Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages.
Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages.
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DOI：
10.1101/gr.276286.121
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发表时间：
2022-05
期刊：
影响因子：
7
通讯作者：
Tsai, Isheng Jason
中科院分区：
文献类型：
--
作者：
Lee, Tracy Jiaye;Liu, Yu-Ching;Liu, Wei-An;Lin, Yu-Fei;Lee, Hsin-Han;Ke, Huei-Mien;Huang, Jen-Pan;Lu, Mei-Yeh Jade;Hsieh, Chia-Lun;Chung, Kuo-Fang;Liti, Gianni;Tsai, Isheng Jason
在人类驯化之前，模式酵母酿酒酵母的生态学和遗传多样性仍然知之甚少。台湾被认为是这种酵母的地理发源地，在那里发现了最多样化的自然谱系。在这里，我们对这个大陆岛屿上的阔叶林进行了广泛的采样，以探索祖先物种的多样性。我们发现S.酿酒酵母在森林中以低丰度普遍分布。对121个分离株的全基因组测序揭示了9个不同的谱系，这些谱系在更新世期间从亚洲谱系中分离出来，当时一个短暂的大陆架陆桥将台湾与其他主要大陆连接起来。台湾特有三个谱系，亚洲广泛分布六个谱系，使该地区成为生物多样性的焦点热点。古代和最近的混合事件之间的自然谱系，检测和遗传祖先的成分与水果的菌株在大多数混合菌株检测。总体而言，台湾分离物的遗传多样性与整个亚洲大陆相当，即使在同一棵树上，不同的谱系也能在一个很好的空间尺度上共存。每个谱系内的变异模式表明，S。酿酒酵母是高度克隆的，并且在自然界中主要无性繁殖。我们确定了不同的选择模式，塑造自然谱系的编码序列，并发现较少的基因家族扩张和收缩，与驯化的谱系。本研究确定S.酿酒酵母具有丰富的自然多样性，不受人类的影响，使其成为微生物生态学的一个强大的模式系统。
The ecology and genetic diversity of the model yeast Saccharomyces cerevisiae before human domestication remain poorly understood. Taiwan is regarded as part of this yeast's geographic birthplace, where the most divergent natural lineage was discovered. Here, we extensively sampled the broadleaf forests across this continental island to probe the ancestral species’ diversity. We found that S. cerevisiae is distributed ubiquitously at low abundance in the forests. Whole-genome sequencing of 121 isolates revealed nine distinct lineages that diverged from Asian lineages during the Pleistocene, when a transient continental shelf land bridge connected Taiwan to other major landmasses. Three lineages are endemic to Taiwan and six are widespread in Asia, making this region a focal biodiversity hotspot. Both ancient and recent admixture events were detected between the natural lineages, and a genetic ancestry component associated with isolates from fruits was detected in most admixed isolates. Collectively, Taiwanese isolates harbor genetic diversity comparable to that of the whole Asia continent, and different lineages have coexisted at a fine spatial scale even on the same tree. Patterns of variations within each lineage revealed that S. cerevisiae is highly clonal and predominantly reproduces asexually in nature. We identified different selection patterns shaping the coding sequences of natural lineages and found fewer gene family expansion and contractions that contrast with domesticated lineages. This study establishes that S. cerevisiae has rich natural diversity sheltered from human influences, making it a powerful model system in microbial ecology.
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影响因子：
4.9
作者：
Branco S;Bi K;Liao HL;Gladieux P;Badouin H;Ellison CE;Nguyen NH;Vilgalys R;Peay KG;Taylor JW;Bruns TD
通讯作者：
Bruns TD
影响因子：
9.2
作者：
Chang CC;Chow CC;Tellier LC;Vattikuti S;Purcell SM;Lee JJ
通讯作者：
Lee JJ
影响因子：
11
作者：
Davison, John;Moora, Mari;Zobel, Martin
通讯作者：
Zobel, Martin
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
64.8
作者：
D'Angiolo, Melania;De Chiara, Matteo;Liti, Gianni
通讯作者：
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