title: Comparative genomics of wild type yeast strains unveils important genome diversity.
abstract: BACKGROUND
  Genome variability generates phenotypic heterogeneity and is of relevance for adaptation to environmental change, but the extent of such variability in natural populations is still poorly understood. For example, selected Saccharomyces cerevisiae strains are variable at the ploidy level, have gene amplifications, changes in chromosome copy number, and gross chromosomal rearrangements. This suggests that genome plasticity provides important genetic diversity upon which natural selection mechanisms can operate.
  
  
  RESULTS
  In this study, we have used wild-type S. cerevisiae (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 ASP3 and YRF1 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal. laura.carreto@ua.pt
authors.forename: Laura
authors.initials: L
authors.lastname: Carreto
authors.forename: Maria F
authors.initials: MF
authors.lastname: Eiriz
authors.forename: Ana C
authors.initials: AC
authors.lastname: Gomes
authors.forename: Patrícia M
authors.initials: PM
authors.lastname: Pereira
authors.forename: Dorit
authors.initials: D
authors.lastname: Schuller
authors.forename: Manuel A S
authors.initials: MA
authors.lastname: Santos
mesh_terms: D055028:Comparative Genomic Hybridization; D004265:DNA Helicases / Q000235:genetics; D004271:DNA, Fungal; D018628:Gene Dosage; D005800:Genes, Fungal; D014644:Genetic Variation / Q000235:genetics*; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods*; D018626:Retroelements; D012441:Saccharomyces cerevisiae / Q000145:classification / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D013045:Species Specificity; D016615:Telomere / Q000235:genetics
chemical_list: D004271:DNA, Fungal; D018626:Retroelements; D029701:Saccharomyces cerevisiae Proteins; D004265:DNA Helicases; C116427:Y'-helicase protein 1, S cerevisiae