Chromosome-level genome and transcriptome analysis of <i>Trichophyton verrucosum</i> reveals pathogenicity mechanisms and antifungal response

<i>Trichophyton verrucosum</i> 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 <i>T. verrucosum</i> 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 <i>T</i>. <i>verrucosum</i> closest to <i>Trichophyton rubrum</i>. 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 <i>T. verrucosum</i> 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.