Consistent patterns of rate asymmetry and gene loss indicate widespread neofunctionalization of yeast genes after whole-genome duplication
Consistent patterns of rate asymmetry and gene loss indicate widespread neofunctionalization of yeast genes after whole-genome duplication
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DOI：
10.1534/genetics.106.066951
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发表时间：
2007-03-01
期刊：
影响因子：
3.3
通讯作者：
Wolfe, Kenneth H.
中科院分区：
文献类型：
--
作者：
Byrne, Kevin P.;Wolfe, Kenneth H.
我们研究了酵母物种中由全基因组复制(WGD)形成的基因对之间的序列进化的速率不对称模式。通过将三个经过WGD的物种(酿酒酵母、光滑假丝酵母和卡氏假丝酵母)与一个非重复外群(Kluyvermyces Lactis)进行比较，并在每个重复基因座上建立同源和同源关系，我们发现56%的Ohnolog对表现出显著的不对称蛋白质序列进化。对于在两个物种中保持重复的同源基因对，一个物种中进化得更快的拷贝与另一个物种中进化得更快的拷贝存在强烈的同源趋势，这表明进化速率差异是在物种形成之前建立的，因此在WGD之后不久就建立了。我们还提供了证据，在WGD后物种的基因组中丢失了一个同源基因的情况下，丢失的副本很可能是该物种在丢失之前进化得更快的成员。这些结果表明，酵母物种中保留的很大一部分同源基因在复制后不久就发生了新的功能化。
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.