Genome Evolution, Commensalism, and Pathogenecity in the Diploid Fungust Candida albicans

Fungal pathogens exhibit considerable genetic plasticity, with both microvariation and chromosome-level rearrangements frequently enabling adaptation to host and environmental pressures.  Several genera of fungi are important human pathogens, with invasive fungal infections responsible for the death of approximately 1.5 to 2 million people worldwide each year. Candida species are the most prominent cause of invasive fungal disease in the US, with the major protagonist being Candida albicans. This is a highly adaptive species with the ability to occupy diverse niches in the human body, either as a benign commensal or as an invasive opportunistic pathogen.

 This project seeks to define microevolution of C. albicans diploid genomes over relatively short time scales during growth in vitro or during infection of the mammalian host. The C. albicans genome consists of eight heterozygous chromosomes that can undergo de novo mutation, loss of heterozygosity (LOH), or large scale rearrangements including variations in chromosome copy number. To define microevolutionary changes, clinical isolates will be sequenced before and after passaging in different murine models of infection and the full spectrum of genetic changes determined by deep-sequencing analysis. Preliminary experiments have established higher mutation rates during mammalian infection and that genome evolution in C. albicans is shaped by strong purifying selection. Analyses reveal that ‘micro-scale’ changes are key drivers of microevolution, including frequent de novo mutations and short LOH events. This project looks to build on these studies and to use C. albicans as a model species for understanding the generation of genetic diversity in a heterozygous diploid eukaryote.

The experiments will address how genetic change drives host adaptation, including changes in fitness and virulence. Gene expression changes will be examined before and after passaging, and mechanisms underlying host adaptation will be genetically dissected. Exciting preliminary data suggests that LOH and aneuploidy are important mechanisms by which C. albicans readily adapts to host niches. This research also seeks to develop new tools, including methods to define fungal growth rates in the mammalian host, phasing of diploid genomes, as well as bioinformatic pipelines for high resolution analysis of heterozygous genomes. These experiments will provide a detailed insight into how C. albicans adapts to its host, and the capacity for genomic variation to drive microevolution. 

Candida species are a frequent and serious cause of bloodstream infections in the clinical setting.  Despite the prevalence of these infections, it is unknown how the diploid Candida albicans genome adapts to its host, and the capacity for genomic variation to drive microevolution. This study will define genome dynamics and selection during growth of C. albicans isolates in the mammalian host and examine how de novo genetic variation alters commensalism and pathogenesis.