Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq.
Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq.
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DOI：
10.1534/g3.113.007492
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发表时间：
2013-12-09
期刊：
影响因子：
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通讯作者：
Fay JC
中科院分区：
文献类型：
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作者：
Cromie GA;Hyma KE;Ludlow CL;Garmendia-Torres C;Gilbert TL;May P;Huang AA;Dudley AM;Fay JC
芽殖酵母酿酒酵母对于人类食品生产很重要，并且作为生物学研究的模式生物。全球酵母菌株群体中包含的遗传多样性是许多领域的宝贵资源，包括遗传学、生物工程以及进化和群体结构研究。在这里，我们应用多重、精简的基因组测序策略（限制性位点相关测序或 RAD-seq）对从广泛的地理位置和环境生态位中分离出的大量酿酒酵母菌株进行基因分型。该方法允许对所有基因组中相同的 1% 进行测序，产生跨 262 个菌株的 116,880 个碱基的多重序列比对。我们发现这些菌株的多样性主要是按地理分布的，包括欧洲、北美、亚洲和非洲/南美。 E. 亚洲人群定义了遗传变异的主轴。在更精细的范围内，来自可可、橄榄和清酒的一小群菌株是由其他菌株中不存在的独特变体定义的。一个群体包含来自各种发酵的菌株，表现出高水平的杂合性和来自欧洲和亚洲群体的等位基因的混合物，表明该群体的混合起源。我们提出了一种地理分化模型，随后是与人类相关的混合，主要是欧洲和亚洲人群之间的混合，最近是欧洲和北美人群之间的混合。这里描述的大量基因型酵母菌株将为广大酵母研究人员提供有用的资源。
The budding yeast Saccharomyces cerevisiae is important for human food production and as a model organism for biological research. The genetic diversity contained in the global population of yeast strains represents a valuable resource for a number of fields, including genetics, bioengineering, and studies of evolution and population structure. Here, we apply a multiplexed, reduced genome sequencing strategy (restriction site−associated sequencing or RAD-seq) to genotype a large collection of S. cerevisiae strains isolated from a wide range of geographical locations and environmental niches. The method permits the sequencing of the same 1% of all genomes, producing a multiple sequence alignment of 116,880 bases across 262 strains. We find diversity among these strains is principally organized by geography, with European, North American, Asian, and African/S. E. Asian populations defining the major axes of genetic variation. At a finer scale, small groups of strains from cacao, olives, and sake are defined by unique variants not present in other strains. One population, containing strains from a variety of fermentations, exhibits high levels of heterozygosity and a mixture of alleles from European and Asian populations, indicating an admixed origin for this group. We propose a model of geographic differentiation followed by human-associated admixture, primarily between European and Asian populations and more recently between European and North American populations. The large collection of genotyped yeast strains characterized here will provide a useful resource for the broad community of yeast researchers.