9 votes

Population genomics of domestic and wild yeasts

David M. Carter¹, Gianni Liti², Alan M. Moses³, Leopold Parts¹, Stephen A. James⁴, Robert P. Davey⁴, Ian N. Roberts⁴, Anders Blomberg⁵, Jonas Warringer⁵, Austin Burt⁶, Vassiliki Koufopanou⁶, Isheng J. Tsai⁶, Casey M. Bergman⁷, Douda Bensasson⁷, Michael J. T. O’Kelly⁸, Alexander van Oudenaarden⁸, David B. H. Barton², Elizabeth Bailes², Matthew Jones¹, Michael A. Quail¹, Ian Goodhead¹, Sarah Sims¹, Frances Smith¹, Richard Durbin¹ & Edward Louis²

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1. Wellcome Trust Sanger Institute
2. University of Nottingham
3. University of Toronto
4. National Collection of Yeast Cultures
5. University of Gothenburg
6. Imperial College London
7. University of Manchester
8. Massachusetts Institute of Technology

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Document Type:

Manuscript

Date:

Received 19 June 2008 10:26 UTC; Posted 20 June 2008

Subjects:

Ecology, Genetics & Genomics, Bioinformatics, Evolutionary Biology

Tags:

• population genomics
• genome evolution
• genetic variation
• yeast

Abstract:

The natural genetics of an organism is determined by the distribution of sequences of its genome. Here we present one- to four-fold, with some deeper, coverage of the genome sequences of over seventy isolates of the domesticated baker’s yeast, Saccharomyces cerevisiae, and its closest relative, the wild S. paradoxus, which has never been associated with human activity. These were collected from numerous geographic locations and sources (including wild, clinical, baking, wine, laboratory and food spoilage). These sequences provide an unprecedented view of the population structure, natural (and artificial) selection and genome evolution in these species. Variation in gene content, SNPs, indels, copy numbers and transposable elements provide insights into the evolution of different lineages. Phenotypic variation broadly correlates with global genome-wide phylogenetic relationships however there is no correlation with source. S. paradoxus populations are well delineated along geographic boundaries while the variation among worldwide S. cerevisiae isolates show 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 shows a few well defined geographically isolated lineages and many different mosaics of these lineages, supporting the notion that human influence provided the opportunity for outbreeding and production of new combinations of pre-existing variation.

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This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Carter, David, Liti, Gianni, Moses, Alan, Parts, Leopold, James, Stephen, Davey, Robert, Roberts, Ian, Blomberg, Anders, Warringer, Jonas, Burt, Austin, Koufopanou, Vassiliki, Tsai, Isheng, Bergman, Casey, Bensasson, Douda, O’Kelly, Michael, van Oudenaarden, Alexander, Barton, David, Bailes, Elizabeth, Jones, Matthew, Quail, Michael, Goodhead, Ian, Sims, Sarah, Smith, Frances, Durbin, Richard, and Louis, Edward. Population genomics of domestic and wild yeasts. Available from Nature Precedings <http://hdl.handle.net/10101/npre.2008.1988.1> (2008)

Version info:

Published version:

10.1038/nature07743 (Peer Reviewed) Published in Nature (11 February 2009)

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