Elucidating the Regulation of Alternative Splicing in Mungbean (Vigna radiata)

Recent studies indicated that alternative splicing (AS) is a ubiquitous phenomenon in plants, but it is unclear whether it represents another layer of gene expression regulation or simply the result of stochastic noise from the splicing machinery. To assess the regulation of AS in mungbean, global transcript splicing profile was examined in RNA-Seq data from root, leaf, flower, and pod tissues. Among the 22,427 annotated genes, 78% has AS and produce 59,230 AS isoforms where the dominant form is intron retention (45%), followed by alternative acceptor (24%), alternative donor (13%), and exon skipping (7%). Several observations corroborate the role of stochastic splicing as the source of numerous AS isoforms in mungbean. For example, 36% of AS isoforms may not even exist as a single complete RNA in an average cell, making them unlikely to have any function. Moreover, around 24.4% of AS isoform is present at less than 1/10th of the default transcript. The proportion of missense splicing, which has more potential to generate non-functional transcript, is close to the expected frequency if splicing occur at random (67%). However, alternative donor and acceptor types have more tendency to occur at multiples of codon length. Genes with high exon number and expression level, which should have the most AS if splicing is stochastic, were found to have less AS, consistent with negative selection for accumulation of large quantity of non-functional AS that could be detrimental to cell’s survival. These observations suggest that cataloguing global AS events will mostly yield non-functional isoforms.