title: The genomic and phenotypic diversity of Schizosaccharomyces pombe.
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.
authors: Department of Genetics, Evolution and Environment, University College London, London, UK.
authors: Daniel C
authors: 0000000173200706
authors: DC
authors: Jeffares
authors: Department of Genetics, Evolution and Environment, University College London, London, UK.
authors: Charalampos
authors: C
authors: Rallis
authors: 1] Department of Genetics, Evolution and Environment, University College London, London, UK. [2] University College London Genetics Institute, University College London, London, UK.
authors: Adrien
authors: A
authors: Rieux
authors: 1] Department of Genetics, Evolution and Environment, University College London, London, UK. [2] University College London Genetics Institute, University College London, London, UK.
authors: Doug
authors: D
authors: Speed
authors: Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic.
authors: Martin
authors: M
authors: Převorovský
authors: Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
authors: Tobias
authors: T
authors: Mourier
authors: Department of Genetics, Evolution and Environment, University College London, London, UK.
authors: Francesc X
authors: FX
authors: Marsellach
authors: Wellcome Trust Centre for Human Genetics, Oxford, UK.
authors: Zamin
authors: Z
authors: Iqbal
authors: Department of Genetics, Evolution and Environment, University College London, London, UK.
authors: Winston
authors: W
authors: Lau
authors: Cell Cycle Laboratory, Cancer Research UK London Research Institute, London, UK.
authors: Tammy M K
authors: TM
authors: Cheng
authors: Department of Genetics, Evolution and Environment, University College London, London, UK.
authors: Rodrigo
authors: R
authors: Pracana
authors: Department of Biochemistry, University of Cambridge, Cambridge, UK.
authors: Michael
authors: M
authors: Mülleder
authors: 1] Department of Genetics, University of Cambridge, Cambridge, UK. [2] Gurdon Institute, University of Cambridge, Cambridge, UK.
authors: Jonathan L D
authors: JL
authors: Lawson
authors: Department of Biochemistry, University of Cambridge, Cambridge, UK.
authors: Anatole
authors: A
authors: Chessel
authors: Wellcome Trust Sanger Institute, Cambridge, UK.
authors: Sendu
authors: S
authors: Bala
authors: 1] Department of Genetics, Evolution and Environment, University College London, London, UK. [2] University College London Genetics Institute, University College London, London, UK.
authors: Garrett
authors: G
authors: Hellenthal
authors: Associated Regional and University Pathologists, Inc. University of Utah, Salt Lake City, Utah, USA.
authors: Brendan
authors: B
authors: O'Fallon
authors: Wellcome Trust Sanger Institute, Cambridge, UK.
authors: Thomas
authors: T
authors: Keane
authors: Wellcome Trust Sanger Institute, Cambridge, UK.
authors: Jared T
authors: JT
authors: Simpson
authors: Commonwealth Scientific and Industrial Research Organisation (CSIRO) Mathematics, Informatics and Statistics, North Ryde, New South Wales, Australia.
authors: Leanne
authors: L
authors: Bischof
authors: Department of Genetics, Evolution and Environment, University College London, London, UK.
authors: Bartlomiej
authors: B
authors: Tomiczek
authors: Department of Genetics, Evolution and Environment, University College London, London, UK.
authors: Danny A
authors: DA
authors: Bitton
authors: Department of Genetics, Evolution and Environment, University College London, London, UK.
authors: Theodora
authors: T
authors: Sideri
authors: Department of Genetics, Evolution and Environment, University College London, London, UK.
authors: Sandra
authors: S
authors: Codlin
authors: Department of Genetics, Evolution and Environment, University College London, London, UK.
authors: Josephine E E U
authors: JE
authors: Hellberg
authors: Department of Genetics, Evolution and Environment, University College London, London, UK.
authors: Laurent
authors: L
authors: van Trigt
authors: Cell Cycle Laboratory, Cancer Research UK London Research Institute, London, UK.
authors: Linda
authors: L
authors: Jeffery
authors: Cell Cycle Laboratory, Cancer Research UK London Research Institute, London, UK.
authors: Juan-Juan
authors: JJ
authors: Li
authors: Department of Genetics, Evolution and Environment, University College London, London, UK.
authors: Sophie
authors: S
authors: Atkinson
authors: Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
authors: Malte
authors: M
authors: Thodberg
authors: Genome Analysis Centre, Norwich, UK.
authors: Melanie
authors: M
authors: Febrer
authors: Genome Analysis Centre, Norwich, UK.
authors: Kirsten
authors: K
authors: McLay
authors: Genome Analysis Centre, Norwich, UK.
authors: Nizar
authors: N
authors: Drou
authors: Centre for Genetics and Genomics, University of Nottingham, Nottingham, UK.
authors: William
authors: W
authors: Brown
authors: Cell Cycle Laboratory, Cancer Research UK London Research Institute, London, UK.
authors: Jacqueline
authors: J
authors: Hayles
authors: 1] Department of Genetics, University of Cambridge, Cambridge, UK. [2] Gurdon Institute, University of Cambridge, Cambridge, UK.
authors: Rafael E
authors: 0000000259433981
authors: RE
authors: Carazo Salas
authors: 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.
authors: Markus
authors: 0000000195357413
authors: M
authors: Ralser
authors: Department of Genetics, Evolution and Environment, University College London, London, UK.
authors: Nikolas
authors: N
authors: Maniatis
authors: 1] Department of Genetics, Evolution and Environment, University College London, London, UK. [2] University College London Genetics Institute, University College London, London, UK.
authors: David J
authors: 0000000214806115
authors: DJ
authors: Balding
authors: 1] Department of Genetics, Evolution and Environment, University College London, London, UK. [2] University College London Genetics Institute, University College London, London, UK.
authors: Francois
authors: F
authors: Balloux
authors: Wellcome Trust Sanger Institute, Cambridge, UK.
authors: Richard
authors: R
authors: Durbin
authors: 1] Department of Genetics, Evolution and Environment, University College London, London, UK. [2] University College London Genetics Institute, University College London, London, UK.
authors: Jürg
authors: J
authors: Bähler
mesh_terms: D014644:Genetic Variation; D016681:Genome, Fungal; D055106:Genome-Wide Association Study / Q000379:methods; D023281:Genomics / Q000379:methods; D005838:Genotype; D006801:Humans; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D012568:Schizosaccharomyces / Q000235:genetics*