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. One of the key reasons JAY270 is favored by many bioethanol distilleries is that it does not normally display flocculation or other mechanisms of cellular co-aggregation. However, genome instability processes known to occur during long-term fermentations may cause genetic alterations that trigger the appearance of this undesirable phenotype in the yeast population. From pure cultures of JAY270, we identified the spontaneous appearance of colonies displaying altered rough morphology in agar media and fast sedimentation in liquid culture analogous to flocculation. The rough colonies were abundant (~1 in every 3,000 normal smooth colonies), a very high frequency that was inconsistent with de novo nucleotide mutagenesis, especially in a diploid genome. We investigated the genetic control of this phenotype, and found that JAY270 is heterozygous for a frameshift mutation in the ACE2 gene (ACE2/ace2-A7) on chromosome 12 (Chr12). ACE2 encodes a transcription factor that regulates the expression of genes required for the degradation of the septum that links mother and daughter cells post-budding. Twenty seven spontaneous rough colony JAY270-derived isolates analyzed displayed the characteristic mother-daughter cell separation defect associated with ace2 null mutants, and carried copy-neutral loss-of-heterozygosity (LOH) on Chr12 at the ACE2 locus (ace2-A7/ace2-A7). We sequenced the full genomes of all 27 rough colony isolates and characterized the LOH tracts spanning the ACE2 locus, which extended for up to hundreds of kilobases, but did not span the centromere. In addition, many of the isolates carried concomitant LOH tracts in chromosomes other than Chr12, suggesting the occurrence of systemic genomic instability processes. The genomic sequence data associated with this project includes reads obtained from JAY270, from 27 rough colony isolates derived from JAY270, and 44 haploid spores derived from JAY270.
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