UBC Theses and Dissertations
The effects of abiotic stress on isoform composition in polyploid Brassica napus Bailey, Ryan Edward
Polyploidy has played a major role throughout the evolution of plants and has long been considered a powerful driver of evolution across a broad range of plant lineages. Polyploidization events have occurred many times during the evolution of flowering plants (angiosperms). Following a polyploidization event, a set of duplicated genes is created which can diverge in function or new functions can evolve. Brassica napus, an allopolyploid derived from the hybridization of B. rapa and B. oleracea, more commonly known as canola, serves as an excellent model to study the complexities between duplicate gene pairs, also known as homeologous pairs. One of these complexities is the process of alternative splicing (AS) by which precursor mRNAs from multiexon genes are spliced to form mature mRNAs producing a vast repertoire of isoforms. The effects of abiotic stress conditions on isoform diversity and variability across homeologous pairs has received little attention. We conducted a global isoform sequencing analysis of Brassica napus using long-read sequencing of plants subjected to heat and cold stress. Analysis of AS events reveal a heat-responsive increase in the number of AS events. Furthermore, we discovered that cold stress reduces the number of isoforms produced by a given gene, whereas heat stress increases the number of isoforms produced by a given gene. This heat-responsive increase in the number of isoforms produced was paired with the observation that heat-stress also induces a higher number of transcripts predicted to be likely targets of nonsense-mediated decay (NMD), a common mechanism by which AS exerts transcriptional regulation. Our analysis also revealed that across homeologous pairs, C homeologs are more likely to produce more isoforms relative to A homeologs, across all three conditions tested. These shifted isoform distributions do not lead to shifted distributions in the predicted likelihood of NMD-targeting. In all, our analysis reveals opposing shifts in isoform composition in response to cold and heat stress as well as skewed isoform distributions across subgenomes, in which C homeologs are more likely to produce more isoforms relative to A homeologs, across each of the conditions we tested.
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