Genome-wide transcriptome expands the published gene repertoire of castor bean (Ricinus communis. L).

Abstract

Castorbean (Ricinus communis L) is an industrial important crop primarily for its ricinoleic acid-rich seed-oil. India is the prominent regulator of world market in castorbean seed by being the largest producer of the seed in the world. Given the economic impact of the crop, castorbean was one among the first industrial oil-seed crop whose genome was sequenced. The published genome of castorbean is reported to harbor 31221 protein coding gene models of which only for about 6000 there were experimental evidence of transcripts. With the aim of improving the empirical evidence for the expressed set of genes, we set out to develop a genome wide transcriptome for this important oilseed crop. Pooled RNA obtained from twelve distinct tissues representing seedling, root, shoot apex, leaf, male and femal flowers at different stages, and developing capsule at different stages and 34 cotyledonary leaf samples from a different experimental set up, was subjected to RNA-sequencing (RNA-seq). Using 150 X 2 paired read lengths for pooled tissues and 100 X 2 paired read lengths for 34 coltyledonary-leaf samples, strand-specific RNA-seq was performed using Illumina HiSeq. With genome-as-reference, reads were assembled into transcripts using Cufflinks and the individual transcriptomes of each sample was merged into a single, unified transcriptome using cuffmerge. The resulting transcriptome contained 133,520 transcripts derived from 45,004 loci. The underlying gene-models revealed the expression of 41 miRNA transcripts belonging to 21 miRNA genes, 21 tRNA transcripts, 49 large-sub-unit (28S)-rRNA transcripts, 58 small nuclear transcripts and 15,056 natural anti-sense transcripts. Further, 5’ and 3’ UTRs could be modeled based on the transcript sequence using TransDecoder. Such information obtained would aid in conventional breeding and biotechnological interventions for the improvement of key agronomical and economical traits of the crop.