Candida albicans is a diploid fungus and common human commensal that colonizes the skin, gastrointestinal tract, and urogenital system of its host. It is also one of the most clinically relevant fungal pathogens, capable of overgrowing its natural niches and causing cutaneous or mucosal infections in immunocompromised individuals. Access to the bloodstream can facilitate dissemination through the body and progress to life-threatening systemic infections associated with high mortality rates, presenting a significant healthcare burden. As such, C. albicans – in particular the genome reference strain SC5314 – has been the subject of many investigations to better understand the mechanisms behind its ability to cause human disease.One of the key factors allowing C. albicans to function as both a commensal and a pathogen is its ability to transition between a variety of phenotypically distinct morphologies. While it typically grows as a round-to-ovoid yeast (also known as the white state), C. albicans can adopt a range of cell states and morphologies including pseudohyphae, hyphae, opaque, and other less common cell types. Different morphologies interact with the human host to produce commensal or pathogenic outcomes. For example, hyphae are more readily recognized by immune cells and inflict damage upon the host by penetrating through tissue and lysing phagocytic cells. In contrast, opaque cells are phagocytosed less efficiently by macrophage and neutrophils relative to their white state counterparts and colonize the gastrointestinal tract more thoroughly in some cases. Advancing our understanding of the mechanisms regulating these morphological transitions between them is critical to understanding how this pathogenic yeast interacts with the host.In Chapter 2, we investigate the role of the histone deacetylase SIR2 in C. albicans phenotypic switching. Preliminary work using a previously-constructed strain set in the BWP17 background – an SC5314 derivative – identified increased frequencies of white-to-opaque switching. However, sir2Δ/Δ mutants constructed in a wildtype SC5314 background failed to reproduce this phenotype. We found that the canonical function of SIR2 in subtelomeric silencing was similar between strains in the BWP17 and SC5314 backgrounds. Furthermore, altered growth rates in the original BWP17 strain set were not sufficient to explain the high-frequency switching. Reconstruction of sir2Δ/Δ mutants in other SC5314 lineages (as well as BWP17 itself) also failed to phenocopy the original BWP17 sir2Δ/Δ mutants. Utilizing whole genome sequencing, we revealed the high-switching strain set possessed multiple aneuploidies and loss of heterozygosity tracts not found in related strains, likely interacting with SIR2 to increase the switching frequency. These findings highlight the need for more thorough validation of strain backgrounds, as altered karyotypes can significantly impair the interpretation of phenotypes.We also describe ongoing work characterizing an expanded subtelomeric gene family – the telomere-associated (TLO) genes – in Chapter 3. Tlos function as interchangeable Med2 subunits in the transcriptional coactivator Mediator complex. A previous study generated strains lacking all TLO paralogs (tlo-null) in SC5314, but these strains possessed major chromosomal rearrangements. We constructed two new tlo-null mutants with a modified deletion strategy and verified karyotypes using a hybrid sequencing method. We also generated a de novo, telomere-to-telomere, haplotype-phased assembly of the SC5314 genome for comparison to our tlo-null strains. Both newly constructed tlo-null strains lacked large-scale rearrangements, and analysis of our assembly revealed major errors in previously annotated SC5314 subtelomeres, where sequences were often misassigned and omitted up to 15 kilobases at some ends. SC5314 subtelomeres also possessed two unidentified TLO homologs on the left arm of chromosome 4 and another subtelomeric gene family homologous to telomere-associated DNA helicase genes (YRF1) in Saccharomyces cerevisiae. Our work has revealed previously hidden aspects of the C. albicans genome, providing a more complete understanding of its genomic landscape and opening new avenues for future investigations. Finally, Chapter 4 explores transcriptional variation among C. albicans isolates and combines this information with quantitative phenotyping to identify the function of previously uncharacterized genes. Surprisingly, this work revealed that transcriptional profiles of C. albicans isolates do not recapitulate their phylogenetic relationships. Closely related isolates differentially expressed up to a third of their annotated genes under identical conditions. Using weighted gene correlation network analyses to link transcription and phenotypes, we produced coexpression modules for genes that could be associated with specific phenotypes, including those linked to virulence. Importantly, these modules frequently recapitulated the transcriptional architecture of previously characterized pathways. Genes in a module that were not previously linked to filamentation were shown to be responsible for hyphal initiation. These findings suggest that in C. albicans, transcriptional profiles are better indicators for phenotypic outcomes than genotypic information. more...