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. 2021 Nov;7(11):000707.
doi: 10.1099/mgen.0.000707.

The taxonomy of the Trichophyton rubrum complex: a phylogenomic approach

Luc Cornet  1 , Elizabet D'hooge  1 , Nicolas Magain  2 , Dirk Stubbe  1 , Ann Packeu  1 , Denis Baurain  3 , Pierre Becker  1
Affiliations

The taxonomy of the Trichophyton rubrum complex: a phylogenomic approach

Luc Cornet et al. Microb Genom. 2021 Nov.

Abstract

The medically relevant Trichophyton rubrum species complex has a variety of phenotypic presentations but shows relatively little genetic differences. Conventional barcodes, such as the internal transcribed spacer (ITS) region or the beta-tubulin gene, are not able to completely resolve the relationships between these closely related taxa. T. rubrum, T. soudanense and T. violaceum are currently accepted as separate species. However, the status of certain variants, including the T. rubrum morphotypes megninii and kuryangei and the T. violaceum morphotype yaoundei, remains to be deciphered. We conducted the first phylogenomic analysis of the T. rubrum species complex by studying 3105 core genes of 18 new strains from the BCCM/IHEM culture collection and nine publicly available genomes. Our analyses revealed a highly resolved phylogenomic tree with six separate clades. Trichophyton rubrum, T. violaceum and T. soudanense were confirmed in their status of species. The morphotypes T. megninii, T. kuryangei and T. yaoundei all grouped in their own respective clade with high support, suggesting that these morphotypes should be reinstituted to the species-level. Robinson-Foulds distance analyses showed that a combination of two markers (a ubiquitin-protein transferase and a MYB DNA-binding domain-containing protein) can mirror the phylogeny obtained using genomic data, and thus represent potential new markers to accurately distinguish the species belonging to the T. rubrum complex.

Keywords: Trichophyton rubrum; dermatophytes; fungi; gene marker; mycopathology; phylogenomics.

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Conflict of interest statement

The authors declare that there are no conflicts of interest.

Figures

Fig. 1.
Fig. 1.
Graphical abstract. We used 18 newly sequenced BCCM/IHEM strains and 11 public genomes assemblies, of which one BCCM/IHEM strain, to reconstruct the phylogeny of the Trichophyton rubrum complex on a dataset composed of 3105 core genes. We used two independent methods, namely bootstrapping and jackknife, to assess the robustness of our phylogenomic results. Robinson-Foulds (1981) distance comparison allowed the identification of two new single-gene markers. Based on our phylogenomic results, we propose to consider morphotypes of this complex as separate species.
Fig. 2.
Fig. 2.
Comparison between consensus jackknife phylogenomic trees. Phylogenomic analyses were conducted on 3105 core genes in DNA and in proteins. 100×100000 concatenation of genes were produced with SCaFoS and the corresponding trees computed with RAML under the models GTRGAMMA for DNA and PROTGAMMALGF for proteins. T. rubrum is in red, T. kuryangei in orange, T. megninii in purple, T. soudanense in brown and T. violaceum - T. yaoundei is in blue. Jackknife support values are shown at the nodes.
Fig. 3.
Fig. 3.
Large-scale protein analysis of 27 strains belonging to the T. rubrum complex. The maximum likelihood tree was inferred on 3105 core genes under the PROTGAMMALGF model with RAxML from a supermatrix of 29×1688754 unambiguously aligned amino-acid positions. T. rubrum is in red, T. kuryangei in orange, T. megninii in purple, T. soudanense in brown and T. violaceum is in blue and - T. yaoundei is in green. Bootstrap support values are shown at the nodes. Branch length of outgroup are divided by five.
Fig. 4.
Fig. 4.
Comparison of the reference tree with marker gene phylogenies. The reference tree is the one of Fig. 3. Marker gene trees were computed on DNA sequences under the GTRGAMMA model. Nodes are enumerated according to the reference tree.
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