Format

Send to

Choose Destination
Nat Genet. 2015 Mar;47(3):235-41. doi: 10.1038/ng.3215. Epub 2015 Feb 9.

The genomic and phenotypic diversity of Schizosaccharomyces pombe.

Author information

1
Department of Genetics, Evolution and Environment, University College London, London, UK.
2
1] Department of Genetics, Evolution and Environment, University College London, London, UK. [2] University College London Genetics Institute, University College London, London, UK.
3
Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic.
4
Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
5
Wellcome Trust Centre for Human Genetics, Oxford, UK.
6
Cell Cycle Laboratory, Cancer Research UK London Research Institute, London, UK.
7
Department of Biochemistry, University of Cambridge, Cambridge, UK.
8
1] Department of Genetics, University of Cambridge, Cambridge, UK. [2] Gurdon Institute, University of Cambridge, Cambridge, UK.
9
Wellcome Trust Sanger Institute, Cambridge, UK.
10
Associated Regional and University Pathologists, Inc. University of Utah, Salt Lake City, Utah, USA.
11
Commonwealth Scientific and Industrial Research Organisation (CSIRO) Mathematics, Informatics and Statistics, North Ryde, New South Wales, Australia.
12
Genome Analysis Centre, Norwich, UK.
13
Centre for Genetics and Genomics, University of Nottingham, Nottingham, UK.
14
1] Department of Biochemistry, University of Cambridge, Cambridge, UK. [2] Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK. [3] Division of Physiology and Metabolism, Medical Research Council (MRC) National Institute for Medical Research, London, UK.

Abstract

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.

PMID:
25665008
PMCID:
PMC4645456
DOI:
10.1038/ng.3215
[Indexed for MEDLINE]
Free PMC Article

Publication type, MeSH terms, Secondary source ID, Grant support

Publication type

MeSH terms

Secondary source ID

Grant support

Supplemental Content

Full text links

Icon for Nature Publishing Group Icon for PubMed Central
Loading ...
Support Center