Analysis of yeast genome instability during industrial-scale bioethanol fermentation. Saccharomyces cerevisiae

The Saccharomyces cerevisiae strain JAY270/PE-2 is a highly efficient biocatalyst used in the production of bioethanol from sugarcane feedstock. This strain is heterothallic and diploid, and its genome is characterized by abundant structural and nucleotide polymorphisms between most pairs of homologous chromosomes. Genome instability processes known to occur during long-term fermentations may cause genetic alterations that trigger the appearance of undesirable phenotypes in the yeast population. From a pure culture of JAY270, we initiated a batch sugarcane fermentation at a bioethanol distillery. After 30 days of successive yeast cell recycling, we harvested the microbial culture and characterized its composition. We used markers for four different polymorphic loci to identify yeast clones derived from the original JAY270 inoculum. We then used pulse field gel electrophoresis (PFGE) to analyze the karyotypes of these clones, finding that approximately 30% carried chromosomal size polymorphisms. The fitness of eleven clones (FDY) carrying such genome rearrangements was assessed through competition assays in co-culture with the JAY270 parent strain. In competitions that simulated the conditions present during industrial fermentation, ten of the clones did not show alterations in fitness, while one (FDY6) displayed superior growth relative to JAY270. We then sequenced the genomes of all eleven clones and found that most of them carried loss-of-heterozygosity events at various chromosomes, explaining the nature of the size polymorphisms observed in PFGE. In some cases, multiple LOH tracts were observed per clone, suggesting the occurrence of systemic genomic instability processes. The genomic sequence data associated with this project includes reads obtained 11 fermentation isolates derived from JAY270.