The Australian Wine Research Institute, Adelaide, Australia.
PLoS Genet. 2011 Feb 3;7(2):e1001287. doi: 10.1371/journal.pgen.1001287.
Human intervention has subjected the yeast Saccharomyces cerevisiae to multiple rounds of independent domestication and thousands of generations of artificial selection. As a result, this species comprises a genetically diverse collection of natural isolates as well as domesticated strains that are used in specific industrial applications. However the scope of genetic diversity that was captured during the domesticated evolution of the industrial representatives of this important organism remains to be determined. To begin to address this, we have produced whole-genome assemblies of six commercial strains of S. cerevisiae (four wine and two brewing strains). These represent the first genome assemblies produced from S. cerevisiae strains in their industrially-used forms and the first high-quality assemblies for S. cerevisiae strains used in brewing. By comparing these sequences to six existing high-coverage S. cerevisiae genome assemblies, clear signatures were found that defined each industrial class of yeast. This genetic variation was comprised of both single nucleotide polymorphisms and large-scale insertions and deletions, with the latter often being associated with ORF heterogeneity between strains. This included the discovery of more than twenty probable genes that had not been identified previously in the S. cerevisiae genome. Comparison of this large number of S. cerevisiae strains also enabled the characterization of a cluster of five ORFs that have integrated into the genomes of the wine and bioethanol strains on multiple occasions and at diverse genomic locations via what appears to involve the resolution of a circular DNA intermediate. This work suggests that, despite the scrutiny that has been directed at the yeast genome, there remains a significant reservoir of ORFs and novel modes of genetic transmission that may have significant phenotypic impact in this important model and industrial species.
人为干预使酵母酿酒酵母经历了多轮独立驯化和数千代的人工选择。因此，该物种包含了遗传多样性的天然分离株和用于特定工业应用的驯化菌株。然而，在这个重要生物的驯化进化过程中，所捕获的遗传多样性范围仍有待确定。为了开始解决这个问题，我们已经生成了六个商业酿酒酵母菌株的全基因组组装（四个葡萄酒和两个酿造菌株）。这代表了首次从工业用途的酿酒酵母菌株中产生的基因组组装，也是首次为酿造用酿酒酵母菌株生成的高质量组装。通过将这些序列与六个现有的高覆盖率酿酒酵母基因组组装进行比较，发现了明确的特征，定义了每个工业酵母类别。这种遗传变异包括单核苷酸多态性和大规模的插入和缺失，后者通常与菌株之间的 ORF 异质性有关。这包括发现了二十多个以前在酿酒酵母基因组中未被识别的可能基因。比较大量的酿酒酵母菌株还能够对五个 ORF 簇进行特征描述，这些 ORF 簇已经多次通过似乎涉及解决环状 DNA 中间体的方式整合到葡萄酒和生物乙醇菌株的基因组中，并且位于不同的基因组位置。这项工作表明，尽管对酵母基因组进行了严格的研究，但仍然存在大量的 ORF 和新的遗传传递模式，这些模式可能对这个重要的模型和工业物种具有显著的表型影响。
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