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Mol Ecol.:酿酒酵母生态和群体遗传学研究方面取得新进展

来源:中科院微生物所 2012-11-09 17:20

在发酵工业中广为应用的酿酒酵母(Saccharomyces cerevisiae),也是一种在生命科学研究中常用的模式生物。由于其较清晰的遗传背景、相对较小的基因组、完善的基因组和功能基因组学研究积累、明确的有性生殖循环等优势,除分子生物学领域外,正在成为比较与进化基因组学、生物地理学、群体遗传学、生态学和物种形成与演化机制等研究领域的模式生物。然而,我们对这种也许是被研究得最为透彻的真核微生物在自然界中的生态分布和群体结构仍然所知甚少。以前的研究主要基于实验室和人工环境菌株,真正的野生菌株很少涉及。因此,我们对S. cerevisiae的遗传多样性、驯化群体的起源与演化及人工选择对其表型和基因组变异的影响等基本问题很难进行充分的阐释。

近几年来,中科院微生物研究所真菌学国家重点实验室的白逢彦研究组对S. cerevisiae在自然界的生态分布进行了大规模调查,从分布在不同气候带、人工干扰程度不同的环境,包括人迹罕至的原始森林中,采集了数千份样品,使用特殊的选择性分离方法,成功分离出大量酿酒酵母菌株。进而对99株代表性菌株进行了群体遗传学、分子核型和有性生殖隔离等方面的研究。结果表明,S. cerevisiae在自然界中广泛分布,且存在明显的种群分化;与预想结果相反,树皮、森林土壤和腐木等样品的S. cerevisiae分离率均比各种果实样品的更高。野生S. cerevisiae存在清晰的群体结构,从测序的野生菌株中识别出了8个独立的演化谱系(CHN I-VIII)。来自原始森林的谱系(CHN I-V)位于演化树的底部,且已发生显著的遗传分化;而来自次生林、果园和果实的谱系(CHN VI-VIII)与工业应用(驯化)谱系一起,位于演化树的上部,且群体分化程度较低。这一结果显示了S. cerevisiae从原始森林,到次生林,人工环境,再到工业发酵过程的演化路径。原始森林谱系一般为自交群体,具有不同的分子核型,并已产生一定程度的生殖隔离;而人工环境谱系存在更多的遗传重组事件,人为因素促进了其群体间的杂交。与以前群体遗传和群体基因组学研究中应用的,被认为已代表了S. cerevisiae全球遗传多样性的一批菌株相比,我国菌株的遗传多样性指数高出近1倍。这一结果显示中国,或者东亚,可能是S. cerevisiae的起源中心。此外,该研究还在S. cerevisiae群体结构的塑造因素和葡萄酒及清酒驯化谱系的起源等方面,提出了新观点。

上述研究已发表于Molecular Ecology (21: 5404–5417, 2012),期刊并在同期为本篇论文配发了一篇评论(Perspective)。评论指出,这一研究大幅度地提高了我们对酿酒酵母菌多样性的认识水平,并将大大提升我们对其生态、驯化和演化等方面的研究能力。(生物谷Bioon.com)

Surprisingly diverged populations of Saccharomyces cerevisiae in natural environments remote from human activity

Wang QM, Liu WQ, Liti G, Wang SA, Bai FY.

The budding yeast, Saccharomyces cerevisiae, is a leading system in genetics, genomics and molecular biology and is becoming a powerful tool to illuminate ecological and evolutionary principles. However, little is known of the ecology and population structure of this species in nature. Here, we present a field survey of this yeast at an unprecedented scale and have performed population genetics analysis of Chinese wild isolates with different ecological and geographical origins. We also included a set of worldwide isolates that represent the maximum genetic variation of S. cerevisiae documented so far. We clearly show that S. cerevisiae is a ubiquitous species in nature, occurring in highly diversified substrates from human-associated environments as well as habitats remote from human activity. Chinese isolates of S. cerevisiae exhibited strong population structure with nearly double the combined genetic variation of isolates from the rest of the world. We identified eight new distinct wild lineages (CHN I-VIII) from a set of 99 characterized Chinese isolates. Isolates from primeval forests occur in ancient and significantly diverged basal lineages, while those from human-associated environments generally cluster in less differentiated domestic or mosaic groups. Basal lineages from primeval forests are usually inbred, exhibit lineage-specific karyotypes and are partially reproductively isolated. Our results suggest that greatly diverged populations of wild S. cerevisiae exist independently of and predate domesticated isolates. We find that China harbours a reservoir of natural genetic variation of S. cerevisiae and perhaps gives an indication of the origin of the species.

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