Print Email Facebook Twitter De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology Title De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology Author Nijkamp, J.F. Van den Broek, M.A. Datema, E. De Kok, S. Bosman, L. Luttik, M.A.H. Daran-Lapujade, P.A.S. Vongsangnak, W. Nielsen, J. Heijne, W.H.M. Klaassen, P. Paddon, C.J. Platt, D. Kötter, P. Van Ham, R.C. Reinders, M.J.T. Pronk, J.T. De Ridder, D. Daran, J.M. Faculty Electrical Engineering, Mathematics and Computer Science Department Intelligent Systems Date 2012-01-27 Abstract 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. Subject OA-Fund TU Delft To reference this document use: http://resolver.tudelft.nl/uuid:69c3e926-0517-4dbc-8635-df290f0e5889 DOI https://doi.org/10.1186/1475-2859-11-36 Publisher BioMed Central ISSN 1475-2859 Source http://www.microbialcellfactories.com/content/11/1/36 Source Microbial Cell Factories, 11, 2012 Part of collection Institutional Repository Document type journal article Rights © 2012 The Author(s)Licensee BioMed Central Ltd. Files PDF Nijkamp_2012.pdf 2.46 MB Close viewer /islandora/object/uuid:69c3e926-0517-4dbc-8635-df290f0e5889/datastream/OBJ/view