Consistent Patterns of Rate Asymmetry and Gene Loss Indicate Widespread Neofunctionalization of Yeast Genes After Whole-Genome Duplication

摘要

We investigated patterns of rate asymmetry in sequence evolution among the gene pairs (ohnologs)nformed by whole-genome duplication (WGD) in yeast species. By comparing three species (Saccharomycesncerevisiae, Candida glabrata, and S. castellii) that underwent WGD to a nonduplicated outgroupn(Kluyveromyces lactis), and by using a synteny framework to establish orthology and paralogy relationshipsnat each duplicated locus, we show that 56% of ohnolog pairs show significantly asymmetric proteinnsequence evolution. For ohnolog pairs that remain duplicated in two species there is a strong tendency fornthe faster-evolving copy in one species to be orthologous to the faster copy in the other species, whichnindicates that the evolutionary rate differences were established before speciation and hence soon afternthe WGD. We also present evidence that in cases where one ohnolog has been lost from the genome of anpost-WGD species, the lost copy was likely to have been the faster-evolving member of the pair prior to itsnloss. These results suggest that a significant fraction of the retained ohnologs in yeast species underwentnneofunctionalization soon after duplication.