Network Centralities and the Retention of Genes Following Whole Genome Duplication in Saccharomyces cerevisiae




Imrie, Matthew J.

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The yeast Saccharomyces cerevisiae genome is descendant from a whole genome duplication event approximately 150 million years ago. Following this duplication many genes were lost however, a certain class of genes, termed ohnologs, persist in duplicate. In this thesis we investigate network centrality as it relates to ohnolog re- tention with the goal of determining why only certain genes were retained. With this in mind, we compare physical and genetic interaction networks and genetic and pro- tein sequence data in order to reveal how network characteristics and post-duplication retention are related. We show that there are two subclasses of ohnologs, those that interact with their duplication sister and those that do not and that these two classes have distinct characteristics that provide insight into the evolutionary mechanisms that affected their retention following whole genome duplication. Namely, a very low ratio of non-synonymous mutations per non-synonymous site for ohnologs that retain an interaction with their duplicate. The opposite observation is seen for ohnologs that have lost their interaction with their duplicate. We interpret this in the fol- lowing way: ohnologs that have retained their interaction with their duplicate are functionally constrained to buffer for the other ohnolog. For this reason they are retained; ohnologs that have lost their interaction with their duplicate are retained because they are functionally divergent to the point of being individually essential. Additionally we investigate small scale duplications and show that, generally, the mechanism of duplication (smale scale or whole genomes) does not affect the distri- bution of network characteristics. Nor do these network characteristics correlate to the selective pressure observed by retained paralogous genes, including both ohnologs and small scale duplicates. In contrast, we show that the network characteristics of individual genes, particularly the magnitude of their physical and genetic network centralities, do influence their retention following whole genome duplication.



Yeast, Network Analysis, Saccharomyces cerevisiae, Centralities, Evolution, Whole Genome Duplication