Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains

Joseph Schacherer, Douglas M. Ruderfer, David Gresham, Kara Dolinski, David Botstein, Leonid Kruglyak

Research output: Contribution to journalArticle

Abstract

Ten years have passed since the genome of Saccharomyces cerevisiae-more precisely, the S288c strain-was completely sequenced. However, experimental work in yeast is commonly performed using strains that are of unknown genetic relationship to S288c. Here, we characterized the nucleotide-level similarity between S288c and seven commonly used lab strains (A364A, W303, FL100, CEN.PK, ∑1278b, SK1 and BY4716) using 25mer oligonucleotide microarrays that provide complete and redundant coverage of the ∼12 Mb Saccharomyces cerevisiae genome. Using these data, we assessed the frequency and distribution of nucleotide variation in comparison to the sequenced reference genome. These data allow us to infer the relationships between experimentally important strains of yeast and provide insight for experimental designs that are sensitive to sequence variation. We propose a rational approach for near complete sequencing of strains related to the reference using these data and directed re-sequencing. These data and new visualization tools are accessible online in a new resource: the Yeast SNPs Browser (YSB; http://gbrowse.princeton.edu/cgi-bin/gbrowse/yeast_strains_snps) that is available to all researchers.

Original languageEnglish (US)
Article numbere322
JournalPLoS One
Volume2
Issue number3
DOIs
StatePublished - Mar 28 2007

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Yeast
Saccharomyces cerevisiae
Nucleotides
Genes
Yeasts
nucleotides
Genome
genome
yeasts
Oligonucleotide Array Sequence Analysis
Single Nucleotide Polymorphism
Research Design
Research Personnel
Bins
Microarrays
oligonucleotides
Oligonucleotides
Design of experiments
genetic relationships
Visualization

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. / Schacherer, Joseph; Ruderfer, Douglas M.; Gresham, David; Dolinski, Kara; Botstein, David; Kruglyak, Leonid.

In: PLoS One, Vol. 2, No. 3, e322, 28.03.2007.

Research output: Contribution to journalArticle

Schacherer, Joseph ; Ruderfer, Douglas M. ; Gresham, David ; Dolinski, Kara ; Botstein, David ; Kruglyak, Leonid. / Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. In: PLoS One. 2007 ; Vol. 2, No. 3.
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