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Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq.

Cromie GA, Hyma KE, Ludlow CL, Garmendia-Torres C, Gilbert TL, May P, Huang AA, Dudley AM, Fay JC - G3 (Bethesda) (2013)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Institute for Systems Biology, Seattle, Washington 98109.

ABSTRACT
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.

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Related in: MedlinePlus

Clustered genotypes with inferred population structure and membership. Sites were clustered by complete hierarchical clustering by use of the Euclidean distance of allele sharing (identity by state). Strains were grouped by population structure and memberships inferred using InStruct. Minor alleles are shown in red, heterozygous sites in yellow, common alleles in black, and missing data are gray. Populations are labeled by the most common source and/or geographic location from which they were originally isolated.
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fig2: Clustered genotypes with inferred population structure and membership. Sites were clustered by complete hierarchical clustering by use of the Euclidean distance of allele sharing (identity by state). Strains were grouped by population structure and memberships inferred using InStruct. Minor alleles are shown in red, heterozygous sites in yellow, common alleles in black, and missing data are gray. Populations are labeled by the most common source and/or geographic location from which they were originally isolated.

Mentions: Neighbor-joining tree of the 262 S. cerevisiae strains based on multiple alignments of 116,880 bases. Branch lengths are proportional to sequence divergence measured as P-distance. Scale bar indicates 5 polymorphisms/10 kb of sequence. Geographical and environmental clusters of strains are named and are indicated by black-outlined/gray-filled ovals. Colored ovals with numbering refer to strain populations identified in Figure 2. Seven strains widely used in the laboratory are labeled.


Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq.

Cromie GA, Hyma KE, Ludlow CL, Garmendia-Torres C, Gilbert TL, May P, Huang AA, Dudley AM, Fay JC - G3 (Bethesda) (2013)

Clustered genotypes with inferred population structure and membership. Sites were clustered by complete hierarchical clustering by use of the Euclidean distance of allele sharing (identity by state). Strains were grouped by population structure and memberships inferred using InStruct. Minor alleles are shown in red, heterozygous sites in yellow, common alleles in black, and missing data are gray. Populations are labeled by the most common source and/or geographic location from which they were originally isolated.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3852379&req=5

fig2: Clustered genotypes with inferred population structure and membership. Sites were clustered by complete hierarchical clustering by use of the Euclidean distance of allele sharing (identity by state). Strains were grouped by population structure and memberships inferred using InStruct. Minor alleles are shown in red, heterozygous sites in yellow, common alleles in black, and missing data are gray. Populations are labeled by the most common source and/or geographic location from which they were originally isolated.
Mentions: Neighbor-joining tree of the 262 S. cerevisiae strains based on multiple alignments of 116,880 bases. Branch lengths are proportional to sequence divergence measured as P-distance. Scale bar indicates 5 polymorphisms/10 kb of sequence. Geographical and environmental clusters of strains are named and are indicated by black-outlined/gray-filled ovals. Colored ovals with numbering refer to strain populations identified in Figure 2. Seven strains widely used in the laboratory are labeled.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Institute for Systems Biology, Seattle, Washington 98109.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus