Wong Simon, Butler Geraldine, Wolfe Kenneth H
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland.
Proc Natl Acad Sci U S A. 2002 Jul 9;99(14):9272-7. doi: 10.1073/pnas.142101099. Epub 2002 Jul 1.
The wealth of comparative genomics data from yeast species allows the molecular evolution of these eukaryotes to be studied in great detail. We used "proximity plots" to visually compare chromosomal gene order information from 14 hemiascomycetes, including the recent Génolevures survey, to Saccharomyces cerevisiae. Contrary to the original reports, we find that the Génolevures data strongly support the hypothesis that S. cerevisiae is a degenerate polyploid. Using gene order information alone, 70% of the S. cerevisiae genome can be mapped into "sister" regions that tile together with almost no overlap. This map confirms and extends the map of sister regions that we constructed previously by using duplicated genes, an independent source of information. Combining gene order and gene duplication data assigns essentially the whole genome into sister regions, the largest gap being only 36 genes long. The 16 centromere regions of S. cerevisiae form eight pairs, indicating that an ancestor with eight chromosomes underwent complete doubling; alternatives such as segmental duplications can be ruled out. Gene arrangements in Kluyveromyces lactis and four other species agree quantitatively with what would be expected if they diverged from S. cerevisiae before its polyploidization. In contrast, Saccharomyces exiguus, Saccharomyces servazzii, and Candida glabrata show higher levels of gene adjacency conservation, and more cases of imperfect conservation, suggesting that they split from the S. cerevisiae lineage after polyploidization. This finding is confirmed by sequences around the C. glabrata TRP1 and IPP1 loci, which show that it contains sister regions derived from the same duplication event as that of S. cerevisiae.
来自酵母物种的丰富比较基因组学数据，使得对这些真核生物的分子进化能够进行非常详细的研究。我们使用“邻近图谱”直观地比较了14种半子囊菌（包括最近的酵母基因组测序计划）与酿酒酵母的染色体基因顺序信息。与最初的报道相反，我们发现酵母基因组测序计划的数据有力地支持了酿酒酵母是一种退化多倍体的假说。仅使用基因顺序信息，酿酒酵母基因组的70%可以映射到几乎没有重叠地拼接在一起的“姐妹”区域。这一图谱证实并扩展了我们之前通过使用重复基因（一种独立的信息来源）构建的姐妹区域图谱。结合基因顺序和基因重复数据，基本上可以将整个基因组划分到姐妹区域，最大的间隔仅36个基因长。酿酒酵母的16个着丝粒区域形成八对，这表明一个具有八条染色体的祖先经历了完全加倍；可以排除诸如片段重复等其他可能性。乳酸克鲁维酵母和其他四个物种的基因排列在数量上与如果它们在酿酒酵母多倍体化之前就与其分化所预期的情况相符。相比之下，微小酿酒酵母、塞尔瓦齐酿酒酵母和光滑念珠菌表现出更高水平的基因邻接保守性，以及更多不完全保守的情况，这表明它们在多倍体化之后从酿酒酵母谱系中分化出来。光滑念珠菌TRP1和IPP1基因座周围的序列证实了这一发现，这些序列表明它包含与酿酒酵母相同复制事件产生的姐妹区域。
