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Comparative genomics of wild type yeast strains unveils important genome diversity.

Carreto L, Eiriz MF, Gomes AC, Pereira PM, Schuller D, Santos MA - BMC Genomics (2008)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal. laura.carreto@ua.pt

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.

Conclusion: 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.

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Chromosomal location and classification of ORFs with variable copy number. Panel-A shows the distribution of variable ORFs indicated by CGH-Miner in terms of chromosome location, that is, sub-telomeric, centromeric or chromosome arms. Panel-B shows the distribution of the same ORFs in terms of abundance of Ty elements, hypothetical or annotated ORFs. In both panels, each bar represents the total number of variable ORFs for a given strain.
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Figure 4: Chromosomal location and classification of ORFs with variable copy number. Panel-A shows the distribution of variable ORFs indicated by CGH-Miner in terms of chromosome location, that is, sub-telomeric, centromeric or chromosome arms. Panel-B shows the distribution of the same ORFs in terms of abundance of Ty elements, hypothetical or annotated ORFs. In both panels, each bar represents the total number of variable ORFs for a given strain.

Mentions: The karyoscope maps displaying the relative hybridization data derived for each strain revealed that the majority of the genome alterations corresponded to deletions relative to strain S288C, while ORF amplifications were rare (Figure 3 and Additional File 2, Figures S2A–S2P). ORF amplification clusters were found in some strains, mostly located in sub-telomeric regions (Figure 3A) and within 20 Kb of the S288C respective chromosome end, but only few corresponded to genes with annotated function. Clusters of depleted ORFs were found in sub-telomeric regions and contained large percentage of Ty elements and hypothetical ORFs (Figure 4). In the group of wine strains, up to one third of the observed gene copy number alterations were found in sub-telomeric regions (Figure 4A) – within 50 Kb from the S288C chromosome ends, using the criterion of Edwards-Ingram and colleagues [40]. On average, the clinical strains showed slightly higher percentage (almost 40%) of depleted ORFs localized near the telomeres. However, this is mostly explained by the massive loss of chromosomes VII and X right arms in strains J940557 and J940915 (see karyoscope map of J940915 in Figure 3B). The depletion of ORFs around the centromeric regions- within 20 Kb of the centromere, according to the criterion of Schacherer and colleagues [41]- was reduced and only slightly above average in some of the wine strains.


Comparative genomics of wild type yeast strains unveils important genome diversity.

Carreto L, Eiriz MF, Gomes AC, Pereira PM, Schuller D, Santos MA - BMC Genomics (2008)

Chromosomal location and classification of ORFs with variable copy number. Panel-A shows the distribution of variable ORFs indicated by CGH-Miner in terms of chromosome location, that is, sub-telomeric, centromeric or chromosome arms. Panel-B shows the distribution of the same ORFs in terms of abundance of Ty elements, hypothetical or annotated ORFs. In both panels, each bar represents the total number of variable ORFs for a given strain.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2588607&req=5

Figure 4: Chromosomal location and classification of ORFs with variable copy number. Panel-A shows the distribution of variable ORFs indicated by CGH-Miner in terms of chromosome location, that is, sub-telomeric, centromeric or chromosome arms. Panel-B shows the distribution of the same ORFs in terms of abundance of Ty elements, hypothetical or annotated ORFs. In both panels, each bar represents the total number of variable ORFs for a given strain.
Mentions: The karyoscope maps displaying the relative hybridization data derived for each strain revealed that the majority of the genome alterations corresponded to deletions relative to strain S288C, while ORF amplifications were rare (Figure 3 and Additional File 2, Figures S2A–S2P). ORF amplification clusters were found in some strains, mostly located in sub-telomeric regions (Figure 3A) and within 20 Kb of the S288C respective chromosome end, but only few corresponded to genes with annotated function. Clusters of depleted ORFs were found in sub-telomeric regions and contained large percentage of Ty elements and hypothetical ORFs (Figure 4). In the group of wine strains, up to one third of the observed gene copy number alterations were found in sub-telomeric regions (Figure 4A) – within 50 Kb from the S288C chromosome ends, using the criterion of Edwards-Ingram and colleagues [40]. On average, the clinical strains showed slightly higher percentage (almost 40%) of depleted ORFs localized near the telomeres. However, this is mostly explained by the massive loss of chromosomes VII and X right arms in strains J940557 and J940915 (see karyoscope map of J940915 in Figure 3B). The depletion of ORFs around the centromeric regions- within 20 Kb of the centromere, according to the criterion of Schacherer and colleagues [41]- was reduced and only slightly above average in some of the wine strains.

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal. laura.carreto@ua.pt

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.

Conclusion: 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.

Show MeSH
Related in: MedlinePlus