UBC Theses and Dissertations
The evolution of alternative splicing after polyploidy Tack, David Christopher
Gene and genome duplications have made major contributions to the genomes of eukaryotes. Alternative splicing modulates gene expression and alters protein function. First, I examine alternative splicing patterns in the allopolyploid Brassica napus, revealing that the genome-wide trends of alternative splicing in duplicated genes of an evolutionarily new allotetraploid plant are very similar overall to those found in Arabidopsis thaliana. Within Brassica napus, I show that the alternative splicing patterns of the reunited homeologs are not well conserved, highlighting that alternative splicing is a rapidly evolving aspect of gene expression. Second, using Arabidopsis thaliana, I investigated the divergence of alternative splicing between paralogs, revealing about 30% qualitative conservation of alternative splicing events. I determined that qualitatively conserved events most often are not quantitatively conserved, indicating either incomplete divergence or specialization. I examined the duplicate gene pair of CCA1/LHY in detail, showing a case of subfunctionalization of alternative splicing after gene duplication that has implications for the cold response pathway of A. thaliana. By analyzing a transcriptome data set from nonsense mediated decay mutants, I showed that alternative splicing mediated nonsense mediated decay has significantly diverged between both pairs of whole genome and pairs of tandem duplicates. Third, I investigated the immediate effects of allopolyploidzation on gene expression and alternative splicing using three resynthesized Brassica napus lines. Many of the effects of allopolyploidization are repeatable, however some changes to gene expression and alternative splicing are unique to an instance of polyploidy. In all three polyploids surveyed, intron retention events that changed their frequency did so in an overwhelmingly negative fashion (i.e. the levels of alternatively spliced transcripts went down) and the majority of these changes were parallel between polyploids. Other classes of alternative splicing events showed a far more balanced set of changes in response to polyploidy. Natural B. napus showed significantly more increases in intron retention frequency vs. the parental species than any of the resynthesized lines. I assert that much of the changes in levels of alternatively spliced transcripts can be attributed the stochastic nature of polyploidization.
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