Reshaped Patterns of Alternative Splicing after Allopolyploidy in Brassica napus

In allopolyploids, when two genomes are amalgamated into a common nucleus, the native cis-architectures of genes are placed in a new hybrid and polyploid trans-environment, releasing novel expression profiles with respect to parental patterns. In conjunction with changes in transcript levels, transcript splicing patterns undergo changes to create novel forms. We studied the degree to which these changes differ from the parental splicing patterns and the degree to which they are reciprocated between individual instances of allopolyploidy. Using RNA-seq, we analyzed the transcriptomes of four Brassica napus lines and from the B. rapa and B. oleracea parents.  The results revealed myriad qualitative and quantitative differences in alternative splicing events among the genotypes. Several thousand alternatively spliced transcript forms were gained or lost in the polyploids.  We show that allopolyplody generates a variety of splicing landscapes from the same genetic merger, revealing both plastic and static changes in splicing, and our results complement studies of gene expression levels and patterns in allopolyploids. Our results show that changes in splicing patterns are a common occurrence after allopolyploidy and they contribute to the “transcriptome shock” experienced by newly formed allopolyploids.