DOI: 10.5061/dryad.zpc866tjn
title: Data from: 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

description: 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) and T. interdigitale. Our results challenge the species
 status of T. indotineae because of insufficient genetic divergence from
 T. mentagrophytes. Therefore, we propose designating T. indotineae as
 T. mentagrophytes var. indotineae (or T. mentagrophytes ITS genotype VIII)
 to avoid further splitting of the complex and taxonomic inflation.
 Although T. interdigitale shows clearer genetic differentiation, its
 separation is incomplete, and identification of some isolates is ambiguous
 when using routine methods, leading us to consider it a variety as well:
 T. mentagrophytes var. interdigitale. We recommend using T. mentagrophytes
 as the overarching species name for all complex isolates. Where precise
 molecular identification is possible, the use of variety ranks is
 encouraged. Since identical resistance mechanisms are not specific to any
 genotype or dermatophyte species, identifying antifungal resistance is
 more important than differentiating closely related genotypes or
 populations.
description: # 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
 analysis. Quality control was performed using TASSEL v5.2.91, with initial
 filtering removing taxa that had more than 10% missing sites, leaving 87
 individuals. Further filtering applied a Site Minimum Count of Alleles Not
 Unknown parameter set to 80 and a Site Minimum Minor Allele Frequency
 threshold of 0.1 (10%), reducing the dataset to 6,996 sites. ####
 Description of the data and file structure **Dataset Overview** This
 Variant Call Format (VCF) file contains Single Nucleotide Polymorphism
 (SNP) data from 87 individuals. It comprises 6996 SNPs with an average
 coverage of 212.5x per individual. **populations.snps.vcf** **File
 Details** * **File Name**: mentagrophytes.vcf * **File Format**: VCF
 (Variant Call Format) Version 4.0 * **Date**: November 28, 2024 **Data
 Description** The VCF file includes the following columns standard to the
 format: * `#CHROM`: Chromosome number * `POS`: Position of the SNP on the
 chromosome * `ID`: Identifier of the SNP * `REF`: Reference base * `ALT`:
 Alternate base(s) * `QUAL`: Quality score of the SNP * `FILTER`: Filter
 status * `INFO`: Additional information (e.g., allele frequency, number of
 samples) * `FORMAT`: Data format * Sample columns: One per individual,
 containing genotype information Specific Fields in `INFO` * `NS`: Number
 of samples with data * `AF`: Allele frequency * `DP`: Total depth of reads
 Specific Fields in `FORMAT` * `GT`: Genotype * `AD`: Allele depth * `DP`:
 Read depth * `GQ`: Genotype quality * `GL`: Genotype likelihood