A survey of the sorghum transcriptome using single-molecule long reads

Alternative splicing (AS) and alternative polyadenylation (APA) of pre-mRNAs greatly contribute to transcriptome diversity, coding capacity of a genome and gene regulatory mechanisms in eukaryotes. Short-read sequencing of transcriptomes using second-generation sequencing has been extensively used to analyze gene expression and the extent of AS in eukaryotes. However, a major limitation with short-read data is that it is difficult to accurately predict the full-length splice isoforms produced from a gene. Here we sequenced the sorghum transcriptome using Pacific Biosciences single molecule real time long-read isoform sequencing (Iso-Seq) to identify full-length splice isoforms and APA sites. Analysis of these data revealed transcriptome-wide full-length isoforms at an unprecedented scale with over 8000 novel splice isoforms, first for any plant system. In addition, these data uncovered APA of about 5000 expressed genes, and >1400 novel genes that were not previously annotated. These results complement available sorghum genome in refining its transcriptome and study gene regulation in this important bioenergy crop.