Chromosome-level genome and transcriptome analysis of Trichophyton verrucosum reveals pathogenicity mechanisms and antifungal response.

Trichophyton verrucosum is a zoophilic dermatophyte and the primary cause of bovine dermatophytosis, a contagious and economically significant skin disease with zoonotic potential. Despite its importance, high-quality genomic and transcriptomic resources for this species remain scarce, limiting insights into its pathogenic mechanisms and antifungal responses. Here, we present a chromosome-level genome assembly of T. verrucosum OR056436.1, generated using single-molecule real-time (SMRT), Illumina paired-end and high-throughput chromosomal conformation capture (Hi-C) technologies, followed by comprehensive annotation and comparative analyses with six other fungal pathogens. Transcriptome profiling under itraconazole (ITR) and Xuanjing - Compound Chinese Herbal Spray (CCM) treatments revealed antifungal-responsive genes. The final 23.44 Mb genome comprises 7,936 protein-coding genes, with 4.98% repetitive sequences, and shows 98.8% completeness based on BUSCO analysis. Functional annotation identified 262 Kyoto Encyclopedia of Genes and Genomes pathways, 4,861 Eukaryotic Orthologous Groups proteins, 34 secondary metabolite biosynthetic gene clusters, 1,157 carbohydrate-active enzymes, 2,920 pathogen-host interaction genes, and 59 virulence factor genes. Comparative genomics identified 45,425 orthogroups including 393 core and 184 single-copy orthogroups, placing T. verrucosum closest to Trichophyton rubrum. Transcriptomic analysis highlighted differentially expressed genes enriched in amino acid metabolism, ABC transporters, drug metabolism, and stress response pathways. Notably, subtilisin-like proteases and LysM-domain proteins were significantly regulated under antifungal treatments. This integrative genomic-transcriptomic study provides the most complete T. verrucosum genome to date, identifies key genes involved in pathogenicity and antifungal adaptation, and offers valuable resources for diagnostics, therapeutic development, and improved strategies for bovine dermatophytosis.