The genome sequence of the popular hexose transport deficient Saccharomyces cerevisiae strain EBY.VW4000 reveals LoxP/Cre-induced translocations and gene loss.

Saccharomyces cerevisiae harbours a large group of tightly controlled transporters with different characteristics for glucose uptake. A milestone in the characterization of S. cerevisiae's transporters was the construction of EBY.VW4000, a strain devoid of glucose import. Since its construction, EBY.VW4000 has become a widely used platform for the discovery and characterization of transporters from a wide range of organisms. To abolish glucose uptake, 21 genes were knocked-out across 16 successive deletion rounds with the LoxP/Cre system. While these genetic approaches notoriously trigger genome alterations, the genome of EBY.VW4000 has hitherto never been characterized. Based on a combination of whole genome sequencing, karyotyping and molecular confirmation, the present study reveals that the construction of EBY.VW4000 resulted in many gene losses and chromosomal rearrangements. Recombinations between the LoxP scars has led to the assembly of four neo-chromosomes, the truncation of two chromosomes and the loss of two telomeric regions. Karyotyping of the EBY.VW400 lineage retraced the current chromosomal architecture to four translocations events that occurred between the 6th and the 12th rounds of deletion/marker recycling. The presented data provide support for further targeted genetic modifications of EBY.VW4000. Furthermore, the present study identified that sporulation and spore germination are severely impaired in EBY.VW4000.