Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication

Abstract

Among yeasts that underwent whole-genome duplication (WGD), Kluyveromyces polysporus represents the lineage most distant from Saccharomyces cerevisiae. By sequencing the K. polysporus genome and comparing it with the S. cerevisiae genome using a likelihood model of gene loss, we show that these species diverged very soon after the WGD, when their common ancestor contained >9,000 genes. The two genomes subsequently converged onto similar current sizes (5,600 protein-coding genes each) and independently retained sets of duplicated genes that are strikingly similar. Almost half of their surviving single-copy genes are not orthologs but paralogs formed by WGD, as would be expected if most gene pairs were resolved independently. In addition, by comparing the pattern of gene loss among K. polysporus, S. cerevisiae, and three other yeasts that diverged after the WGD, we show that the patterns of gene loss changed over time. Initially, both members of a duplicate pair were equally likely to be lost, but loss of the same gene copy in independent lineages was increasingly favored at later time points. This trend parallels an increasing restriction of reciprocal gene loss to more slowly evolving gene pairs over time and suggests that, as duplicate genes diverged, one gene copy became favored over the other. The apparent low initial sequence divergence of the gene pairs leads us to propose that the yeast WGD was probably an autopolyploidization.genomics ͉ polyploidy ͉ reciprocal gene loss ͉ Vanderwaltozyma polyspora A n ancestor of Saccharomyces cerevisiae underwent wholegenome duplication (WGD) after it had diverged from non-WGD yeast lineages such as Kluyveromyces lactis, Kluyveromyces waltii, and Ashbya gossypii (1-4). The WGD had a major impact on the evolution of S. cerevisiae and its relatives, most notably by facilitating their adaptation to anaerobic growth (5) and contributing to their rapid speciation (6). In S. cerevisiae, Ϸ20% of genes are members of duplicated pairs that were formed in the WGD (7). The other loci became single-copy again during the sorting-out process (genome reduction) that occurred after the WGD. Similar large-scale loss of copies of duplicated genes from paleopolyploid genomes has occurred during the evolution of plants such as grasses and crucifers (8-11).Because the S. cerevisiae genome sequence is a single observation of the evolutionary result of the WGD that occurred in a yeast ancestor, it has not been clear whether the set of genes that survived the sorting-out process in S. cerevisiae was an inevitable outcome of the WGD, or whether stochastic processes played a major role. Two questions need to be answered. First, are the loci that remain duplicated in S. cerevisiae a special subset of the pre-WGD genome, that were somehow more amenable to retention in duplicate after WGD? Second, for loci that are now single-copy in S. cerevisiae, was retention of one particular gene copy preferred over the other? These questions are best addressed by studying the genomes of other yeast species tha...

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