MOROKOSHI: transcriptome database in Sorghum bicolor.

Area of Science:

• Plant genomics
• Transcriptome analysis
• Gene expression profiling

Background:

• Accurate annotation of transcriptional units and their expression profiles is crucial for transcriptome analysis.
• Full-length cDNA (FL-cDNA) collections and precise transcription start sites aid in refining annotation and understanding transcriptional regulation.

Purpose of the Study:

• To construct a normalized FL-cDNA library from Sorghum bicolor for enhanced transcriptome annotation.
• To analyze gene expression profiles using RNA sequencing (RNA-Seq) and identify novel genes and isoforms.
• To provide a publicly accessible resource for Sorghum bicolor transcriptome data.

Main Methods:

• Construction of a normalized FL-cDNA library from eight growth stages of Sorghum bicolor aerial tissues.
• Sanger sequencing of FL-cDNA clones to generate expressed sequence tags (ESTs).
• RNA sequencing (RNA-Seq) analysis of spikelet, seed, and stem tissues, combined with public sorghum RNA-Seq data.

Main Results:

• Generated 38,981 high-quality expressed sequence tags (ESTs) from 37,607 FL-cDNA clones.
• Annotated 272 novel genes, 323 antisense transcripts, and 1,672 candidate isoforms.
• Confirmed expression of 70.6% of newly identified genes and developed comprehensive gene expression profiles and co-expression networks.

Conclusions:

• The developed FL-cDNA library and expression data significantly enhance Sorghum bicolor transcriptome annotation.
• The study identified novel genetic elements and provided insights into gene regulation and expression patterns.
• A comprehensive transcriptome data resource for Sorghum bicolor is now available at http://sorghum.riken.jp for public access and comparison.