Resolving phylogenetic relationships within the <em>Trichophyton mentagrophytes</em> complex: A RADseq genomic approach challenges status of ‘terbinafine‐resistant’ <em>Trichophyton indotineae</em> as distinct species

The Trichophyton mentagrophytes complex encompasses common dermatophytes causing superficial mycoses in humans and animals. The taxonomy of the complex is unstable, with conflicting views on the species status of some taxa, particularly T. indotineae and T. interdigitale. Due to the presence of intermediate genotypes, neither MALDI-TOF MS nor ITS rDNA sequencing can accurately distinguish all taxa in the complex, potentially contributing to clinical misdiagnoses. This research resolves phylogenetic relationships within the T. mentagrophytes complex. Based on these data, the taxonomical recommendations are suggested. In order to resolve the phylogenetic relationship of the T. mentagrophytes complex, we employed Restriction Site-Associated DNA Sequencing (RADseq) to produce a high-resolution single-nucleotide polymorphism (SNP) dataset from 95 isolates. The SNP-based analyses indicated the presence of two major genetic clusters corresponding to T. mentagrophytes (including T. indotineae) ..., , , # Data from: Resolving phylogenetic relationships within the *Trichophyton mentagrophytes* complex: A RADseq genomic approach challenges status of ‘terbinafine‐resistant’ *Trichophyton indotineae* as distinct species We have submitted the resulting mentagrophytes.vcf (Variant Call Format) file, created to explore population genetics within the Trichophyton mentagrophytes complex. Library preparation, enzyme selection, and RAD sequencing were performed by Floragenex Inc. (9590 SW Gemini Dr, Beaverton, OR, USA), using the PstI enzyme for digestion. The sequencing generated 409.8 million reads, providing an average coverage of 20,187.5× per variant, enabling the identification of 16,795 variable loci. The reference genome for strain ME 517/15 was assembled using VELVET v1.2.10, and the remaining samples were aligned to this reference genome. Variant calling was conducted using BOWTIE v1.1.1, BWA v0.6.1, and SAMTOOLS v0.1.16. The generated VCF file was subsequently processed for SNP data a...,