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UBC Theses and Dissertations

Evolution of duplicate gene sequences, expression patterns, and functions in the Brassicaceae and other rosids Liu, Shao-Lun


Duplicated genes are considered as raw materials for evolutionary innovations. They are common in eukaryotic genomes, particularly in plants due to the high incidence of whole genome duplication. Thus, understanding the factors that contribute to the retention of duplicated genes is a fundamental topic in evolutionary biology. I tackle this topic by examining how reciprocal expression (RE) among different organ and tissue types, as well as protein subcellular relocalization (PSR), contributes to the retention of duplicated genes. From analyses of microarray data across 83 different organ/cell types and developmental stages in Arabidopsis thaliana, I determined that more than 30% of duplicate pairs showed RE patterns (chapter 2). Reconstructing their ancestral expression pattern, more RE cases resulted from gain of a new expression pattern (neofunctionalization) than from partitioning of ancestral expression patterns (subfunctionalization), with pollen being a common location for expression gain (chapter 2). During the analysis on RE, I found a dramatic example of neofunctionalization for a pair of protein kinase genes, SSP and BSK1, in the Brassicaceae (chapter 3). BSK1 and SSP have opposite expression patterns in pollen compared with all other parts of the plant. I determined that BSK1 retains the ancestral expression pattern and function and that the ancestral function of SSP was lost by deletions in the kinase domain. I revealed that SSP changed its function from a component of the brassinosteroid signaling pathway to being a paternal regulator of embryogenesis. I also found that two reciprocally expressed duplicated gene pairs, a peroxidase gene pair and a CDPK gene pair, in Brassicaceae showed PSR and evidence for neofunctionalization (chapter 2). To better understand how PSR can contribute to the retention of duplicated genes, I focused on a particular example for a pair of the chloroplast-origin ribosomal protein S13 (rps13) genes in rosids (chapter 4). One encodes chloroplast-imported RPS13 (nucp rps13), while the other encodes mitochondria-imported RPS13 (numit rps13). I provided evidence that numit rps13 genes have experienced adaptive and convergent evolution. My thesis provides important insights into the evolutionary importance of RE and PSR on the retention of duplicated genes in plants.

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