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Originally published as Genetics Published Articles Ahead of Print on December 28, 2006.
Genetics, Vol. 175, 1341-1350, March 2007, Copyright © 2007
doi:10.1534/genetics.106.066951
Consistent Patterns of Rate Asymmetry and Gene Loss Indicate Widespread Neofunctionalization of Yeast Genes After Whole-Genome Duplication
Kevin P. Byrne and Kenneth H. Wolfe1
Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
1 Corresponding author: Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland.
E-mail: khwolfe{at}tcd.ie
We investigated patterns of rate asymmetry in sequence evolution among the gene pairs (ohnologs) formed by whole-genome duplication (WGD) in yeast species. By comparing three species (Saccharomyces cerevisiae, Candida glabrata, and S. castellii) that underwent WGD to a nonduplicated outgroup (Kluyveromyces lactis), and by using a synteny framework to establish orthology and paralogy relationships at each duplicated locus, we show that 56% of ohnolog pairs show significantly asymmetric protein sequence evolution. For ohnolog pairs that remain duplicated in two species there is a strong tendency for the faster-evolving copy in one species to be orthologous to the faster copy in the other species, which indicates that the evolutionary rate differences were established before speciation and hence soon after the WGD. We also present evidence that in cases where one ohnolog has been lost from the genome of a post-WGD species, the lost copy was likely to have been the faster-evolving member of the pair prior to its loss. These results suggest that a significant fraction of the retained ohnologs in yeast species underwent neofunctionalization soon after duplication.
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Genetics 2007 175: NP.
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