About this web site

This web site (the Budding Yeast Gene Evolution database) complements a paper describing the genome-wide analysis of the evolutionary dynamics of Saccharomyces (PLoS ONE, submitted). In the paper we analyze patterns of polymorphism and divergence to infer natural selection in the context of these GSR categories, and associate this variation with Gene Ontology terms. We discuss the relationship between evolutionary forces and population structure, and suggest two mechanisms for species divergence. We also estimate the divergence time between species and population coalescence times within species.

This site was created to foster future comparative and phenotype association studies in yeast and provides access to relevant DNA sequences, multiple alignments, and statistics. Specifically you can obtain estimates of polymorphism and divergence based on sequence alignments for 10 categories corresponding to unique genic structural regions for 6,575 S. cerevisiae and 5,250 S. paradoxus protein-coding genes from 39 S. cerevisiae and 28 S. paradoxus publicly available genome sequence assemblies.

In particular we would like to acknowledge the Sanger Institute and the laboratory of Dr. Ed Louis for making their yeast genome sequence collection publicly available. This collection constitutes the bulk of DNA sequences included in our study.

Project blurb

Despite the historical importance of budding yeast in science, industry, and culture, the natural history of the Saccharomyces sensu stricto clade has received little attention until the past decade. Hundreds of Saccharomyces strains have now been isolated from several environments, including vineyards, fruit, saké fermenters, human hosts, and oak trees. With the recent release of genome sequences for several dozen S. cerevisiae and S. paradoxus strains, it has become possible to investigate both population and gene structure at a whole-genome scale. While protein-coding DNA naturally encodes polypeptides, various gene-associated non-coding sequences are functionally important for the proper production and maintenance of these proteins. These promoters, untranslated regions, and introns tend to exhibit unique regulatory roles, so understanding how they are shaped by evolutionary forces should provide broad insights into the interface between microevolution and speciation.

• Hosted by the laboratory of Junhyong Kim
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