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Zhan P, Dukik K, Li D, Sun J, Stielow JB, Gerrits van den Ende B, Brankovics B, Menken SBJ, Mei H, Bao W, Lv G, Liu W, de Hoog GS. Phylogeny of dermatophytes with genomic character evaluation of clinically distinct Trichophyton rubrum and T. violaceum. Stud Mycol 2018; 89:153-175. [PMID: 29910521 PMCID: PMC6002342 DOI: 10.1016/j.simyco.2018.02.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Trichophyton rubrum and T. violaceum are prevalent agents of human dermatophyte infections, the former being found on glabrous skin and nail, while the latter is confined to the scalp. The two species are phenotypically different but are highly similar phylogenetically. The taxonomy of dermatophytes is currently being reconsidered on the basis of molecular phylogeny. Molecular species definitions do not always coincide with existing concepts which are guided by ecological and clinical principles. In this article, we aim to bring phylogenetic and ecological data together in an attempt to develop new species concepts for anthropophilic dermatophytes. Focus is on the T. rubrum complex with analysis of rDNA ITS supplemented with LSU, TUB2, TEF3 and ribosomal protein L10 gene sequences. In order to explore genomic differences between T. rubrum and T. violaceum, one representative for both species was whole genome sequenced. Draft sequences were compared with currently available dermatophyte genomes. Potential virulence factors of adhesins and secreted proteases were predicted and compared phylogenetically. General phylogeny showed clear gaps between geophilic species of Arthroderma, but multilocus distances between species were often very small in the derived anthropophilic and zoophilic genus Trichophyton. Significant genome conservation between T. rubrum and T. violaceum was observed, with a high similarity at the nucleic acid level of 99.38 % identity. Trichophyton violaceum contains more paralogs than T. rubrum. About 30 adhesion genes were predicted among dermatophytes. Seventeen adhesins were common between T. rubrum and T. violaceum, while four were specific for the former and eight for the latter. Phylogenetic analysis of secreted proteases reveals considerable expansion and conservation among the analyzed species. Multilocus phylogeny and genome comparison of T. rubrum and T. violaceum underlined their close affinity. The possibility that they represent a single species exhibiting different phenotypes due to different localizations on the human body is discussed.
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Affiliation(s)
- P Zhan
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China.,Dermatology Hospital of Jiangxi Provinces, Jiangxi Dermatology Institute, Nanchang, China.,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - K Dukik
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - D Li
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China.,Georgetown University Medical Center, Department of Microbiology and Immunology, Washington, DC, USA
| | - J Sun
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - J B Stielow
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Thermo Fisher Scientific, Landsmeer, The Netherlands.,Center of Expertise in Mycology of Radboudumc/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | | | - B Brankovics
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - S B J Menken
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - H Mei
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - W Bao
- Nanjing General Hospital of Nanjing Command, Nanjing, China
| | - G Lv
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - W Liu
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - G S de Hoog
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.,Thermo Fisher Scientific, Landsmeer, The Netherlands.,Center of Expertise in Mycology of Radboudumc/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
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Verkley G, Dukik K, Renfurm R, Göker M, Stielow J. Novel genera and species of coniothyrium-like fungi in Montagnulaceae (Ascomycota). Persoonia 2014; 32:25-51. [PMID: 25264382 PMCID: PMC4150078 DOI: 10.3767/003158514x679191] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 08/08/2013] [Indexed: 11/25/2022]
Abstract
Based on analyses of concatenated internal transcribed spacer regions of the nrDNA operon (ITS), large subunit rDNA (LSU), γ-actin and β-tubulin gene sequences the taxonomy of coniothyrium-like fungi belonging in the family Montagnulaceae, order Pleosporales, was re-assessed. Two new genera are proposed, Alloconiothyrium, to accommodate A. aptrootii sp. nov., and Dendrothyrium for D. longisporum sp. nov. and D. variisporum sp. nov. One new species is described in Paraconiothyrium, viz. Parac. archidendri sp. nov., while two species so far classified in Paraconiothyrium are transferred to Paraphaeosphaeria, viz. Paraph. minitans comb. nov. and Paraph. sporulosa comb. nov. In Paraphaeosphaeria five new species are described based on asexual morphs, viz. Paraph. arecacearum sp. nov., Paraph. neglecta sp. nov., Paraph. sardoa sp. nov., Paraph. verruculosa sp. nov., and Paraph. viridescens sp. nov. Macro- and micromorphological characteristics are fully described.
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Affiliation(s)
- G.J.M. Verkley
- CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - K. Dukik
- CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - R. Renfurm
- CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - M. Göker
- DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| | - J.B. Stielow
- CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
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