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UBC Theses and Dissertations

Evolution and neofunctionalization of imprinted genes after duplication in Brassicaceae Qiu, Yichun


Plant genomes have large numbers of duplicated genes. After duplication one duplicate can acquire a new function or expression pattern, referred to as neofunctionalization. Some duplicated genes are imprinted, where only one allele is expressed depending on its parental origin. I hypothesized that duplicated imprinted genes frequently show an accelerated rate of amino acid sequence evolution and have a new expression pattern compared with their paralogs, which together are suggestive of neofunctionalization. I first studied four imprinted genes in Arabidopsis, FIS2, MPC, FWA, and HDG3 that have flower and/or seed specific expression. I found that they all have considerably accelerated rates of sequence evolution compared to their paralogs. To determine the ancestral expression pattern I assayed expression patterns in outgroup species, the results of which strongly suggested that the imprinted genes have acquired a novel organ-specific expression pattern restricted to flowers and/or seeds. Using data from recent large-scale identification studies of imprinted genes, I detected by phylogenetic tree analyses 133 imprinted genes that arose from gene duplication events in Brassicaceae. Analyses of 48 alpha whole genome duplicated gene pairs indicated that many imprinted genes show an accelerated rate of amino acid changes compared to their paralogs. Analyses of microarray data indicated that many imprinted genes have expression patterns restricted to flowers and/or seeds, compared with their broadly-expressed paralogs. Both the accelerated sequence rate evolution and the new expression pattern in the imprinted genes suggest that after evolutionarily recent duplication events, imprinted genes frequently underwent neofunctionalization. In particular, neofunctionalization of the FIS2 gene has led to a change in the mechanism of regulating seed development in Brassicaceae. Multiple lines of evidence, when considered together, are highly suggestive of many origins of imprinting in Brassicaceae. This study reveals that the origin of genetic imprinting can arise over short evolutionary time periods and gene duplication serves as an important factor generating imprinted genes.

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