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 Bischof; Bartlomiej 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

doi:10.1038/ng.3215

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

Research output: Contribution to journal › Article (Academic Journal) › peer-review

134 Citations (Scopus)

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.

Original language	English
Pages (from-to)	235-241
Number of pages	7
Journal	Nature Genetics
Volume	47
Issue number	3
Early online date	9 Feb 2015
DOIs	https://doi.org/10.1038/ng.3215
Publication status	Published - 1 Mar 2015

Research Groups and Themes

Jean Golding

Keywords

Genetic Variation
Genome, Fungal
Genome-Wide Association Study
Genomics
Genotype
Humans
Phenotype
Polymorphism, Single Nucleotide
Schizosaccharomyces
Journal Article
Research Support, Non-U.S. Gov't

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Professor Rafael E Carazo Salas
- rafael.carazosalasbristol.acuk
- School of Cellular and Molecular Medicine - Chair in Biomedical Sciences
Person: Academic

Cite this

Jeffares, D. C., Rallis, C., Rieux, A., Speed, D., Převorovský, M., Mourier, T., Marsellach, F. X., Iqbal, Z., Lau, W., Cheng, T. M. K., Pracana, R., Mülleder, M., Lawson, J. L. D., Chessel, A., Bala, S., Hellenthal, G., O'Fallon, B., Keane, T., Simpson, J. T., ... Bähler, J. (2015). The genomic and phenotypic diversity of Schizosaccharomyces pombe. Nature Genetics, 47(3), 235-241. https://doi.org/10.1038/ng.3215

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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.",

keywords = "Genetic Variation, Genome, Fungal, Genome-Wide Association Study, Genomics, Genotype, Humans, Phenotype, Polymorphism, Single Nucleotide, Schizosaccharomyces, Journal Article, Research Support, Non-U.S. Gov't",

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Jeffares, DC, Rallis, C, Rieux, A, Speed, D, Převorovský, M, Mourier, T, Marsellach, FX, Iqbal, Z, Lau, W, Cheng, TMK, Pracana, R, Mülleder, M, Lawson, JLD, Chessel, A, Bala, S, Hellenthal, G, O'Fallon, B, Keane, T, Simpson, JT, Bischof, L, Tomiczek, B, Bitton, DA, Sideri, T, Codlin, S, Hellberg, JEEU, van Trigt, L, Jeffery, L, Li, J-J, Atkinson, S, Thodberg, M, Febrer, M, McLay, K, Drou, N, Brown, W, Hayles, J, Carazo Salas, RE, Ralser, M, Maniatis, N, Balding, DJ, Balloux, F, Durbin, R & Bähler, J 2015, 'The genomic and phenotypic diversity of Schizosaccharomyces pombe', Nature Genetics, vol. 47, no. 3, pp. 235-241. https://doi.org/10.1038/ng.3215

TY - JOUR

T1 - The genomic and phenotypic diversity of Schizosaccharomyces pombe

AU - Jeffares, Daniel C

AU - Rallis, Charalampos

AU - Rieux, Adrien

AU - Speed, Doug

AU - Převorovský, Martin

AU - Mourier, Tobias

AU - Marsellach, Francesc X

AU - Iqbal, Zamin

AU - Lau, Winston

AU - Cheng, Tammy M K

AU - Pracana, Rodrigo

AU - Mülleder, Michael

AU - Lawson, Jonathan L D

AU - Chessel, Anatole

AU - Bala, Sendu

AU - Hellenthal, Garrett

AU - O'Fallon, Brendan

AU - Keane, Thomas

AU - Simpson, Jared T

AU - Bischof, Leanne

AU - Tomiczek, Bartlomiej

AU - Bitton, Danny A

AU - Sideri, Theodora

AU - Codlin, Sandra

AU - Hellberg, Josephine E E U

AU - van Trigt, Laurent

AU - Jeffery, Linda

AU - Li, Juan-Juan

AU - Atkinson, Sophie

AU - Thodberg, Malte

AU - Febrer, Melanie

AU - McLay, Kirsten

AU - Drou, Nizar

AU - Brown, William

AU - Hayles, Jacqueline

AU - Carazo Salas, Rafael E

AU - Ralser, Markus

AU - Maniatis, Nikolas

AU - Balding, David J

AU - Balloux, Francois

AU - Durbin, Richard

AU - Bähler, Jürg

PY - 2015/3/1

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N2 - 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.

AB - 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.

KW - Genetic Variation

KW - Genome, Fungal

KW - Genome-Wide Association Study

KW - Genomics

KW - Genotype

KW - Humans

KW - Phenotype

KW - Polymorphism, Single Nucleotide

KW - Schizosaccharomyces

KW - Journal Article

KW - Research Support, Non-U.S. Gov't

U2 - 10.1038/ng.3215

DO - 10.1038/ng.3215

M3 - Article (Academic Journal)

C2 - 25665008

SN - 1061-4036

VL - 47

SP - 235

EP - 241

JO - Nature Genetics

JF - Nature Genetics

IS - 3

ER -

The genomic and phenotypic diversity of Schizosaccharomyces pombe

Abstract

Research Groups and Themes

Keywords

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Professor Rafael E Carazo Salas

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