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In the environment, they grow as multicellular filaments (hyphae) that produce vegetative spores called arthroconidia. Upon inhalation by mammals, arthroconidia undergo a process called spherulation. They enlarge and undergo numerous nuclear divisions to form a spherical structure, and then internally segment until the spherule is filled with multiple cells called endospores. Mature spherules rupture and release endospores, each of which can form another spherule, in a process thought to facilitate dissemination. Spherulation is unique to <jats:italic>Coccidioides<\/jats:italic>, and its molecular determinants remain largely unknown. Here, we report the first high-density transcriptomic analyses of <jats:italic>Coccidioides<\/jats:italic> development, defining morphology-dependent transcripts and those whose expression is regulated by <jats:italic>RYP1<\/jats:italic>, a major regulator required for spherulation and virulence. Of approximately 9,000 predicted transcripts, we discovered 273 transcripts with consistent spherule-associated expression, 82 of which are <jats:italic>RYP1<\/jats:italic>-dependent, a set likely to be critical for <jats:italic>Coccidioides<\/jats:italic> virulence. ChIP-Seq revealed two distinct regulons of Ryp1: one shared between hyphae and spherules and the other unique to spherules. Spherulation regulation was elaborate, with the majority of 227 predicted transcription factors in <jats:italic>Coccidioides<\/jats:italic> displaying spherule-enriched expression. We identified provocative targets, including 20 transcripts whose expression is endospore-enriched and 14 putative secreted effectors whose expression is spherule-enriched, of which six are secreted proteases. To highlight the utility of these data, we selected a cluster of <jats:italic>RYP1<\/jats:italic>-dependent, arthroconidia-associated transcripts and found that they play a role in arthroconidia cell wall biology, demonstrating the power of this resource in illuminating <jats:italic>Coccidioides<\/jats:italic> biology and virulence.<\/jats:p>","DOI":"10.1371\/journal.pbio.3003066","type":"journal-article","created":{"date-parts":[[2025,4,15]],"date-time":"2025-04-15T13:40:58Z","timestamp":1744724458000},"page":"e3003066","update-policy":"https:\/\/doi.org\/10.1371\/journal.pbio.corrections_policy","source":"Crossref","is-referenced-by-count":16,"title":["Transcriptomic atlas throughout Coccidioides development reveals key phase-enriched transcripts of this important fungal pathogen"],"prefix":"10.1371","volume":"23","author":[{"given":"Christina 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