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Open Access Research article

Comparative genomics among Saccharomyces cerevisiae × Saccharomyces kudriavzevii natural hybrid strains isolated from wine and beer reveals different origins

David Peris1, Christian A Lopes23, Carmela Belloch2, Amparo Querol2 and Eladio Barrio1*

Author Affiliations

1 ‘Cavanilles’ Institute of Biodiversity and Evolutionary Biology, University of Valencia, Parc Científic, P.O. Box 22085, E-46071, Valencia, Spain

2 Department of Biotechnology, Institute of Agrochemistry and Food Technology (CSIC), Valencia, Spain

3 Yeast Biodiversity & Biotechnology Group. Instituto Multidisciplinario de Investigación y Desarrollo de la Patagonia Norte (IDEPA), CONICET, Universidad Nacional del Comahue, Neuquén, Argentina

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BMC Genomics 2012, 13:407  doi:10.1186/1471-2164-13-407

Published: 20 August 2012

Additional files

Additional file 1:

Figure S1. Caryoscope representation of microarray data of S.kudriavzevii IFO1802. Array CGH data are shown in numerical order with chromosome I at the top and chromosome XVI at the bottom. Red signal indicates hybridization signal but it’s important to note the high normalization factor applied to the red signal (2) and the correction applied to the green one (0.49). This figure indicate that no cross hybridization has occurred between S. kudriavzevii genes and S. cerevisiae genes. (PPTX 106 kb)

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Additional file 2:

able S1. Binary table showing the presence/absence of a particular event for each hybrid strain (coded as 1/0 respectively). kud, S. kudriavzevii; loss, chromosome loss; rec, recombination generating a chimerical chromosome. Roman numerals indicate chromosome numbers and Arabic numerals the types of chimerical chromosomes or the restriction sites in the analysis of RFLP patterns in 34 genes. Parsimony tree was computed using a mixture model in which chimerical chromosomes, S. kudriavzevii chromosome losses and double S. cerevisiae chromosome were considered under the Camin-Sokal criterion and restriction site gains/losses under the Wagner criterion. (XLS 32 kb)

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Additional file 3:

Figure S2. Caryoscope representation of microarray data of 11 S. cerevisiae × S.kudriavzevii hybrids. Array CGH data are shown in numerical order with chromosome I at the top and chromosome XVI at the bottom for each strain. Regions with higher red signal correspond to S. cerevisiae genome regions that are overrepresented in the hybrid genome and those with higher green signal to those regions that are underrepresented. aCGH of wine and brewery hybrids are depicted on black and gray backgrounds, respectively. Arrows indicate potential non-reciprocal recombination events between homeologous chromosomes involved in the generation of chimerical chromosomes. (PPT 607 kb)

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Additional file 4:

Table S2. List of S. cerevisiae genes depleted in all S. cerevisiae × S. kudriavzevii hybrids under analysis. (XLS 29 kb)

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Additional file 5:

Table S3. S. kudriavzevii gene composition for each hybrid. A cross indicates the putative presence of that gene by considering colinearity between S. kudriavzevii and S. cerevisiae genomes. R indicates interspecies recombinant genes. Wine and brewing hybrids are indicated in black and gray lettering, respectively. (XLS 2001 kb)

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Additional file 6:

Table S4. Metabolic pathways and biological processes obtained from a Gene Ontology analysis using the S. kudriavzevii genes retained in each hybrid grouping. (XLS 38 kb)

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