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

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

130 Scopus citations

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 (US)
Pages (from-to)	235-241
Number of pages	7
Journal	Nature Genetics
Volume	47
Issue number	3
DOIs	https://doi.org/10.1038/ng.3215
State	Published - Feb 25 2015
Externally published	Yes

ASJC Scopus subject areas

Genetics

Access to Document

10.1038/ng.3215

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

@article{ab1ae773932745ecaf68e692f57e6333,

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.",

author = "Jeffares, {Daniel C.} and Charalampos Rallis and Adrien Rieux and Doug Speed and Martin P{\v r}evorovsk{\'y} and Tobias Mourier and Marsellach, {Francesc X.} and Zamin Iqbal and Winston Lau and Cheng, {Tammy M.K.} and Rodrigo Pracana and Michael M{\"u}lleder and Lawson, {Jonathan L.D.} and Anatole Chessel and Sendu Bala and Garrett Hellenthal and Brendan O'Fallon and Thomas Keane and Simpson, {Jared T.} and Leanne Bischof and Bartlomiej Tomiczek and Bitton, {Danny A.} and Theodora Sideri and Sandra Codlin and Hellberg, {Josephine E.E.U.} and {Van Trigt}, Laurent and Linda Jeffery and Li, {Juan Juan} and Sophie Atkinson and Malte Thodberg and Melanie Febrer and Kirsten McLay and Nizar Drou and William Brown and Jacqueline Hayles and Salas, {Rafael E.Carazo} and Markus Ralser and Nikolas Maniatis and Balding, {David J.} and Francois Balloux and Richard Durbin and J{\"u}rg B{\"a}hler",

year = "2015",

month = feb,

day = "25",

doi = "10.1038/ng.3215",

language = "English (US)",

volume = "47",

pages = "235--241",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Publishing Group",

number = "3",

}

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, JJ, Atkinson, S, Thodberg, M, Febrer, M, McLay, K, Drou, N, Brown, W, Hayles, J, Salas, REC, 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 - Salas, Rafael E.Carazo

AU - Ralser, Markus

AU - Maniatis, Nikolas

AU - Balding, David J.

AU - Balloux, Francois

AU - Durbin, Richard

AU - Bähler, Jürg

PY - 2015/2/25

Y1 - 2015/2/25

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.

UR - http://www.scopus.com/inward/record.url?scp=84924074129&partnerID=8YFLogxK

U2 - 10.1038/ng.3215

DO - 10.1038/ng.3215

M3 - Article

C2 - 25665008

AN - SCOPUS:84924074129

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

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this