Despite bread being one of the most historically and culturally important fermented products, its history and influence on the evolution of associated microbial species remains largely unknown. The first evidence of leavened bread dates to the second millenium BCE in Egypt and since, the art of bread-making developed and spread worldwide. Nowadays, leavened bread is made either by using a pure commercial culture of the yeast Saccharomyces cerevisiae or by propagating a sourdough, which is a mix of flour and water spontaneously fermented by yeast and bacteria. We studied the domestication of S. cerevisiae populations originating from industry and sourdough and tested whether these different bread-making processes led to population divergence. We found that the origin of S. cerevisiae bakery strains is polyphyletic with 67 % of strains clustering in two main clades: most commercial strains were tetraploid and clustered with strains having diverse origins, including beer. By contrast, most sourdough strains were diploids and found in a second clade of strains having mosaic genomes and diverse origins including fruits, or clinical and wild environments. When compared to the others, sourdough strains harboured in average a higher copy number of genes involved in maltose utilization, a common sugar produced from dough starch. Overall, a high level of gene flow from multiple contributors was detected. Phenotyping of bakery and non bakery strains further showed that sourdough and industrial bakery populations have undergone human selection for rapidly starting fermentations and for high CO2 production. Interestingly, sourdough strains also showed a better adaptation to a sourdough mimicking environment, suggesting that natural selection occurred as well. In summary, our results revealed that the domestication of bakery yeast populations has been accompanied by dispersion, hybridization and divergent selection through industrial and artisanal bakery processes. In addition, they unveiled for the first time a case of fungus domestication where species divergence occurred through autotetraploidisation.

中文翻译：

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酿酒酵母中两种主要驯化轨迹的证据与不同的面包制作过程有关

尽管面包是历史上和文化上最重要的发酵产品之一，但其历史和对相关微生物物种进化的影响仍然未知。发酵面包的最早证据可以追溯到公元前第二个千年，自此，面包制作技术就发展起来并传播到全世界。如今，发酵面包是通过使用啤酒酵母的纯商业培养或通过发酵发酵面团而制成的，发酵面团是面粉和水的混合物，发酵液是由酵母和细菌自发发酵而成的。我们研究了源自工业和酵母的酿酒酵母种群的驯化，并测试了这些不同的面包制作过程是否导致了种群差异。我们发现了S的起源。酿酒酵母菌株是多系的，其中67％的菌株聚集在两个主要进化枝中：大多数商业菌株为四倍体，并且聚集有多种来源的菌株，包括啤酒。相比之下，大多数酵母菌株是二倍体，存在于具有镶嵌基因组和多种起源的菌株的第二类中，这些起源包括水果，临床或野生环境。与其他酵母菌相比，酵母菌株平均具有更高的拷贝数，涉及麦芽糖利用的基因，这是一种由面团淀粉产生的常见糖。总体而言，检测到来自多个贡献者的高水平基因流。面包房和非面包房菌株的表型进一步表明，为了快速开始发酵并产生高二氧化碳，已经对酵母和工业面包房进行了人工选择。有趣的是 酵母菌株还显示出对酵母模拟环境的更好适应性，表明自然选择也发生了。总而言之，我们的结果表明，烘焙酵母种群的驯化伴随着通过工业和手工烘焙过程的分散，杂交和发散选择。此外，他们首次揭露了真菌驯化案例，该物种通过自身四倍体化发生了物种分化。