In order to understand yeast natural genome and transcriptome variability and evaluate whether such variability correlates with phenotypic diversity, we have isolated approximately 1000 yeast strains from Portuguese vineyards, namely from the Bairrada and Minho wine regions, genotyped them and selected the most divergent ones for genome and transcriptome characterization, using comparative genome hybridization on array (aCGH) and mRNA profiling, respectively. For comparative purposes, strains isolated from opportunistic clinical infections and commercial strains used by the wine industry were also included in the study. Approximately 3 % of the ORFeome showed copy number alterations relative to the reference strain S288C, which was associated with sub-telomeric instability and Ty element transposition. Interestingly, one third of the Ty elements identified in the genome of the reference laboratory strain (S288C) were absent in the wine strains, but were present in the clinical isolates. Distinct gene functional classes were affected by copy number changes in wine and clinical strains. However, no correlation was found between genome alterations and geographical origin. Transcriptome profiling of the same strains grown in synthetic must, using a common reference design, showed important variation in mRNA levels during fermentation, in particular in the wine isolates. Some genes showed patterns of activation that were consistent with gene copy number differences, while others pointed to strain specific regulation. Substantial variability in expression levels were detected among genes associated with fermentation in the wine strains. Therefore, transcriptome variability is relevant to understand yeast adaptation to new ecological niches, yeast evolution, and also to design strategies to select strains with particular phenotypes.National Facility for DNAInstitute of Electronics and Telecommunications of the University of Aveiro (IEETA)Microarray - projecto Ref: CTS 12 (Instituto de Investigação da Universidade de Aveiro)Fundação para a Ciência e a Tecnologia (FCT) - Bolsas CONC-REEQ/737/200, POCI/SAU-MMO/55476/2004, FEDER/POCI/BIA-PRO/55472/2004Biocant Institute, Cantanhede, Portugal
