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.
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.
authors.affiliation: The Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands.
authors.forename: Jurgen F
authors.initials: JF
authors.lastname: Nijkamp
authors.forename: Marcel
authors.initials: M
authors.lastname: van den Broek
authors.forename: Erwin
authors.initials: E
authors.lastname: Datema
authors.forename: Stefan
authors.initials: S
authors.lastname: de Kok
authors.forename: Lizanne
authors.initials: L
authors.lastname: Bosman
authors.forename: Marijke A
authors.initials: MA
authors.lastname: Luttik
authors.forename: Pascale
authors.initials: P
authors.lastname: Daran-Lapujade
authors.forename: Wanwipa
authors.initials: W
authors.lastname: Vongsangnak
authors.forename: Jens
authors.initials: J
authors.lastname: Nielsen
authors.forename: Wilbert H M
authors.initials: WH
authors.lastname: Heijne
authors.forename: Paul
authors.initials: P
authors.lastname: Klaassen
authors.forename: Chris J
authors.initials: CJ
authors.lastname: Paddon
authors.forename: Darren
authors.initials: D
authors.lastname: Platt
authors.forename: Peter
authors.initials: P
authors.lastname: Kötter
authors.forename: Roeland C
authors.initials: RC
authors.lastname: van Ham
authors.forename: Marcel J T
authors.initials: MJ
authors.lastname: Reinders
authors.forename: Jack T
authors.initials: JT
authors.lastname: Pronk
authors.forename: Dick
authors.initials: D
authors.lastname: de Ridder
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Daran
mesh_terms: D001709:Biotechnology; D056915:DNA Copy Number Variations; D004271:DNA, Fungal / Q000235:genetics; D005800:Genes, Fungal; D016681:Genome, Fungal; D060847:Metabolic Engineering / Q000379:methods; D016366:Open Reading Frames; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA
chemical_list: D004271:DNA, Fungal; D029701:Saccharomyces cerevisiae Proteins