Non-coding RNAs drive transcriptional network rewiring underlying thermal dimorphism in a human pathogenic fungus

As fungal pathogens pose mounting global challenges, decoding their complex adaptive traits remains a paramount academic priority. While previous studies have provided foundational insights into protein-coding variations and orphan genes, fully understanding such traits requires exploring upstream non-coding regulatory networks. Here, we present a high-resolution, rRNA-depleted temporal transcriptomic framework across reciprocal dimorphic transitions to decode how non-coding network rewiring involving in fungal adaption. Integrating temporal profiling with comparative genomics reveals that early ATP-related metabolic reprogramming and melanin biosynthesis direct morphogenesis via species-specific motifs. Further temporal network modeling uncovers a functional stratification where long non-coding RNAs orchestrate early stress responses, whereas circular RNAs drive morphological conversion. Functional validation confirms that hub non-coding transcripts mediate stress adaptation, with cross-species perturbation in the closest non-pathogen species altering phenotypic outcomes. Together, these findings demonstrate how system-level non-coding dynamics underlie the evolutionary innovation of thermal dimorphism, establishing a robust paradigm for understanding specialized fungal pathogenicity and evolution adaption.