The genomic and phenotypic diversity of Schizosaccharomyces pombe

被引：120

作者：

Jeffares, Daniel C. ^{[1
]}

Rallis, Charalampos ^{[1
]}

Rieux, Adrien ^{[1
,2
]}

Speed, Doug ^{[1
,2
]}

Prevorovsky, Martin ^{[3
]}

Mourier, Tobias ^{[4
]}

Marsellach, Francesc X. ^{[1
]}

Iqbal, Zamin ^{[5
]}

Lau, Winston ^{[1
]}

Cheng, Tammy M. K. ^{[6
]}

Pracana, Rodrigo ^{[1
]}

Muelleder, Michael ^{[7
]}

Lawson, Jonathan L. D. ^{[8
,9
]}

Chessel, Anatole ^{[7
]}

Bala, Sendu ^{[10
]}

Hellenthal, Garrett ^{[1
,2
]}

O'Fallon, Brendan ^{[11
]}

Keane, Thomas ^{[10
]}

Simpson, Jared T. ^{[10
]}

Bischof, Leanne ^{[12
]}

Tomiczek, Bartlomiej ^{[1
]}

Bitton, Danny A. ^{[1
]}

Sideri, Theodora ^{[1
]}

Codlin, Sandra ^{[1
]}

Hellberg, Josephine E. E. U. ^{[1
]}

van Trigt, Laurent ^{[1
]}

Jeffery, Linda ^{[6
]}

Li, Juan-Juan ^{[6
]}

Atkinson, Sophie ^{[1
]}

Thodberg, Malte ^{[4
]}

Febrer, Melanie ^{[13
]}

McLay, Kirsten ^{[13
]}

Drou, Nizar ^{[13
]}

Brown, William ^{[14
]}

Hayles, Jacqueline ^{[6
]}

Salas, Rafael E. Carazo ^{[8
,9
]}

Ralser, Markus ^{[7
,15
,16
]}

Maniatis, Nikolas ^{[1
]}

Balding, David J. ^{[1
,2
]}

Balloux, Francois ^{[1
,2
]}

Durbin, Richard ^{[10
]}

Baehler, Juerg ^{[1
,2
]}

机构：

[1] UCL, Dept Genet Evolut & Environm, London, England

[2] UCL, Genet Inst, London, England

[3] Charles Univ Prague, Fac Sci, Dept Cell Biol, Prague, Czech Republic

[4] Univ Copenhagen, Nat Hist Museum Denmark, Copenhagen, Denmark

[5] Wellcome Trust Ctr Human Genet, Oxford, England

[6] Canc Res UK London Res Inst, Cell Cycle Lab, London, England

[7] Univ Cambridge, Dept Biochem, Cambridge CB2 1QW, England

[8] Univ Cambridge, Dept Genet, Cambridge CB2 3EH, England

[9] Univ Cambridge, Gurdon Inst, Cambridge CB2 3EH, England

[10] Wellcome Trust Sanger Inst, Cambridge, England

[11] Univ Utah, Associated Reg & Univ Pathologists Inc, Salt Lake City, UT USA

[12] CSIRO Math Informat & Stat, N Ryde, NSW, Australia

[13] Genome Anal Ctr, Norwich, Norfolk, England

[14] Univ Nottingham, Ctr Genet & Gen, Nottingham NG7 2RD, England

[15] Univ Cambridge, Cambridge Syst Biol Ctr, Cambridge, England

[16] Natl Inst Med Res, MRC, Div Physiol & Metab, London NW7 1AA, England

来源：

NATURE GENETICS | 2015年 / 47卷 / 03期

基金：

英国生物技术与生命科学研究理事会; 英国医学研究理事会; 欧洲研究理事会; 英国惠康基金;

关键词：

POPULATION-STRUCTURE; SEQUENCE; DNA; MODEL; INTEGRATION; GENERATION; DISCOVERY; SELECTION; YEAST; MAPS;

D O I：

10.1038/ng.3215

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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 (pi = 3 x 10(-3) substitutions/site) and weak global population structure. We estimate that dispersal of S. pombe began during human antiquity (similar to 340 BCE), and ancestors of these strains reached the Americas at similar to 1623 CE. We quantified 74 traits, finding substantial heritable phenotypic diversity. We conducted 223 genomewide 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.

引用

页码：235 / +

页数：10

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