Transcript isoforms and alternative splicing in polyploid Brassica napus under heat and cold stress

Background and Aims Polyploidization events have occurred many times during the evolution of flowering plants and have played a major role in genome evolution. Genes duplicated by polyploidy, termed homeologues, can diverge in function or new functions can evolve. There has been considerable interest in characterizing the transcriptomes of polyploid plants. One aspect of gene expression is alternative splicing (AS) by which precursor mRNAs are differentially spliced to form multiple mature mRNA isoforms. The effects of abiotic stress conditions on transcript isoform diversity of homeologues in polyploids has received little attention. Brassica napus, an allopolyploid derived from B. rapa and B. oleracea, is a model to study genetic complexities in polyploids. Brassica napus contains A homeologues that are derived from B. rapa, and C homeologues that are derived from B. oleracea. Methods We conducted global analyses of transcript isoforms in B. napus using single molecule long-read sequencing of plants subjected to heat and cold stress treatments. Key Results Cold stress reduced the number of isoforms produced by a given gene, whereas heat stress increased the number of isoforms. There was also a heat-responsive increase in the number of AS events. Heat stress induced a higher number of transcripts predicted to be probable targets of nonsense-mediated decay. C homeologues were more likely to produce more isoforms relative to A homeologues. A large proportion of homeologous pairs display shifts in their relative isoform distributions across homeologues in response to stress. Conclusions Overall, our analyses reveal opposing shifts in isoform composition in response to cold and heat stress, as well as skewed isoform distributions across subgenomes. These results indicate that heat and cold stress can have considerable effects on the isoform composition of homeologous transcripts, which may help polyploids respond to temperature stresses.