Multiple Stochastic Parameters Influence Genome Dynamics in a Heterozygous Diploid Eukaryotic Model

Area of Science:

• Genetics and Genomics
• Microbial Pathogenesis
• Evolutionary Biology

Background:

• The opportunistic fungal pathogen *Candida albicans* is a heterozygous diploid organism prone to frequent genomic rearrangements, particularly loss-of-heterozygosity (LOH) events.
• LOH events, often resulting from DNA repair mechanisms, occur across all chromosomes and are observed in both laboratory and clinical isolates, especially under host-relevant stress conditions.
• In other diploid organisms like *Saccharomyces cerevisiae*, LOH facilitates the adaptation process by enabling recessive beneficial mutations to become expressed, a mechanism also relevant for antifungal resistance and niche adaptation in *C. albicans*.

Purpose of the Study:

• To investigate the genome-wide dynamics and heterogeneity of loss-of-heterozygosity (LOH) events in *Candida albicans* under both standard and stress conditions.
• To determine if stress responses uniformly increase genome-wide instability or if LOH frequencies are locus- and strain-specific.
• To understand the adaptive significance of LOH heterogeneity in *C. albicans*.

Main Methods:

• Construction of a collection of 15 *C. albicans* strains, each equipped with a loss-of-heterozygosity (LOH) reporter system on a distinct chromosome arm.
• The LOH reporter system utilizes two fluorescent marker genes, allowing spontaneous LOH events to be detected via loss of fluorescence using flow cytometry.
• Analysis of LOH frequencies across different genomic loci and strains under standard laboratory conditions and upon exposure to various stresses.

Main Results:

• Significant differences in loss-of-heterozygosity (LOH) frequencies were observed between different genomic loci under standard laboratory conditions.
• Comparable heterogeneity in LOH frequency was found for a specific genomic locus across independent strains.
• Exposure to stress resulted in varied outcomes, with individual strains showing increased, decreased, or unchanged LOH frequencies, refuting a general stress-induced genome instability response.

Conclusions:

• The heterogeneity of loss-of-heterozygosity (LOH) frequency in *Candida albicans* is pervasive, occurring at inter-strain, intra-strain, and inter-chromosomal levels.
• LOH events appear to occur stochastically, influenced by the genetic background, rather than being uniformly driven by stress.
• This genome-wide LOH heterogeneity likely serves as a key adaptive strategy for *C. albicans*, enabling rapid generation of genetic variation for survival in dynamic environments.