Molecular Genetics and Genomics

, Volume 287, Issue 6, pp 485–494 | Cite as

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

  • Farbod Babrzadeh
  • Roxana Jalili
  • Chunlin Wang
  • Shadi Shokralla
  • Sarah Pierce
  • Avi Robinson-Mosher
  • Pål Nyren
  • Robert W. Shafer
  • Luiz C. Basso
  • Henrique V. de Amorim
  • Antonio J. de Oliveira
  • Ronald W. Davis
  • Mostafa Ronaghi
  • Baback Gharizadeh
  • Boris U. StambukEmail author
Original Paper


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.


Bioethanol Genome Saccharomyces Sugarcane Industrial strains 



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

Supplementary material

438_2012_695_MOESM1_ESM.docx (61 kb)
Supplementary material 1 (DOCX 60 kb)


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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Farbod Babrzadeh
    • 1
  • Roxana Jalili
    • 1
  • Chunlin Wang
    • 1
  • Shadi Shokralla
    • 1
  • Sarah Pierce
    • 1
  • Avi Robinson-Mosher
    • 1
  • Pål Nyren
    • 2
  • Robert W. Shafer
    • 3
  • Luiz C. Basso
    • 4
  • Henrique V. de Amorim
    • 5
  • Antonio J. de Oliveira
    • 5
  • Ronald W. Davis
    • 1
  • Mostafa Ronaghi
    • 1
  • Baback Gharizadeh
    • 1
  • Boris U. Stambuk
    • 6
    Email author
  1. 1.Stanford Genome Technology Center, Stanford UniversityStanfordUSA
  2. 2.Department of BiochemistrySchool of Biotechnology, KTH Royal Institute of TechnologyStockholmSweden
  3. 3.Department of MedicineSchool of Medicine, Stanford UniversityStanfordUSA
  4. 4.Biological Science DepartmentEscola Superior de Agricultura Luiz de Queiroz, Universidade de São PauloSão PauloBrazil
  5. 5.Fermentec LtdaPiracicabaBrazil
  6. 6.Departamento de BioquímicaCentro de Ciências Biológicas, Universidade Federal de Santa CatarinaFlorianópolisBrazil

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