Identification of LncRNAs Involved in the Salt Stress Responses of Eurotium cristatum and Functional Analysis of Their Roles in Morphological Differentiation and Metabolic Regulation

Long non-coding RNAs (lncRNAs) are crucial regulators in eukaryotic organisms, yet their roles in filamentous fungi, particularly in environmental adaptation and metabolic changes, remain largely unexplored. Here, we investigated the roles of lncRNAs in salt stress response, morphological differentiation, and metabolic regulation in <i>Eurotium cristatum</i>. Using strand-specific RNA sequencing, we identified lncRNAs in sexual and asexual mycelia of <i>E. cristatum</i> and analyzed their expression profiles. We identified 203 lncRNAs, with 120 significantly differentially expressed (FDR < 0.01; |log₂ (fold change)| ≥ 1) under salt stress, including 57 upregulated and 63 downregulated in the asexual morph compared to the sexual morph. These lncRNAs correlated with physiological indicators like mycelial biomass, polysaccharide content, and melanin production. Target gene prediction and functional enrichment analysis revealed that these lncRNAs influenced morphogenesis and secondary metabolite synthesis in <i>E. cristatum</i> by regulating pathways including carbohydrate metabolism, peroxisome function, and protein ubiquitination. The lncRNA MSTRG.10627.3 showed the highest upregulation (log₂FC = 10.53, FDR < 1 × 10^-105), while MSTRG.3124.1 was significantly downregulated in the sexual morph (log₂FC = -4.94, FDR < 1 × 10^-88). A regulatory network of lncRNAs involved in salt stress responses was constructed, providing insights into fungal environmental adaptation mechanisms and potential targets for industrial strain improvement.