Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq
Gareth A. Cromie,Katie E. Hyma,Catherine L. Ludlow,Cecilia Garmendia-Torres,Teresa L. Gilbert,Patrick May,Patrick May,Angela A. Huang,Aimée M. Dudley,Justin C. Fay +9 more
TLDR
This paper applied 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, finding diversity among these strains is principally organized by geography, with European, North American, Asian, and African populations defining the major axes of genetic variation.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.read more
Citations
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The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen
Pooja K Strope,Daniel A. Skelly,Stanislav G. Kozmin,Gayathri Mahadevan,Eric A. Stone,Paul M. Magwene,Fred S. Dietrich,John H. McCusker +7 more
TL;DR: Most phenotypic variation in S. cerevisiae strains is found to be quantitative and identified population, genotype, and phenotype associations, suggesting that copper resistance contributes to fitness in the human host.
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A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes
Anders Bergström,Jared T. Simpson,Francisco Salinas,Benjamin Barré,Leopold Parts,Leopold Parts,Amin Zia,Amin Zia,Alex N. Nguyen Ba,Alan M. Moses,Edward J. Louis,Ville Mustonen,Jonas Warringer,Richard Durbin,Gianni Liti +14 more
TL;DR: It is found that genome content variation, in the form of presence or absence as well as copy number of genetic material, is higher inside S. cerevisiae than within S. paradoxus, despite genetic distances as measured in single-nucleotide polymorphisms being vastly smaller within the former species.
Journal ArticleDOI
A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum
Pedro Almeida,Carla Gonçalves,Sara Teixeira,Diego Libkind,Martin Bontrager,Isabelle Masneuf-Pomarède,Warren Albertin,Pascal Durrens,David James Sherman,Philippe Marullo,Chris Todd Hittinger,Paula Gonçalves,José Paulo Sampaio +12 more
TL;DR: A population genomics approach uses a collection of isolates obtained from fermented beverages and from natural environments on five continents to investigate the global phylogeography and domestication fingerprints of Saccharomyces cerevisiae.
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Distinct Domestication Trajectories in Top-Fermenting Beer Yeasts and Wine Yeasts.
Margarida Gonçalves,Ana Pontes,Pedro Almeida,Raquel Barbosa,Marta Serra,Diego Libkind,Mathias Hutzler,Paula Gonçalves,José Paulo Sampaio +8 more
TL;DR: The results revealed that top-fermenting beer yeasts are polyphyletic, with a main clade composed of at least three subgroups, dominantly represented by the German, British, and wheat beer strains.
Journal ArticleDOI
The genomic and phenotypic diversity of Schizosaccharomyces pombe
Daniel C. Jeffares,Charalampos Rallis,Adrien Rieux,Doug Speed,Martin Převorovský,Tobias Mourier,Francesc Xavier Marsellach,Zamin Iqbal,Winston Lau,Tammy M. K. Cheng,Rodrigo Pracana,Michael Mülleder,Jonathan L.D. Lawson,Anatole Chessel,Sendu Bala,Garrett Hellenthal,Brendan D. O'Fallon,Thomas M. Keane,Jared T. Simpson,Leanne Bischof,Bartlomiej Tomiczek,Danny A. Bitton,Theodora C. Sideri,Sandra Codlin,Josephine E. E. U. Hellberg,Laurent van Trigt,Linda Jeffery,Juan Juan Li,Sophie R. Atkinson,Malte Thodberg,Melanie Febrer,Kirsten McLay,Nizar Drou,William Brown,Jacqueline Hayles,Rafael E. Carazo Salas,Markus Ralser,Nikolas Maniatis,David J. Balding,Francois Balloux,Richard Durbin,Jürg Bähler +41 more
TL;DR: The fission yeast Schizosaccharomyces pombe is an important model for eukaryotic biology, but researchers typically use one standard laboratory strain, so this analysis represents a rich resource to examine genotype-phenotype relationships in a tractable model.
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