基于RAD-seq的酿酒酵母基因组序列多样性及群体结构分析
Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq
摘要：
芽殖酵母Saccharomyces cerevisiae对人类食品生产和生物学研究具有重要意义。全球酵母菌株群体中所含的遗传多样性〈动〉<动>代表了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的研究。在这里，我们应用一种多重的，简化的基因组测序策略（称为RAD-seq）对大量的S。酿酒酵母菌株，分离自广泛的地理位置和环境小生境。该方法允许对所有基因组中相同的1%进行测序，从而在262个菌株中产生116，880个碱基的多重序列比对。我们发现这些菌株之间的多样性主要是由地理组织的，与欧洲，北美，亚洲和非洲/S。E.亚洲人群定义了遗传变异的主轴。在更精细的尺度上，来自可可、橄榄和清酒的小群体菌株由其他菌株中不存在的独特变体定义。一个人口，含有各种发酵菌株，表现出高水平的杂合性和混合物的等位基因从欧洲和亚洲的人口，这组混合的起源。在这种全球多样性的背景下，我们证明，在实验室中常用的7种菌株的集合只包括在菌株的完整集合中存在的遗传多样性〈动〉性<动>的四分之一，强调相对有限的遗传多样性〈动〉性<动>捕获的当前一组实验室菌株。我们提出了一个模型的地理分化，其次是人类相关的混合物，主要是欧洲和亚洲人口之间，最近欧洲和北美人口之间。大量收集的基因型酵母菌株的特点，这里将提供一个有用的资源，为广大社区的酵母研究人员。
英文摘要：
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 (known as 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 mixtures of alleles from European and Asian populations, indicating an admixed origin for this group. In the context of this global diversity, we demonstrate that a collection of seven strains commonly used in the laboratory encompasses only one quarter of the genetic diversity present in the full collection of strains, underscoring the relatively limited genetic diversity captured by the current set of lab strains. 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.
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