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Whole-genome sequencing of the efficient industrial fuel-ethanol fermentative Saccharomyces cerevisiae strain CAT-1

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Abstract

The Saccharomyces cerevisiae strains widely used for industrial fuel-ethanol production have been developed by selection, but their underlying beneficial genetic polymorphisms remain unknown. Here, we report the draft whole-genome sequence of the S. cerevisiae strain CAT-1, which is a dominant fuel-ethanol fermentative strain from the sugarcane industry in Brazil. Our results indicate that strain CAT-1 is a highly heterozygous diploid yeast strain, and the ~12-Mb genome of CAT-1, when compared with the reference S228c genome, contains ~36,000 homozygous and ~30,000 heterozygous single nucleotide polymorphisms, exhibiting an uneven distribution among chromosomes due to large genomic regions of loss of heterozygosity (LOH). In total, 58 % of the 6,652 predicted protein-coding genes of the CAT-1 genome constitute different alleles when compared with the genes present in the reference S288c genome. The CAT-1 genome contains a reduced number of transposable elements, as well as several gene deletions and duplications, especially at telomeric regions, some correlated with several of the physiological characteristics of this industrial fuel-ethanol strain. Phylogenetic analyses revealed that some genes were likely associated with traits important for bioethanol production. Identifying and characterizing the allelic variations controlling traits relevant to industrial fermentation should provide the basis for a forward genetics approach for developing better fermenting yeast strains.

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Acknowledgments

The work of B.U.S. at Stanford University was possible through a visiting fellowship (BEX2793-05-9) from CAPES, Brazil.

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Authors and Affiliations

  1. Stanford Genome Technology Center, Stanford University, Stanford, CA, USA

    Farbod Babrzadeh, Roxana Jalili, Chunlin Wang, Shadi Shokralla, Sarah Pierce, Avi Robinson-Mosher, Ronald W. Davis, Mostafa Ronaghi & Baback Gharizadeh

  2. Department of Biochemistry, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden

    Pål Nyren

  3. Department of Medicine, School of Medicine, Stanford University, Stanford, USA

    Robert W. Shafer

  4. Biological Science Department, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, São Paulo, Brazil

    Luiz C. Basso

  5. Fermentec Ltda, Piracicaba, São Paulo, Brazil

    Henrique V. de Amorim & Antonio J. de Oliveira

  6. Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-970, Brazil

    Boris U. Stambuk

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  1. Farbod Babrzadeh
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Correspondence to Boris U. Stambuk.

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Communicated by T. Ito.

The authors F. Babrzadeh and R. Jalili contributed equally to this work.

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Babrzadeh, F., Jalili, R., Wang, C. et al. Whole-genome sequencing of the efficient industrial fuel-ethanol fermentative Saccharomyces cerevisiae strain CAT-1. Mol Genet Genomics 287, 485–494 (2012). https://doi.org/10.1007/s00438-012-0695-7

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