Stage-specific RNA regulomes of Trichophyton mentagrophytes: mRNA-lncRNA-miRNA interplay in spore-hypha transition

<b>Background</b>: As a globally distributed dermatophyte, <i>Trichophyton mentagrophytes</i> (<i>T. mentagrophytes</i>) causes diverse dermatophytoses in humans and animals. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), which serve as critical regulators of diverse biological processes, have been extensively characterized in numerous fungal species. However, the role of mRNAs, lncRNAs, and miRNAs during <i>T. mentagrophytes</i> germination remains unexplored. <b>Objectives</b>: In this study, the molecular mechanisms involved in the germination of <i>T. mentagrophytes</i> were systematically investigated. <b>Methods</b>: RNA-sequencing technology, small RNA-sequencing technology, related bioinformatics methods, and qRT-PCR were used to systematically characterize the expression profiles of mRNAs, miRNAs, and lncRNAs in <i>T. mentagrophytes</i> spores and hyphae, and analyze the regulatory mechanisms of mRNAs, miRNAs, and lncRNAs during <i>T. mentagrophytes</i> germination. <b>Results</b>: In our study, RNA-sequencing was performed to identify mRNAs, lncRNAs, and miRNAs in spores and hyphae of <i>T. mentagrophytes</i>. A total of 3,193 differentially expressed mRNAs, 409 differentially expressed lncRNAs, and 119 differentially expressed miRNAs were identified, with qRT-PCR subsequently used to verify the dependability of the sequencing data. In addition, an mRNA-lncRNA-miRNA regulatory network containing 2,672 mRNAs, 107 miRNAs, and 329 lncRNAs was constructed. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Gene Set Enrichment Analysis suggested that mRNAs, lncRNAs, and miRNAs may play important roles during spore germination, potentially participating in fundamental biosynthetic, cell wall remodelling, cell cycle regulation, cytoskeletal reorganization, epigenetic regulation, and metabolic processes. <b>Conclusion</b>: Our study revealed the characteristics of mRNAs, lncRNAs, and miRNAs in <i>T. mentagrophytes</i> using transcriptomic methods, and set the stage for future pathogenicity studies and antifungal drug development for <i>T. mentagrophytes</i>.