Isolates following selection for loss of heterozygosity (LOH) in a tetraploid background were analyzed for chromosomal copy numbers by ddRAD-seq after initial LOH selection and following extended passaging (28 days) in standard laboratory media.. Transient aneuploidy during Candida albicans ploidy reduction

The opportunistic pathogen Candida albicans has a large repertoire of mechanisms to generate genetic and phenotypic diversity despite the lack of meiosis in its lifecycle. Its parasexual cycle enables shifts in ploidy, which in turn facilitate recombination, aneuploidy and homozygosis of whole chromosomes to fuel rapid adaptation. Here we show that the tetraploid state potentiates ploidy variation and drives population heterogeneity. Isolates recovered after selection for LOH of one, two or three markers had a wide range of DNA contents between diploid and tetraploid, as measured by flow cytometry. ddRAD-sequencing analysis of these isolates revealed high degrees of aneuploidy, with a broad range of karyotypes including strains with a combination of di-, tri- and tetra-somic chromosomes. We followed the ploidy trajectories, by flow cytometry, for large collection of tetraploid- and aneuploid-derived isolates for 28 days of serial propagation. Terminal isolates were analyzed with ddRAD-sequencing to determine chromosome copy numbers. Isolates derived from either tetraploid or aneuploid isolates most frequently resolved to a stable euploid state. The majority of isolates reduced to the conventional diploid state, however stable triploid and tetraploid states were observed in ~30% of the isolates. While euploidy was most common, Chr6 and/or ChrR aneuploidy persisted in ~35% of terminal isolates. Together, our results indicate that tetraploid progenitors can produce populations of progeny cells with a high degree of genomic diversity, from altered ploidy to homozygosis, providing an excellent source of genetic variation upon which selection can act.