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  The Saccharomyces cerevisiae W303-K6001 cross-platform genome sequence: insights into ancestry and physiology of a laboratory mutt

Ralser, M., Kuhl, H., Ralser, M., Werber, M., Lehrach, H., Breitenbach, M., et al. (2012). The Saccharomyces cerevisiae W303-K6001 cross-platform genome sequence: insights into ancestry and physiology of a laboratory mutt. Open Biology, 2(8): 120093. doi:10.1098/rsob.120093.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-000E-F082-5 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-000E-F083-3
Genre: Journal Article

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© 2012 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/3.0/, which permits unrestricted use, provided the original author and source are credited.
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 Creators:
Ralser, Markus1, 2, Author              
Kuhl, Heiner3, Author              
Ralser, Meryem1, Author
Werber, Martin1, Author              
Lehrach, Hans1, Author              
Breitenbach, Michael4, Author
Timmermann, Bernd3, Author              
Affiliations:
1Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, Berlin, Germany, ou_1433550              
2Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK, ou_persistent22              
3Sequencing (Head: Bernd Timmermann), Scientific Service (Head: Christoph Krukenkamp), Max Planck Institute for Molecular Genetics, Max Planck Society, Berlin, Germany, ou_1479670              
4Department of Cell Biology, University of Salzburg, Salzburg, Austria, ou_persistent22              

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 Abstract: Saccharomyces cerevisiae strain W303 is a widely used model organism. However, little is known about its genetic origins, as it was created in the 1970s from crossing yeast strains of uncertain genealogy. To obtain insights into its ancestry and physiology, we sequenced the genome of its variant W303-K6001, a yeast model of ageing research. The combination of two next-generation sequencing (NGS) technologies (Illumina and Roche/454 sequencing) yielded an 11.8 Mb genome assembly at an N50 contig length of 262 kb. Although sequencing was substantially more precise and sensitive than whole-genome tiling arrays, both NGS platforms produced a number of false positives. At a 378x average coverage, only 74 per cent of called differences to the S288c reference genome were confirmed by both techniques. The consensus W303-K6001 genome differs in 8133 positions from S288c, predicting altered amino acid sequence in 799 proteins, including factors of ageing and stress resistance. The W303-K6001 (85.4%) genome is virtually identical (less than equal to 0.5 variations per kb) to S288c, and thus originates in the same ancestor. Non-S288c regions distribute unequally over the genome, with chromosome XVI the most (99.6%) and chromosome XI the least (54.5%) S288c-like. Several of these clusters are shared with Sigma1278B, another widely used S288c-related model, indicating that these strains share a second ancestor. Thus, the W303-K6001 genome pictures details of complex genetic relationships between the model strains that date back to the early days of experimental yeast genetics. Moreover, this study underlines the necessity of combining multiple NGS and genome-assembling techniques for achieving accurate variant calling in genomic studies.

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 Dates: 2012-08-01
 Publication Status: Published online
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 Rev. Type: Peer
 Identifiers: DOI: 10.1098/rsob.120093
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Title: Open Biology
Source Genre: Journal
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Pages: - Volume / Issue: 2 (8) Sequence Number: 120093 Start / End Page: - Identifier: -