The genomic and phenotypic diversity of Schizosaccharomyces pombe

Daniel C. Jeffares*, Charalampos Rallis, Adrien Rieux, Doug Speed, Martin Převorovský, Tobias Mourier, Francesc X. Marsellach, Zamin Iqbal, Winston Lau, Tammy M.K. Cheng, Rodrigo Pracana, Michael Mülleder, Jonathan L.D. Lawson, Anatole Chessel, Sendu Bala, Garrett Hellenthal, Brendan O'Fallon, Thomas Keane, Jared T. Simpson, Leanne BischofBartlomiej Tomiczek, Danny A. Bitton, Theodora Sideri, Sandra Codlin, Josephine E.E.U. Hellberg, Laurent Van Trigt, Linda Jeffery, Juan Juan Li, Sophie 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

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

112 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)235-241
Number of pages7
JournalNature Genetics
Issue number3
StatePublished - Feb 25 2015

Bibliographical note

Funding Information:
We thank L. Clissold, H. Musk, D. Baker and R. Davey for their contributions to sequencing, H. Levin for discussions about transposons, and J. Mata and S. Marguerat for comments on the manuscript. This work was supported by a Wellcome Trust Senior Investigator Award to J.B. (grant 095598/Z/11/Z), by the Wellcome Trust to S.B., T.K., J.T.S. and R.D., by grant 260801-BIG-IDEA from the European Research Council (ERC) and grant BB/H005854/1 from the Biotechnology and Biological Sciences Research Council (BBSRC) to A.R. and F.B., by UK Medical Research Council grant G0901388 to D.S. and D.J.B., by a Cancer Research UK Postdoctoral Fellowship to T.M.K.C., by an ERC Starting Grant (SYSGRO) to R.E.C.S., a Wellcome Trust PhD studentship to J.L.D.L. and BBSRC grant BB/K006320/1 to R.E.C.S. and A.C., by a Wellcome Trust grant (RG 093735/Z/10/Z) and ERC Starting Grant 260809 to M.R. (M.R. is a Wellcome Trust Research Career Development and Wellcome-Beit Prize Fellow), by Czech Science Foundation grant P305/12/P040 and Charles University grant UNCE 204013 to M.P. and by Cancer Research UK to L.J. and J.H.

Publisher Copyright:
© 2015 Nature America, Inc. All rights reserved.

ASJC Scopus subject areas

  • Genetics


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