Saccharomyces cerevisiae CEN.PK113-7D Genome sequencing and assembly Version 2.0

Saccharomyces cerevisiae CEN.PK113-7D (Mat a MAL2-8c)The haploid Saccharomyces cerevisiae strain CEN.PK113-7D is a popular model system for metabolic engineering and systems biology research. Current genome assemblies are based on short-read sequencing data scaffolded based on homology to model S. cerevisiae strain S288C. The subtelomeric regions, which contain many genes determining industrially-relevant phenotypes, are missing in these assemblies and mistakes may have been introduced due to unwarranted assumption of perfect homology to S288C.Here, we present a near-complete genome assembly of CEN.PK113-7D using only Oxford Nanopore Technology's MinION sequencing platform. The final assembly has 15 of the 16 chromosomes, the mitochondrial genome and the 2-micron plasmid assembled in single contigs and all but one chromosome starts or ends in a telomere cap. This new, near-complete genome assembly contains 844 kbp of added sequence containing 412 gene annotations relative to the previous assembly of CEN.PK113-7D. Many of these genes belong to families with functions which are highly relevant for various industrial applications. This study provides a high-quality reference assembly and annotation of a widely-used biotechnology model organism, demonstrates the power of long-read sequencing and places a caveat on assumed genome stability of model microorganisms.