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Population genomics of domestic and wild yeasts

Since the completion of the genome sequence of Saccharomyces cerevisiae in 1996 (refs 1, 2), there has been a large increase in complete genome sequences, accompanied by great advances in our understanding of genome evolution. Although little is known about the natural and life histories of yeasts i... Full description

Journal Title: Nature 2009-03-19, Vol.458 (7236), p.337-341
Main Author: Parts, Leopold
Other Authors: Blomberg, Anders , O'Kelly, Michael J. T , Sims, Sarah , Koufopanou, Vassiliki , Davey, Robert P , Durbin, Richard , Carter, David M , Jones, Matthew , Tsai, Isheng J , Quail, Michael A , Bergman, Casey M , Bailes, Elizabeth , van Oudenaarden, Alexander , Moses, Alan M , Liti, Gianni , James, Stephen A , Burt, Austin , Barton, David B. H , Warringer, Jonas , Bensasson, Douda , Nguyen, Alex N , Smith, Frances , Goodhead, Ian , Louis, Edward J , Roberts, Ian N
Format: Electronic Article Electronic Article
Language: English
Subjects:
Publisher: London: Nature Publishing Group
ID: ISSN: 0028-0836
Zum Text:
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title: Population genomics of domestic and wild yeasts
format: Article
creator:
  • Parts, Leopold
  • Blomberg, Anders
  • O'Kelly, Michael J. T
  • Sims, Sarah
  • Koufopanou, Vassiliki
  • Davey, Robert P
  • Durbin, Richard
  • Carter, David M
  • Jones, Matthew
  • Tsai, Isheng J
  • Quail, Michael A
  • Bergman, Casey M
  • Bailes, Elizabeth
  • van Oudenaarden, Alexander
  • Moses, Alan M
  • Liti, Gianni
  • James, Stephen A
  • Burt, Austin
  • Barton, David B. H
  • Warringer, Jonas
  • Bensasson, Douda
  • Nguyen, Alex N
  • Smith, Frances
  • Goodhead, Ian
  • Louis, Edward J
  • Roberts, Ian N
subjects:
  • Article
  • Biochemistry and Molecular Biology
  • Biokemi och molekylärbiologi
  • Biological and medical sciences
  • Brewer's yeast
  • Cell Biology
  • Cellbiologi
  • classification
  • Fundamental and applied biological sciences. Psychology
  • Fungal
  • Genetic aspects
  • Genetics
  • Genetics of eukaryotes. Biological and molecular evolution
  • Genetics, Population
  • Genetik
  • Genome
  • Genome, Fungal - genetics
  • Genomics
  • Geography
  • Identification and classification
  • INDEL Mutation
  • INDEL Mutation - genetics
  • Microbial colonies
  • Phenotype
  • Phylogeny
  • Polymorphism
  • Polymorphism, Single Nucleotide - genetics
  • Population
  • Population genetics
  • Population genetics, reproduction patterns
  • Saccharomyces
  • Saccharomyces - classification
  • Saccharomyces - genetics
  • Saccharomyces cerevisiae
  • Saccharomyces cerevisiae - genetics
  • Saccharomyces paradoxus
  • Selection (Genetics)
  • Selection, Genetic
  • Single Nucleotide
  • Single nucleotide polymorphisms
  • Thallophyta, bryophyta
  • Vegetals
ispartof: Nature, 2009-03-19, Vol.458 (7236), p.337-341
description: Since the completion of the genome sequence of Saccharomyces cerevisiae in 1996 (refs 1, 2), there has been a large increase in complete genome sequences, accompanied by great advances in our understanding of genome evolution. Although little is known about the natural and life histories of yeasts in the wild, there are an increasing number of studies looking at ecological and geographic distributions, population structure and sexual versus asexual reproduction. Less well understood at the whole genome level are the evolutionary processes acting within populations and species that lead to adaptation to different environments, phenotypic differences and reproductive isolation. Here we present one- to fourfold or more coverage of the genome sequences of over seventy isolates of the baker's yeast S. cerevisiae and its closest relative, Saccharomyces paradoxus. We examine variation in gene content, single nucleotide polymorphisms, nucleotide insertions and deletions, copy numbers and transposable elements. We find that phenotypic variation broadly correlates with global genome-wide phylogenetic relationships. S. paradoxus populations are well delineated along geographic boundaries, whereas the variation among worldwide S. cerevisiae isolates shows less differentiation and is comparable to a single S. paradoxus population. Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of S. cerevisiae consists of a few well-defined, geographically isolated lineages and many different mosaics of these lineages, supporting the idea that human influence provided the opportunity for cross-breeding and production of new combinations of pre-existing variations.
language: eng
source:
identifier: ISSN: 0028-0836
fulltext: no_fulltext
issn:
  • 0028-0836
  • 1476-4687
  • 1476-4687
  • 1476-4679
url: Link


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creatorParts, Leopold ; Blomberg, Anders ; O'Kelly, Michael J. T ; Sims, Sarah ; Koufopanou, Vassiliki ; Davey, Robert P ; Durbin, Richard ; Carter, David M ; Jones, Matthew ; Tsai, Isheng J ; Quail, Michael A ; Bergman, Casey M ; Bailes, Elizabeth ; van Oudenaarden, Alexander ; Moses, Alan M ; Liti, Gianni ; James, Stephen A ; Burt, Austin ; Barton, David B. H ; Warringer, Jonas ; Bensasson, Douda ; Nguyen, Alex N ; Smith, Frances ; Goodhead, Ian ; Louis, Edward J ; Roberts, Ian N
creatorcontribParts, Leopold ; Blomberg, Anders ; O'Kelly, Michael J. T ; Sims, Sarah ; Koufopanou, Vassiliki ; Davey, Robert P ; Durbin, Richard ; Carter, David M ; Jones, Matthew ; Tsai, Isheng J ; Quail, Michael A ; Bergman, Casey M ; Bailes, Elizabeth ; van Oudenaarden, Alexander ; Moses, Alan M ; Liti, Gianni ; James, Stephen A ; Burt, Austin ; Barton, David B. H ; Warringer, Jonas ; Bensasson, Douda ; Nguyen, Alex N ; Smith, Frances ; Goodhead, Ian ; Louis, Edward J ; Roberts, Ian N ; Naturvetenskapliga fakulteten ; Faculty of Sciences ; Göteborgs universitet ; Institutionen för cell- och molekylärbiologi ; Gothenburg University ; Department of Cell and Molecular Biology
descriptionSince the completion of the genome sequence of Saccharomyces cerevisiae in 1996 (refs 1, 2), there has been a large increase in complete genome sequences, accompanied by great advances in our understanding of genome evolution. Although little is known about the natural and life histories of yeasts in the wild, there are an increasing number of studies looking at ecological and geographic distributions, population structure and sexual versus asexual reproduction. Less well understood at the whole genome level are the evolutionary processes acting within populations and species that lead to adaptation to different environments, phenotypic differences and reproductive isolation. Here we present one- to fourfold or more coverage of the genome sequences of over seventy isolates of the baker's yeast S. cerevisiae and its closest relative, Saccharomyces paradoxus. We examine variation in gene content, single nucleotide polymorphisms, nucleotide insertions and deletions, copy numbers and transposable elements. We find that phenotypic variation broadly correlates with global genome-wide phylogenetic relationships. S. paradoxus populations are well delineated along geographic boundaries, whereas the variation among worldwide S. cerevisiae isolates shows less differentiation and is comparable to a single S. paradoxus population. Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of S. cerevisiae consists of a few well-defined, geographically isolated lineages and many different mosaics of these lineages, supporting the idea that human influence provided the opportunity for cross-breeding and production of new combinations of pre-existing variations.
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subjectArticle ; Biochemistry and Molecular Biology ; Biokemi och molekylärbiologi ; Biological and medical sciences ; Brewer's yeast ; Cell Biology ; Cellbiologi ; classification ; Fundamental and applied biological sciences. Psychology ; Fungal ; Genetic aspects ; Genetics ; Genetics of eukaryotes. Biological and molecular evolution ; Genetics, Population ; Genetik ; Genome ; Genome, Fungal - genetics ; Genomics ; Geography ; Identification and classification ; INDEL Mutation ; INDEL Mutation - genetics ; Microbial colonies ; Phenotype ; Phylogeny ; Polymorphism ; Polymorphism, Single Nucleotide - genetics ; Population ; Population genetics ; Population genetics, reproduction patterns ; Saccharomyces ; Saccharomyces - classification ; Saccharomyces - genetics ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae - genetics ; Saccharomyces paradoxus ; Selection (Genetics) ; Selection, Genetic ; Single Nucleotide ; Single nucleotide polymorphisms ; Thallophyta, bryophyta ; Vegetals
ispartofNature, 2009-03-19, Vol.458 (7236), p.337-341
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7Carter, David M
8Jones, Matthew
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17Burt, Austin
18Barton, David B. H
19Warringer, Jonas
20Bensasson, Douda
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22Smith, Frances
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24Louis, Edward J
25Roberts, Ian N
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28Göteborgs universitet
29Institutionen för cell- och molekylärbiologi
30Gothenburg University
31Department of Cell and Molecular Biology
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0Population genomics of domestic and wild yeasts
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descriptionSince the completion of the genome sequence of Saccharomyces cerevisiae in 1996 (refs 1, 2), there has been a large increase in complete genome sequences, accompanied by great advances in our understanding of genome evolution. Although little is known about the natural and life histories of yeasts in the wild, there are an increasing number of studies looking at ecological and geographic distributions, population structure and sexual versus asexual reproduction. Less well understood at the whole genome level are the evolutionary processes acting within populations and species that lead to adaptation to different environments, phenotypic differences and reproductive isolation. Here we present one- to fourfold or more coverage of the genome sequences of over seventy isolates of the baker's yeast S. cerevisiae and its closest relative, Saccharomyces paradoxus. We examine variation in gene content, single nucleotide polymorphisms, nucleotide insertions and deletions, copy numbers and transposable elements. We find that phenotypic variation broadly correlates with global genome-wide phylogenetic relationships. S. paradoxus populations are well delineated along geographic boundaries, whereas the variation among worldwide S. cerevisiae isolates shows less differentiation and is comparable to a single S. paradoxus population. Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of S. cerevisiae consists of a few well-defined, geographically isolated lineages and many different mosaics of these lineages, supporting the idea that human influence provided the opportunity for cross-breeding and production of new combinations of pre-existing variations.
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1Biochemistry and Molecular Biology
2Biokemi och molekylärbiologi
3Biological and medical sciences
4Brewer's yeast
5Cell Biology
6Cellbiologi
7classification
8Fundamental and applied biological sciences. Psychology
9Fungal
10Genetic aspects
11Genetics
12Genetics of eukaryotes. Biological and molecular evolution
13Genetics, Population
14Genetik
15Genome
16Genome, Fungal - genetics
17Genomics
18Geography
19Identification and classification
20INDEL Mutation
21INDEL Mutation - genetics
22Microbial colonies
23Phenotype
24Phylogeny
25Polymorphism
26Polymorphism, Single Nucleotide - genetics
27Population
28Population genetics
29Population genetics, reproduction patterns
30Saccharomyces
31Saccharomyces - classification
32Saccharomyces - genetics
33Saccharomyces cerevisiae
34Saccharomyces cerevisiae - genetics
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36Selection (Genetics)
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titlePopulation genomics of domestic and wild yeasts
authorParts, Leopold ; Blomberg, Anders ; O'Kelly, Michael J. T ; Sims, Sarah ; Koufopanou, Vassiliki ; Davey, Robert P ; Durbin, Richard ; Carter, David M ; Jones, Matthew ; Tsai, Isheng J ; Quail, Michael A ; Bergman, Casey M ; Bailes, Elizabeth ; van Oudenaarden, Alexander ; Moses, Alan M ; Liti, Gianni ; James, Stephen A ; Burt, Austin ; Barton, David B. H ; Warringer, Jonas ; Bensasson, Douda ; Nguyen, Alex N ; Smith, Frances ; Goodhead, Ian ; Louis, Edward J ; Roberts, Ian N
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4Brewer's yeast
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8Fundamental and applied biological sciences. Psychology
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10Genetic aspects
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18Geography
19Identification and classification
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22Microbial colonies
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32Saccharomyces - genetics
33Saccharomyces cerevisiae
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0Author Contributions R.D. and E.J.L. conceived and designed the project. G.L. selected and manipulated yeast strains and extracted DNA samples. M.J., M.A.Q., I.G., S.S., F.S. performed the subcloning and sequencing. D.M.C. did the reference comparison and assembly of the sequences. D.M.C. and G.L. coordinated the collection of data. D.M.C. and R.D. performed much of the global analysis, which was the basis for specific analyses performed by the rest. A.M.M. did the selection studies. E.J.L., G.L. D.M.C., L.B. did the population structure and novel genes analysis. C.M.B. and D.B. performed the analysis of Ty elements abundance. S.A.J., R.P.D., M.J.T.O., A.V. and I.N.R. analysed the rDNA. A.B., V.K. and I.J.T. did the sequence variation and recombination analyses. A.M.M. and A.N.N.B. created a BLAST server. J.W. and A.B. generated the phenomics data. E.J.L. and G.L. wrote the paper, coordinating everyone's contributions.
1These authors contributed equally to this work
2Present address: School of Biological Sciences, University of Liverpool, Liverpool, LG9 3BX
abstractSince the completion of the genome sequence of Saccharomyces cerevisiae in 1996 (refs 1, 2), there has been a large increase in complete genome sequences, accompanied by great advances in our understanding of genome evolution. Although little is known about the natural and life histories of yeasts in the wild, there are an increasing number of studies looking at ecological and geographic distributions, population structure and sexual versus asexual reproduction. Less well understood at the whole genome level are the evolutionary processes acting within populations and species that lead to adaptation to different environments, phenotypic differences and reproductive isolation. Here we present one- to fourfold or more coverage of the genome sequences of over seventy isolates of the baker's yeast S. cerevisiae and its closest relative, Saccharomyces paradoxus. We examine variation in gene content, single nucleotide polymorphisms, nucleotide insertions and deletions, copy numbers and transposable elements. We find that phenotypic variation broadly correlates with global genome-wide phylogenetic relationships. S. paradoxus populations are well delineated along geographic boundaries, whereas the variation among worldwide S. cerevisiae isolates shows less differentiation and is comparable to a single S. paradoxus population. Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of S. cerevisiae consists of a few well-defined, geographically isolated lineages and many different mosaics of these lineages, supporting the idea that human influence provided the opportunity for cross-breeding and production of new combinations of pre-existing variations.
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