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

Abstract

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.

Ectopic phytocystatin expression increases nodule numbers and influences the responses of soybean (Glycine max) to nitrogen deficiency

“…5E and H) under LN compared to HN conditions. The abundance of CP3 transcripts (that have not previously not been detected in leaves e.g., by Severin et al, 2010; Table 2) was low under HN conditions in leaves. CP3 transcripts were below the level of detection under LN conditions (Fig.…”

“…Table 2 compares the expression of genes that had previously been measured in young leaves and roots by RNAseq analysis (Severin et al, 2010). The data presented here using qRTPCR analysis provide evidence of changes in transcripts that were below the levels of detection by the RNAseq technique in non-treated tissue samples (Severin et al, 2010).…”

“…Table 2 compares the expression of genes that had previously been measured in young leaves and roots by RNAseq analysis (Severin et al, 2010). The data presented here using qRTPCR analysis provide evidence of changes in transcripts that were below the levels of detection by the RNAseq technique in non-treated tissue samples (Severin et al, 2010). Transcripts encoding the papain-like cysteine proteases CP2, CP3, CP4 and CP5 were either unchanged, or decreased, in abundance under LN when compared to HN conditions in leaves and roots with the exception of root CP4 of line OCI-1 where transcription increased under LN (Fig.…”

“…The recent release of the complete soybean genome (Schmutz et al, 2010) and the RNAseq atlas of genes expressed in fourteen different soybean tissues (Severin et al, 2010) allows the accurate identification and characterisation of soybean cystatins, cysteine proteases and VPEs. The Phytozome database (www.phytozome.…”

“…net) currently contains over 300 cystatin-like sequences from the Viridiplantae kingdom, 706 C1 cysteine protease sequences as well as 362 C13 cysteine protease (VPE-type) sequences. However, the exact functions of most of these proteins remain largely uncharacterised (Severin et al, 2010). In this study, we selected a small number of model cysteine proteases, VPEs and cystatins that were reported to be expressed in leaves and roots in the Phytozome database.…”