走出中国：酿酒酵母的起源、驯养与演化

Out of China: origin, domestication and evolution of Saccharomyces cerevisiae

摘要:

酿酒酵母(Saccharomyces cerevisiae)被广泛应用于酒类酿造和食品发酵等行业，其被人类利用的历史已有近万年。酿酒酵母也是遗传学、分子生物学、基因组学和合成生物学等研究中常用的模式生物。近年来研究者对其自然和驯养种群进行了全球范围的生态学、群体遗传学和群体基因组学等方面的研究，更新了对其生态分布、遗传多样性、自然进化和驯养史以及进化动力等方面的认知。发现酿酒酵母在原始森林等自然环境中普遍存在，并可能偏好阔叶树树干、腐木和周围土壤等生境。中国酿酒酵母的遗传多样性显著高于世界其他地区，该物种最古老的谱系也仅发现于中国，说明中国可能是该物种的起源地。生态适应是塑造该物种群体结构的主要力量，导致其野生和驯养群体之间的明显分化。驯养群体又分化为固态发酵和液态发酵两大类群，每个类群内又形成不同的驯养谱系。该物种野生群体的遗传多样性远高于其驯养群体，而野生群体遗传多样性的形成主要由中性突变引起。中国野生和驯养群体在麦芽糖利用能力、基因组杂合性、子囊孢子形成率和孢子活力等方面表现出显著差异，表明这2个群体采取不同的生活策略来适应其不同的生活环境。驯养群体通过群体或谱系特异性基因拷贝数、基因含量和等位基因分布等变异，并通过横向转移以及基因渐渗获得外源基因等方式，实现对特定生态位的适应。

Abstract:

The budding yeast Saccharomyces cerevisiae has been used by humans in food and beverage fermentation for nearly 10 000 years. It is also a model organism commonly used in genetics, molecular biology, genomics, and synthetic biology research. Ecological, population genetics, and population genomics studies on both wild and domesticated populations of this species conducted globally in recent years have shown that S. cerevisiae distributes ubiquitously in the wild, including in primitive forests, and may prefer habitats such as broad-leaved tree bark, decaying wood, and surrounding soil. The genetic diversity of S. cerevisiae in China is significantly higher than that in other parts of the world, and the oldest lineages of this species have only been found in China, suggesting an out-of-China origin of this species. Ecological adaptation is the main force shaping the population structure of this species, leading to a clear differentiation between the wild and domesticated populations. The domesticated population has further diverged into solid- and liquid-state fermentation groups, each with different domesticated lineages. The genetic diversity of the wild population is significantly higher than that of the domesticated population, and the formation of genetic diversity in the wild population appears to be mainly caused by neutral mutations. The wild and domesticated populations exhibit significant differences in maltose utilization ability, genomic heterozygosity, sporulation rate, and spore viability, indicating that these two populations adopt different life strategies to adapt to their different habitats. The domesticated lineages adapt to specific ecological niches through lineage-specific copy number variation (CNV), gene content and allele distribution variations, horizontal gene transfer, and introgression.