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While previous studies have characterized transcriptomic changes associated with its life stage transitions, the contribution of small RNAs (sRNAs)\u2014key regulators of virulence in other pathogenic fungi\u2014remains unexplored. Here, we profile sRNA expression across three Coccidioides posadasii morphologies\u2014arthroconidia, mycelia, and spherules\u2014analyzing both intracellular and extracellular RNA fractions. Utilizing RiboMarker sRNA and RNA fragment library preparation, we achieved enhanced transcriptome coverage by incorporating RNA species that are typically underrepresented or incompatible with standard sequencing workflows. We observed pronounced transcriptomic remodeling during the transition from arthroconidia to mycelia or spherules, driven primarily by changes in protein-coding transcripts, tRNA, and unannotated loci. These data identify sRNA- and fragment-producing loci that may be required for progression between the saprobic and parasitic life cycles of Coccidioides. In addition, distinct RNA fragmentation patterns were associated with each morphological state. Notably, we detected evidence of RNA export to the extracellular space, particularly snRNAs and tRNA-derived fragments, during these transitions, suggesting potential roles in cell\u2013cell or host\u2013pathogen communication. Together, this intra- and extracellular Coccidioides sRNA atlas provides a resource for biomarker discovery and advances our understanding of the molecular basis of fungal virulence.<\/jats:p>","DOI":"10.1093\/g3journal\/jkag111","type":"journal-article","created":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T08:50:23Z","timestamp":1777366223000},"source":"Crossref","is-referenced-by-count":0,"title":["Transcriptomic characterization of\n                    <i>Coccidioides<\/i>\n                    morphological states using RiboMarker-enhanced RNA sequencing"],"prefix":"10.1093","volume":"16","author":[{"given":"Jonathan M","family":"Howard","sequence":"first","affiliation":[{"name":"RealSeq Biosciences , Santa Cruz 95060 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aidan C","family":"Manning","sequence":"additional","affiliation":[{"name":"RealSeq Biosciences , Santa Cruz 95060 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel C","family":"Clark","sequence":"additional","affiliation":[{"name":"RealSeq Biosciences , Santa Cruz 95060 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tahirah","family":"Williams","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cell Biology, University of California Merced , Merced 95343 ,","place":["United States"]},{"name":"Quantitative and Systems Biology Graduate Program, University of California Merced , Merced 95343 ,","place":["United States"]},{"name":"Health Sciences Research Institute, University of California Merced , Merced 95343 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0799-6499","authenticated-orcid":false,"given":"Clarissa J","family":"Nobile","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cell Biology, University of California Merced , Merced 95343 ,","place":["United States"]},{"name":"Health Sciences Research Institute, University of California Merced , Merced 95343 ,","place":["United States"]},{"name":"Center for Cellular and Biomolecular Machines, University of California Merced , Merced 95343 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergei A","family":"Kazakov","sequence":"additional","affiliation":[{"name":"RealSeq Biosciences , Santa Cruz 95060 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergio","family":"Barberan-Soler","sequence":"additional","affiliation":[{"name":"RealSeq Biosciences , Santa Cruz 95060 ,","place":["United 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