Article (Scientific journals)
Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq
Cromie, Gareth A.; Hyma, Katie E.; Ludlow, Catherine L. et al.
2013In Genes, Genomes and Genomics, 3 (12), p. 2163-2171
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Keywords :
yeast; Genetics; Population
Abstract :
[en] 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.
Research center :
- Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group)
Disciplines :
Genetics & genetic processes
Author, co-author :
Cromie, Gareth A.
Hyma, Katie E.
Ludlow, Catherine L.
Garmendia-Torres, Cecilia
Gilbert, Teresa L.
May, Patrick  ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) ; Institute for Systems Biology - ISB
Huang, Angela A.
Dudley, Aimée M.
Fay, Justin C.
External co-authors :
yes
Language :
English
Title :
Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq
Publication date :
01 December 2013
Journal title :
Genes, Genomes and Genomics
ISSN :
1749-0383
Publisher :
Global Science Books, United Kingdom
Volume :
3
Issue :
12
Pages :
2163-2171
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBilu :
since 15 May 2013

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