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Rapid evolutionary divergence in alternative splicing patterns following whole genome duplication in the Arabidopsis lineage Zhang, Peter G. Y.


Gene and genome duplication are major processes that contribute to increasing proteome diversity in eukaroytes, and gene duplications have occurred throughout eukaryotic evolution. Alternative splicing is another process that increases proteome diversity in eukaroytes. Little is known about the conservation of alternative splicing patterns after gene or genome duplication. Here I have studied alternative splicing patterns in a set of about 2,600 gene pairs in Arabidopsis thaliana that have been retained from the most recent paleopolyploidy event that occurred around 30 million years ago. I identified duplicated genes with putative alternative splicing by comparing cDNA and genomic sequences. To evaluate alternative splicing patterns of those genes, RT-PCR was used to examine the differences among cDNAs from eight different organs for both genes of 50 gene pairs. Differences in splicing patterns were found between the genes in most pairs. These differences include presence/absence of particular splicing patterns or distinct organ specificity. Using three different abiotic stress experiments, I found that alternative splicing patterns in the paleologous pairs respond differently to stress. Furthermore, I analyzed alternative splicing in two gene families to identify when alternative splicing originated and to evaluate gain versus loss of alternative splicing after gene duplication. I found alternative splicing form partitioning between the duplicates and possible sub-functionalization between different splicing variants. My results indicate that alternative splicing is a rapidly evolving process after gene duplication that is poorly conserved between genes duplicated by whole genome duplication during the evolutionary history ofArabidopsis.

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