Genomic Sequence Diversity and Population Structure of<i>Saccharomyces cerevisiae</i>Assessed by RAD-seq
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- Gareth A Cromie
- Institute for Systems Biology, Seattle, Washington 98109
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- Katie E Hyma
- Bioinformatics Facility (CBSU), Institute for Biotechnology, Cornell University, Ithaca, New York 14850
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- Catherine L Ludlow
- Institute for Systems Biology, Seattle, Washington 98109
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- Cecilia Garmendia-Torres
- Institute for Systems Biology, Seattle, Washington 98109
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- Patrick May
- Institute for Systems Biology, Seattle, Washington 98109
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- Angela A Huang
- University of Pennsylvania, Philadelphia, Pennsylvania 19104
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- Aimée M Dudley
- Institute for Systems Biology, Seattle, Washington 98109
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- Justin C Fay
- Department of Genetics, Washington University, St. Louis, Missouri 63108
説明
<jats:title>Abstract</jats:title><jats:p>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.</jats:p>
収録刊行物
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- G3 Genes|Genomes|Genetics
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G3 Genes|Genomes|Genetics 3 (12), 2163-2171, 2013-12-01
Oxford University Press (OUP)