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This suggests that genome plasticity provides important genetic diversity upon which natural selection mechanisms can operate.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>In this study, we have used wild-type<jats:italic>S. cerevisiae<\/jats:italic>(yeast) strains to investigate genome variation in natural and artificial environments. We have used comparative genome hybridization on array (aCGH) to characterize the genome variability of 16 yeast strains, of laboratory and commercial origin, isolated from vineyards and wine cellars, and from opportunistic human infections. Interestingly, sub-telomeric instability was associated with the clinical phenotype, while Ty element insertion regions determined genomic differences of natural wine fermentation strains. Copy number depletion of<jats:italic>ASP3<\/jats:italic>and<jats:italic>YRF1<\/jats:italic>genes was found in all wild-type strains. Other gene families involved in transmembrane transport, sugar and alcohol metabolism or drug resistance had copy number changes, which also distinguished wine from clinical isolates.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>We have isolated and genotyped more than 1000 yeast strains from natural environments and carried out an aCGH analysis of 16 strains representative of distinct genotype clusters. Important genomic variability was identified between these strains, in particular in sub-telomeric regions and in Ty-element insertion sites, suggesting that this type of genome variability is the main source of genetic diversity in natural populations of yeast. The data highlights the usefulness of yeast as a model system to unravel intraspecific natural genome diversity and to elucidate how natural selection shapes the yeast genome.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2164-9-524","type":"journal-article","created":{"date-parts":[[2008,11,4]],"date-time":"2008-11-04T20:23:48Z","timestamp":1225830228000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":107,"title":["Comparative genomics of wild type yeast strains unveils important genome diversity"],"prefix":"10.1186","volume":"9","author":[{"given":"Laura","family":"Carreto","sequence":"first","affiliation":[]},{"given":"Maria F","family":"Eiriz","sequence":"additional","affiliation":[]},{"given":"Ana C","family":"Gomes","sequence":"additional","affiliation":[]},{"given":"Patr\u00edcia M","family":"Pereira","sequence":"additional","affiliation":[]},{"given":"Dorit","family":"Schuller","sequence":"additional","affiliation":[]},{"given":"Manuel AS","family":"Santos","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2008,11,4]]},"reference":[{"key":"1717_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/BF00351734","volume":"22","author":"C Bidenne","year":"1992","unstructured":"Bidenne C, Blondin B, Dequin S, Vezinhet F: Analysis of the chromosomal DNA polymorphism of wine strains of Saccharomyces cerevisiae. 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