Data from: A population genomics insight into the Mediterranean origins of wine yeast domestication

The domestication of the wine yeast Saccharomyces cerevisiae is thought to be contemporary with the development and expansion of viticulture along the Mediterranean basin. Until now, the unavailability of wild lineages prevented the identification of the closest wild relatives of wine yeasts. Here, we enlarge the collection of natural lineages and employ whole-genome data of oak-associated wild isolates to study a balanced number of anthropic and natural S. cerevisiae strains. We identified industrial variants and new geographically delimited populations, including a novel Mediterranean oak population. This population is the closest relative of the wine lineage as shown by a weak population structure and further supported by genomewide population analyses. A coalescent model considering partial isolation with asymmetrical migration, mostly from the wild group into the Wine group, and population growth, was found to be best supported by the data. Importantly, divergence time estimates between the two populations agree with historical evidence for winemaking. We show that three horizontally transmitted regions, previously described to contain genes relevant to wine fermentation, are present in the Wine group but not in the Mediterranean oak group. This represents a major discontinuity between the two populations and is likely to denote a domestication fingerprint in wine yeasts. Taken together, these results indicate that Mediterranean oaks harbour the wild genetic stock of domesticated wine yeasts.人们普遍认为，酿酒酵母（Saccharomyces cerevisiae）的驯化与地中海盆地沿岸葡萄栽培的发展和扩张处于同一时期。此前，野生谱系样本的缺失阻碍了葡萄酒酵母最近缘野生类群的鉴定。本研究扩充了自然谱系的样本库，并利用与橡树共生的野生分离株的全基因组数据，对数量均衡的人为来源与自然来源的酿酒酵母（S. cerevisiae）菌株开展研究。本研究鉴定出若干工业变异株与全新的地理限定种群，其中包括一个新发现的地中海橡树种群。群体结构松散性分析与全基因组群体分析均证实，该种群是葡萄酒酵母谱系的最近缘类群。数据拟合结果显示，考虑部分隔离伴不对称基因流（基因流主要从野生种群流向葡萄酒酵母种群）以及种群扩张的溯祖模型，与实验数据的契合度最高。尤为重要的是，两个种群的分化时间估算结果与酿酒历史的考古证据相吻合。本研究发现，葡萄酒酵母种群中存在三个此前被报道携带与葡萄酒发酵相关基因的水平转移区域，而地中海橡树种群中则无此类区域。这一差异构成了两个种群间的显著遗传间断，很可能代表了葡萄酒酵母的驯化印记。综合以上结果，本研究表明地中海橡树承载着驯化酿酒酵母的野生遗传种质资源。