authors.lastname: Specht
authors.forename: Michelle A
authors.initials: MA
authors.lastname: Graham
authors.forename: Steven B
authors.initials: SB
authors.lastname: Cannon
authors.forename: Gregory D
authors.initials: GD
authors.lastname: May
authors.forename: Carroll P
authors.initials: CP
authors.lastname: Vance
authors.forename: Randy C
authors.initials: RC
authors.lastname: Shoemaker
mesh_terms: D016000:Cluster Analysis; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D035683:MicroRNAs / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D017423:Sequence Analysis, RNA; D013025:Glycine max / Q000235:genetics* / Q000378:metabolism*
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D018749:RNA, Plant