Comparative Transcriptomics of the Saprobic and Parasitic Growth Phases in <em>Coccidioides</em> spp

<div><p><em>Coccidioides immitis</em> and <em>C. posadasii</em>, the causative agents of coccidioidomycosis, are dimorphic fungal pathogens, which grow as hyphae in the saprobic phase in the environment and as spherules in the parasitic phase in the mammalian host. In this study, we use comparative transcriptomics to identify gene expression differences between the saprobic and parasitic growth phases. We prepared Illumina mRNA sequencing libraries for saprobic-phase hyphae and parasitic-phase spherules <em>in vitro</em> for <em>C. immitis</em> isolate RS and <em>C. posadasii</em> isolate C735 in biological triplicate. Of 9,910 total predicted genes in <em>Coccidioides</em>, we observed 1,298 genes up-regulated in the saprobic phase of both <em>C. immitis</em> and <em>C. posadasii</em> and 1,880 genes up-regulated in the parasitic phase of both species. Comparing the saprobic and parasitic growth phases, we observed considerable differential expression of cell surface-associated genes, particularly chitin-related genes. We also observed differential expression of several virulence factors previously identified in <em>Coccidioides</em> and other dimorphic fungal pathogens. These included alpha (1,3) glucan synthase, SOWgp, and several genes in the urease pathway. Furthermore, we observed differential expression in many genes predicted to be under positive selection in two recent <em>Coccidioides</em> comparative genomics studies. These results highlight a number of genes that may be crucial to dimorphic phase-switching and virulence in <em>Coccidioides</em>. These observations will impact priorities for future genetics-based studies in <em>Coccidioides</em> and provide context for studies in other fungal pathogens.</p> </div