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De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology

Jurgen F Nijkamp19, Marcel van den Broek29, Erwin Datema1234, Stefan de Kok279, Lizanne Bosman29, Marijke A Luttik29, Pascale Daran-Lapujade29, Wanwipa Vongsangnak135, Jens Nielsen5, Wilbert HM Heijne6, Paul Klaassen6, Chris J Paddon7, Darren Platt7, Peter Kötter8, Roeland C van Ham1234, Marcel JT Reinders1109, Jack T Pronk29, Dick de Ridder110119* and Jean-Marc Daran1129*

Author Affiliations

1 The Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands

2 Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands

3 Wageningen University Centre for Biosystems Genomics, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands

4 Plant Research International, Business Unit of Bioscience, cluster Applied Bioinformatics, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands

5 Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden

6 DSM Biotechnology Center, PO Box 1, 2600MA Delft, The Netherlands

7 Amyris, Inc, 5885 Hollis Street, Suite 100, Emeryville CA 94608, USA

8 Institute for Molecular Biosciences, Max-von-Laue-Str. 9, Goethe University Frankfurt, D-60438 Frankfurt, Germany

9 Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands

10 Netherlands Bioinformatics Center, 260 NBIC, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands

11 Platform for Green Synthetic Biology, Julianalaan 67, 2628 BC Delft, The Netherlands

12 KeyGene N.V, Agro Business Park 90, 6708 PW Wageningen, The Netherlands

13 Center for Systems Biology, Soochow University, Suzhou 215006, China

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Microbial Cell Factories 2012, 11:36  doi:10.1186/1475-2859-11-36

Published: 26 March 2012


Saccharomyces cerevisiae CEN.PK 113-7D is widely used for metabolic engineering and systems biology research in industry and academia. We sequenced, assembled, annotated and analyzed its genome. Single-nucleotide variations (SNV), insertions/deletions (indels) and differences in genome organization compared to the reference strain S. cerevisiae S288C were analyzed. In addition to a few large deletions and duplications, nearly 3000 indels were identified in the CEN.PK113-7D genome relative to S288C. These differences were overrepresented in genes whose functions are related to transcriptional regulation and chromatin remodelling. Some of these variations were caused by unstable tandem repeats, suggesting an innate evolvability of the corresponding genes. Besides a previously characterized mutation in adenylate cyclase, the CEN.PK113-7D genome sequence revealed a significant enrichment of non-synonymous mutations in genes encoding for components of the cAMP signalling pathway. Some phenotypic characteristics of the CEN.PK113-7D strains were explained by the presence of additional specific metabolic genes relative to S288C. In particular, the presence of the BIO1 and BIO6 genes correlated with a biotin prototrophy of CEN.PK113-7D. Furthermore, the copy number, chromosomal location and sequences of the MAL loci were resolved. The assembled sequence reveals that CEN.PK113-7D has a mosaic genome that combines characteristics of laboratory strains and wild-industrial strains.