Schacherer J, Shapiro JA, Ruderfer DM, Kruglyak L.. Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae. Nature 458: 342-345

Lewis-Sigler Institute for Integrative Genomics, Department of Ecology and Evolutionary Biology and Howard Hughes Medical Institute, Princeton University, Princeton, New Jersey 08544, USA.
Nature (Impact Factor: 41.46). 02/2009; 458(7236):342-5. DOI: 10.1038/nature07670
Source: PubMed


Comprehensive identification of polymorphisms among individuals within a species is essential both for studying the genetic basis of phenotypic differences and for elucidating the evolutionary history of the species. Large-scale polymorphism surveys have recently been reported for human, mouse and Arabidopsis thaliana. Here we report a nucleotide-level survey of genomic variation in a diverse collection of 63 Saccharomyces cerevisiae strains sampled from different ecological niches (beer, bread, vineyards, immunocompromised individuals, various fermentations and nature) and from locations on different continents. We hybridized genomic DNA from each strain to whole-genome tiling microarrays and detected 1.89 million single nucleotide polymorphisms, which were grouped into 101,343 distinct segregating sites. We also identified 3,985 deletion events of length >200 base pairs among the surveyed strains. We analysed the genome-wide patterns of nucleotide polymorphism and deletion variants, and measured the extent of linkage disequilibrium in S. cerevisiae. These results and the polymorphism resource we have generated lay the foundation for genome-wide association studies in yeast. We also examined the population structure of S. cerevisiae, providing support for multiple domestication events as well as insight into the origins of pathogenic strains.

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    • "Specifically, wine strains form a distinct phylogenetic group, with low diversity (Fay & Benavides, 2005; Legras et al., 2007; Liti et al., 2009; Schacherer et al., 2009; Cromie et al., 2013). The diversity between wine strains has been estimated as 1 to 1.4 substitutions per kb and 5 to 6 substitutions per kb between wine and other S. cerevisiae strains from other origins (Fay & Benavides, 2005; Liti et al., 2009; Schacherer et al., 2009). A microsatellite-based study suggested that wine yeast strains could originate from Mesopotamia (Legras et al., 2007; Sicard & Legras, 2011). "
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    ABSTRACT: Saccharomyces cerevisiae and related species, the main workhorses of wine fermentation, have been exposed to stressful conditions for millennia, potentially resulting in adaptive differentiation. As a result, wine yeasts have recently attracted considerable interest for studying the evolutionary effects of domestication. The widespread use of whole genome sequencing during the last decade has provided new insights into the biodiversity, population structure, phylogeography and evolutionary history of wine yeasts. Comparisons between S. cerevisiae isolates from various origins have indicated that a variety of mechanisms, including heterozygosity, nucleotide and structural variations, introgressions, horizontal gene transfer and hybridization, contribute to the genetic and phenotypic diversity of S. cerevisiae. This review will summarize the current knowledge on the diversity and evolutionary history of wine yeasts, focusing on the domestication fingerprints identified in these strains. © FEMS 2015.
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    • "Population analyses often provide valuable insight into the evolutionary history of an organism (Fay & Benavides 2005; Liti et al. 2009; Peris et al. 2014; Ruderfer et al. 2006; Schacherer et al. 2009; Wang et al. 2012). Although S. cerevisiae and S. paradoxus are closely related species and often found in similar natural habitats (Naumov et al. 1998; Sniegowski et al. 2002), our results reveal very distinct characteristics in these two species in response to killer viruses. "
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    ABSTRACT: Microbes have evolved ways of interference competition to gain advantage over their ecological competitors. The use of secreted killer toxins by yeast cells through acquiring double-stranded RNA viruses is one such prominent example. Although the killer behavior has been well studied in laboratory yeast strains, our knowledge regarding how killer viruses are spread and maintained in nature and how yeast cells co-evolve with viruses remains limited. We investigated these issues using a panel of 81 yeast populations belonging to three Saccharomyces sensu stricto species isolated from diverse ecological niches and geographic locations. We found that killer strains are rare among all three species. In contrast, killer toxin resistance is widespread in Saccharomyces paradoxus populations, but not in Saccharomyces cerevisiae or Saccharomyces eubayanus populations. Genetic analyses revealed that toxin resistance in S. paradoxus is often caused by dominant alleles that have independently evolved in different populations. Molecular typing identified one M28 and two types of M1 killer viruses in those killer strains. We further showed that killer viruses of the same type could lead to distinct killer phenotypes under different host backgrounds, suggesting co-evolution between the viruses and hosts in different populations. Taken together, our data suggest that killer viruses vary in their evolutionary histories even within closely related yeast species. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
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    • "Nevertheless , how epistasis takes part among genetic variations within natural populations was still not well understood, and whether it plays a role in the onset of reproductive isolation was unknown. With the advent of sequencing technology, there has been a renewed interest in the understanding of intraspecific diversity in various yeast species in the last decade (Friedrich et al. 2015; Liti et al. 2009; Schacherer et al. 2009; Strope et al. 2015). These advances provided valuable tools to systematically evaluate the onset of intraspecific reproductive isolation across the whole species diversity , to the end of precise characterization of the possible mechanisms involved to a molecular resolution. "
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    ABSTRACT: Exploring the molecular bases of intraspecific reproductive isolation captures the ongoing phenotypic consequences of genetic divergence and provides insights into the early onset of speciation. Recent species-wide surveys using natural populations of yeasts demonstrated that intrinsic post-zygotic reproductive isolation segregates readily within the same species, and revealed the multiplicity of the genetic mechanisms underlying such processes. These advances deepened our current understandings and opened further perspectives regarding the complete picture of molecular and evolutionary origins driving the onset of intraspecific reproductive isolation in yeasts.
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