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The genomic and phenotypic diversity of Schizosaccharomyces pombe

The genomic and phenotypic diversity of Schizosaccharomyces pombe
The genomic and phenotypic diversity of Schizosaccharomyces pombe

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.

Genetic Variation, Genome, Fungal, Genome-Wide Association Study/methods, Genomics/methods, Genotype, Humans, Phenotype, Polymorphism, Single Nucleotide, Schizosaccharomyces/genetics
1061-4036
235-41
Jeffares, Daniel C.
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Rallis, Charalampos
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Rieux, Adrien
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Speed, Doug
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Převorovský, Martin
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Mourier, Tobias
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Marsellach, Francesc X
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Iqbal, Zamin
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Lau, Winston
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Cheng, Tammy M K
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Pracana, Rodrigo
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Mülleder, Michael
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Lawson, Jonathan L.D.
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Chessel, Anatole
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Bala, Sendu
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Hellenthal, Garrett
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O'Fallon, Brendan
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Keane, Thomas
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Simpson, Jared T.
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Bischof, Leanne
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Tomiczek, Bartlomiej
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Bitton, Danny A.
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Sideri, Theodora
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Codlin, Sandra
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Hellberg, Josephine E.E.U
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van Trigt, Laurent
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Jeffery, Linda
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Li, Juan-Juan
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Atkinson, Sophie
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Thodberg, Malte
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Febrer, Melanie
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McLay, Kirsten
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Drou, Nizar
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Brown, William
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Hayles, Jacqueline
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Carazo Salas, Rafael E.
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Ralser, Markus
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Maniatis, Nikolas
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Balding, David J.
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Balloux, Francois
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Durbin, Richard
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Bähler, Jürg
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et al.
Jeffares, Daniel C.
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Rallis, Charalampos
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Rieux, Adrien
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Speed, Doug
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Převorovský, Martin
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Mourier, Tobias
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Marsellach, Francesc X
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Iqbal, Zamin
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Lau, Winston
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Cheng, Tammy M K
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Pracana, Rodrigo
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Mülleder, Michael
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Lawson, Jonathan L.D.
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Chessel, Anatole
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Bala, Sendu
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Hellenthal, Garrett
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O'Fallon, Brendan
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Keane, Thomas
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Simpson, Jared T.
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Bischof, Leanne
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Tomiczek, Bartlomiej
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Bitton, Danny A.
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Sideri, Theodora
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Codlin, Sandra
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Hellberg, Josephine E.E.U
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van Trigt, Laurent
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Jeffery, Linda
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Li, Juan-Juan
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Atkinson, Sophie
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Thodberg, Malte
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Febrer, Melanie
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McLay, Kirsten
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Drou, Nizar
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Brown, William
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Hayles, Jacqueline
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Carazo Salas, Rafael E.
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Ralser, Markus
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Maniatis, Nikolas
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Balding, David J.
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Balloux, Francois
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Durbin, Richard
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Bähler, Jürg
02b71e32-8632-4aed-bd71-444865e2ed2c

Jeffares, Daniel C., Rallis, Charalampos and Rieux, Adrien , et al. (2015) The genomic and phenotypic diversity of Schizosaccharomyces pombe. Nature Genetics, 47 (3), 235-41. (doi:10.1038/ng.3215).

Record type: Article

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.

This record has no associated files available for download.

More information

Accepted/In Press date: 14 January 2015
e-pub ahead of print date: 9 February 2015
Published date: March 2015
Keywords: Genetic Variation, Genome, Fungal, Genome-Wide Association Study/methods, Genomics/methods, Genotype, Humans, Phenotype, Polymorphism, Single Nucleotide, Schizosaccharomyces/genetics

Identifiers

Local EPrints ID: 502113
URI: http://eprints.soton.ac.uk/id/eprint/502113
DOI: doi:10.1038/ng.3215
ISSN: 1061-4036
PURE UUID: 5a6a561a-0fbc-45c2-a306-af4a3c8c3c25
ORCID for Juan-Juan Li: ORCID iD orcid.org/0000-0003-2164-094X

Catalogue record

Date deposited: 17 Jun 2025 16:30
Last modified: 18 Jun 2025 01:56

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Contributors

Author: Daniel C. Jeffares
Author: Charalampos Rallis
Author: Adrien Rieux
Author: Doug Speed
Author: Martin Převorovský
Author: Tobias Mourier
Author: Francesc X Marsellach
Author: Zamin Iqbal
Author: Winston Lau
Author: Tammy M K Cheng
Author: Rodrigo Pracana
Author: Michael Mülleder
Author: Jonathan L.D. Lawson
Author: Anatole Chessel
Author: Sendu Bala
Author: Garrett Hellenthal
Author: Brendan O'Fallon
Author: Thomas Keane
Author: Jared T. Simpson
Author: Leanne Bischof
Author: Bartlomiej Tomiczek
Author: Danny A. Bitton
Author: Theodora Sideri
Author: Sandra Codlin
Author: Josephine E.E.U Hellberg
Author: Laurent van Trigt
Author: Linda Jeffery
Author: Juan-Juan Li ORCID iD
Author: Sophie Atkinson
Author: Malte Thodberg
Author: Melanie Febrer
Author: Kirsten McLay
Author: Nizar Drou
Author: William Brown
Author: Jacqueline Hayles
Author: Rafael E. Carazo Salas
Author: Markus Ralser
Author: Nikolas Maniatis
Author: David J. Balding
Author: Francois Balloux
Author: Richard Durbin
Author: Jürg Bähler
Corporate Author: et al.

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