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The genomic and phenotypic diversity of Schizosaccharomyces pombe

2015; Nature Portfolio; Volume: 47; Issue: 3 Linguagem: Inglês

10.1038/ng.3215

1546-1718

Daniel Jeffares, Charalampos Rallis, Adrien Rieux, Doug Speed, Martin Převorovský, Tobias Mourier, Xavi Marsellach, Zamin Iqbal, Winston Lau, Tammy M. K. Cheng, Rodrigo Pracana, Michael Mülleder, J Lawson, Anatole Chessel, Sendu Bala, Garrett Hellenthal, Brendan O’Fallon, Thomas Keane, Jared T. Simpson, Leanne Bischof, Bartłomiej Tomiczek, Danny A. Bitton, Theodora Sideri, Sandra Codlin, Josephine E. E. U. Hellberg, Laurent van Trigt, Linda Jeffery, Juanjuan Li, Sophie Atkinson, Malte Thodberg, Melanie Febrer, Kirsten McLay, Nizar Drou, William R. Brown, Jacqueline Hayles, Rafael E. Carazo‐Salas, Markus Ralser, Nikolas Maniatis, David J. Balding, François Balloux, Richard Durbin, Jürg Bähler,

Yeasts and Rust Fungi Studies

Daniel Jeffares, Jürg Bähler and colleagues report the genome sequences of 161 natural isolates of Schizosaccharomyces pombe, finding moderate genetic diversity and weak global population structure. They also report genome-wide association studies for 223 quantitative traits. Natural variation within species reveals aspects of genome evolution and function. The fission yeast Schizosaccharomyces pombe is an important model for eukaryotic biology, but researchers typically use one standard laboratory strain. To extend the usefulness of this model, we surveyed the genomic and phenotypic variation in 161 natural isolates. We sequenced the genomes of all strains, finding moderate genetic diversity (π = 3 × 10−3 substitutions/site) and weak global population structure. We estimate that dispersal of S. pombe began during human antiquity (∼340 BCE), and ancestors of these strains reached the Americas at ∼1623 CE. We quantified 74 traits, finding substantial heritable phenotypic diversity. We conducted 223 genome-wide association studies, with 89 traits showing at least one association. The most significant variant for each trait explained 22% of the phenotypic variance on average, with indels having larger effects than SNPs. This analysis represents a rich resource to examine genotype-phenotype relationships in a tractable model.