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doi:10.1534/genetics.106.066951
A more recent version of this article appeared on March 1, 2007.
REGULAR RESEARCH PAPERS |
Consistent patterns of rate asymmetry and gene loss indicate widespread neofunctionalization of yeast genes after whole-genome duplication
Kevin P Byrne 1 and Kenneth H Wolfe 1*
1 Trinity College Dublin
* To whom correspondence should be addressed. E-mail: khwolfe{at}tcd.ie.
Submitted on October 18, 2006
Revised on November 20, 2006
Accepted on 20 December 2006
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 Saccharomyces castellii) that underwent WGD to a non-duplicated outgroup (Kluyveromyces lactis), and by using a synteny framework to establish orthology and paralogy relationships at each duplicated locus, we show that (i) 56% of ohnolog pairs show significantly asymmetric protein sequence evolution; and (ii) 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 (iii) 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.
Key Words: Saccharomyces cerevisiae, gene duplication, gene loss, neofunctionalization, rate asymmetry
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