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.

Nanopore sequencing enables near-completede novoassembly ofSaccharomyces cerevisiaereference strain CEN.PK113-7D

“…Similarly, MAL genes enable utilisation of maltose and maltotriose and FLO genes enable calcium-dependent flocculation, both of which are crucial for the beer brewing industry (Teunissen and Steensma 1995;Lodolo et al 2008;Brown, Murray and Verstrepen 2010). As is the case for Ty-elements, subtelomeric regions are unstable due to repetitive sequences and homology to various regions of the genome, which is likely to cause diversity across strains (Pryde, Huckle and Louis 1995;Brown, Murray and Verstrepen 2010;Nijkamp et al 2012). Characterising and accurately localising subtelomeric gene families is thus crucial for associating strain performance to specific genomic features and for targeted engineering approaches for strain improvement (Bergström et al 2014).…”

“…After scaffolding using MAIA (Nijkamp et al 2010) and linking based on homology with the genome of S288C, it was possible to reconstruct all 16 chromosomes. However, there were large sequence gaps within chromosomes and the subtelomeric regions were left unassembled, both of which could contain relevant open reading frames (ORFs) (Nijkamp et al 2012). Assuming homology to S288C, more than 90% of missing sequence was located in repetitive regions corresponding mostly to subtelomeric regions and Ty-elements.…”

“…This nanopore de novo assembly was compared to the previous short-read assembly of CEN.PK113-7D (Nijkamp et al 2012) with particular attention for previously, poorly assembled subtelomeric regions and for structural variation potentially concealed due to the assumption of homology to S288C.…”

“…Previous genome assemblies of the Saccharomyces cerevisiae strain CEN.PK113-7D have been based on homology with the fully assembled reference genome of S. cerevisiae strain S288C (Cherry et al 2012;Nijkamp et al 2012). CEN.PK113-7D is a haploid strain used as a model organism in biotechnology-related research and systems biology because of its convenient growth characteristics, its robustness under industrially relevant conditions and its excellent genetic accessibility (Canelas et al 2010;Nijkamp et al 2012;González-Ramos et al 2016;Papapetridis et al 2017).…”

“…CEN.PK113-7D is a haploid strain used as a model organism in biotechnology-related research and systems biology because of its convenient growth characteristics, its robustness under industrially relevant conditions and its excellent genetic accessibility (Canelas et al 2010;Nijkamp et al 2012;González-Ramos et al 2016;Papapetridis et al 2017). CEN.PK113-7D was sequenced using a combination of 454 and Illumina short-read libraries, and a draft genome was assembled consisting of over 700 contigs (Nijkamp et al 2012).…”