The Sorghum Transcriptome Database

In transcriptome analysis, accurate annotation of each transcriptional unit and its expression profile is essential. A full-length cDNA (FL-cDNA) collection facilitates the refinement of transcriptional annotation and accurate transcription start sites help to unravel transcriptional regulation. Researchers at the RIKEN Institute constructed a normalized FL-cDNA library from eight growth stages of aerial tissues in Sorghum bicolor and isolated 37,607 clones. These clones were Sanger sequenced from both the 5′ and 3′ ends and in total 38,981 high-quality expressed sequence tags (ESTs) were obtained. About one-third of the transcripts of known genes were captured as FL-cDNA clone resources. In addition to these we also annotated 272 novel genes, 323 antisense transcripts and 1672 candidate isoforms. These clones are available from the RIKEN Bioresource Center. After obtaining accurate annotation of transcriptional units, the researchers performed expression profile analysis. They carried out spikelet-, seed- and stem-specific RNA-Seq analysis and confirmed the expression of 70.6% of the newly identified genes. They also downloaded 23 sorghum RNA-Seq samples that are publicly available and these are shown on a genome browser together with our original FL-cDNA and RNA-Seq data. Using their original and publicly available data, the researchers made an expression profile of each gene and identified the top 20 genes with the most similar expression. In addition, they visualized their relationships in gene co-expression networks.

rna-seq

Availability – Users can access and compare various transcriptome data from Sorghum bicolor at http://sorghum.riken.jp

Makita Y, Shimada S, Kawashima M, Kondou-Kuriyama T, Toyoda T, Matsui M. (2014) MOROKOSHI: Transcriptome Database in Sorghum bicolor. Plant Cell Physiol [Epub ahead of print]. [article]

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