Analysis of the Impact of Ploidy on the Genotypic Effects of Directed Evolution

The role of ploidy—copy number of chromosomes in an organism—on cells under environmental stress is poorly understood. Variations in ploidy such as aneuploidy—deviations in copy number of chromosomes compared to an organisms base ploidy—and polyploidy—more than two sets of each chromosome—are common in cancer so it is important to understand how ploidy impacts evolution. We performed an evolution experiment on strains of Saccharomyces cerevisiae with different ploidy (haploid, diploid, and tetraploid) under selection for growth on a low-glucose, high raffinose media. After 240 generations, the parental strain and seven of the surviving strains (2 diploid and 5 tetraploids) were sequenced via next generation sequencing technology. We analyzed the sequenced strains to identify mutations causal for survival and compared the mutations between the strains of different ploidy. More mutations in the tetraploid strains relative to their diploid counterparts were discovered hinting at the possibility of a positive correlation between ploidy and mutation rate. However, the inability to identify structural variations from the current sequencing dataset prevents complete identification of mutations present in the evolved strains. In addition, we have benchmarked variation-calling software with both “in silico” generated synthetic datasets, as well as our evolved strains for calling SNPs and indels at higher ploidy (N > 2).