Department of Genetics, Genomics and Microbiology, University of Strasbourg/Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7156, Strasbourg, France.
G3 (Bethesda). 2012 Sep;2(9):1103-11. doi: 10.1534/g3.112.003152. Epub 2012 Sep 1.
Mitochondria are organelles, which play a key role in some essential functions, including respiration, metabolite biosynthesis, ion homeostasis, and apoptosis. The vast numbers of mitochondrial DNA (mtDNA) sequences of various yeast species, which have recently been published, have also helped to elucidate the structural diversity of these genomes. Although a large corpus of data are now available on the diversity of yeast species, little is known so far about the mtDNA diversity in single yeast species. To study the genetic variations occurring in the mtDNA of wild yeast isolates, we performed a genome-wide polymorphism survey on the mtDNA of 18 Lachancea kluyveri (formerly Saccharomyces kluyveri) strains. We determined the complete mt genome sequences of strains isolated from various geographical locations (in North America, Asia, and Europe) and ecological niches (Drosophila, tree exudates, soil). The mt genome of the NCYC 543 reference strain is 51,525 bp long. It contains the same core of genes as Lachancea thermotolerans, the nearest relative to L. kluyveri. To explore the mt genome variations in a single yeast species, we compared the mtDNAs of the 18 isolates. The phylogeny and population structure of L. kluyveri provide clear-cut evidence for the existence of well-defined geographically isolated lineages. Although these genomes are completely syntenic, their size and the intron content were found to vary among the isolates studied. These genomes are highly polymorphic, showing an average diversity of 28.5 SNPs/kb and 6.6 indels/kb. Analysis of the SNP and indel patterns showed the existence of a particularly high overall level of polymorphism in the intergenic regions. The dN/dS ratios obtained are consistent with purifying selection in all these genes, with the noteworthy exception of the VAR1 gene, which gave a very high ratio. These data suggest that the intergenic regions have evolved very fast in yeast mitochondrial genomes.
线粒体是细胞器，在一些基本功能中发挥关键作用，包括呼吸作用、代谢物生物合成、离子平衡和细胞凋亡。最近发表的各种酵母物种的大量线粒体 DNA (mtDNA) 序列也有助于阐明这些基因组的结构多样性。尽管现在有大量关于酵母物种多样性的数据，但到目前为止，对单个酵母物种的 mtDNA 多样性知之甚少。为了研究野生酵母分离株的 mtDNA 中发生的遗传变异，我们对 18 株拉曼酵母 (Lachancea kluyveri，以前称为酿酒酵母 Saccharomyces kluyveri) 的 mtDNA 进行了全基因组多态性调查。我们测定了来自不同地理位置（北美、亚洲和欧洲）和生态位（果蝇、树液、土壤）的菌株的完整 mt 基因组序列。NCYC 543 参考菌株的 mt 基因组长 51525bp，包含与拉曼酵母亲缘关系最近的 Lachancea thermotolerans 的相同核心基因。为了探索单个酵母物种的 mt 基因组变异，我们比较了 18 个分离株的 mtDNA。L. kluyveri 的系统发育和种群结构为明确的地理隔离谱系的存在提供了明确的证据。尽管这些基因组完全同源，但我们发现研究的分离株的 mtDNA 大小和内含子含量存在差异。这些基因组高度多态，平均每个 SNP 为 28.5 个/kb，每个 indel 为 6.6 个/kb。对 SNP 和 indel 模式的分析表明，在基因间区存在特别高的整体多态性水平。所有这些基因的 dN/dS 比值都与纯化选择一致，但 VAR1 基因除外，该基因的比值非常高。这些数据表明，酵母线粒体基因组的基因间区进化非常快。
