TitleGenome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains.
Publication TypeJournal Article
Year of Publication2007
AuthorsSchacherer, J, Ruderfer, DM, Gresham, D, Dolinski, K, Botstein, D, Kruglyak, L
JournalPLoS One
Volume2
Issue3
Paginatione322
Date Published2007
KeywordsChromosomes, Fungal, Genetic Variation, Genome, Fungal, Genome-Wide Association Study, Nucleic Acid Hybridization, Nucleotides, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Saccharomyces cerevisiae, Sequence Deletion, Species Specificity, Spores, Fungal
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, summation 1278b, SK1 and BY4716) using 25mer oligonucleotide microarrays that provide complete and redundant coverage of the approximately 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.

Alternate JournalPLoS ONE