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Kabtani J, Ranque S. A Comparative Description of Dermatophyte Genomes: A State-of-the-Art Review. Mycopathologia 2023; 188:1007-1025. [PMID: 37812320 DOI: 10.1007/s11046-023-00802-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/28/2023] [Indexed: 10/10/2023]
Abstract
The nomenclature and phylogeny of dermatophytes is currently based on the nucleotide sequence polymorphisms of a few genomic regions. However, the limitations of this multilocus sequence-based approach makes dermatophyte species identification difficult. Variation and adaptation are key to the persistence of species. Nevertheless, this heterogeneity poses a genuine problem for the classification and nomenclature of dermatophytes. The relatively high intra-species and low inter-species polymorphisms of this keratinophilic group of fungi hampers both species delineation and identification. Establishing the taxonomic boundaries of dermatophyte species complexes remains controversial. Furthermore, until recently, knowledge of molecular biology, genetics and genomics remained limited. This systematic review highlights the added value of whole genome sequencing and analysis data in dermatophyte classification that might enhance identification and, consequently, the diagnosis and management of dermatophytoses. Our approach consisted in describing and comparing the dermatophyte mitochondrial genomes, secretomes (Adhesins, LysM domains, proteases) and metabolic pathways, with the aim to provide new insights and a better understanding of the phylogeny and evolution of dermatophytes.
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Affiliation(s)
- J Kabtani
- IHU Méditerranée Infection, 13005, Marseille, France
| | - S Ranque
- IHU Méditerranée Infection, 13005, Marseille, France.
- AP-HM, IRD, SSA, VITROME, Aix-Marseille Université, 13005, Marseille, France.
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2
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Sahib Sadeq H, Hamed Al-Oebady MA. Detection of LAP1 and LAP2 genes from Trichophyton rubrum. BIONATURA 2022. [DOI: 10.21931/rb/2022.07.04.42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Samples of hair, nails and skin were collected, representing people of different ages and races. The number of isolated people gathered between October 2021 and February 2022 from Al-Hussein Teaching Hospital and a private clinic under the supervision of doctors(118) species was examined. Dermatophytes were found in 80 of them; among the 80 positive Trichophyton rubrum species, 30 were produced, which represents less than half of the dermatophytes for each of the 80 positive species (14 cutaneous, nine hair and seven nail isolates)the study's findings included hair hole testing, which came back negative, and urea degradation testing. The results were either negative or inconsistent across the isolates; the growth test in the PDA was positive, the virulence factors that enable the fungus to penetrate host tissues were studied during leucine aminopeptidase (LAP1) and (LAP2), it was observed that there were no significant differences in gene isolates of T. rubrum.
Keywords: LAP1; LAP2; genus Trichophyton rubrum.
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Affiliation(s)
- Hiba Sahib Sadeq
- Biology Department, College of Science, University of Al-Muthanna, Iraq
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3
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de Melo Teixeira M, Lang BF, Matute DR, Stajich JE, Barker BM. Mitochondrial genomes of the human pathogens Coccidioides immitis and Coccidioides posadasii. G3 (BETHESDA, MD.) 2021; 11:jkab132. [PMID: 33871031 PMCID: PMC8496281 DOI: 10.1093/g3journal/jkab132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/25/2021] [Indexed: 12/25/2022]
Abstract
Fungal mitochondrial genomes encode genes involved in crucial cellular processes, such as oxidative phosphorylation and mitochondrial translation, and the molecule has been used as a molecular marker for population genetics studies. Coccidioides immitis and C. posadasii are endemic fungal pathogens that cause coccidioidomycosis in arid regions across both American continents. To date, approximately 150 Coccidioides isolates have been sequenced to infer patterns of variation in nuclear genomes. However, less attention has been given to the mitochondrial genomes of Coccidioides. In this report, we describe the assembly and annotation of mitochondrial reference genomes for two representative strains of C. posadasii and C. immitis, as well as assess population variation among 77 selected genomes. The sizes of the circular-mapping molecules are 68.2 Kb in C. immitis and 75.1 Kb in C. posadasii. We identify 14 mitochondrial protein-coding genes common to most fungal mitochondria, which are largely syntenic across different populations and species of Coccidioides. Both Coccidioides species are characterized by a large number of group I and II introns, harboring twice the number of elements as compared to closely related Onygenales. The introns contain complete or truncated ORFs with high similarity to homing endonucleases of the LAGLIDADG and GIY-YIG families. Phylogenetic comparisons of mitochondrial and nuclear genomes show extensive phylogenetic discordance suggesting that the evolution of the two types of genetic material is not identical. This work represents the first assessment of mitochondrial genomes among isolates of both species of Coccidioides, and provides a foundation for future functional work.
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Affiliation(s)
- Marcus de Melo Teixeira
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
- Faculty of Medicine, University of Brasília-DF, Brasília, Federal District 70910-3300, Brazil
| | - B Franz Lang
- Robert Cedergren Centre for Bioinformatics and Génomiques, Département de Biochimie, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jason E Stajich
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
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4
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Zheng H, Blechert O, Mei H, Ge L, Liu J, Tao Y, Li D, de Hoog G, Liu W. Assembly and analysis of the whole genome of
Arthroderma uncinatum
strain T10, compared with
Microsporum canis
and
Trichophyton rubrum. Mycoses 2020; 63:683-693. [DOI: 10.1111/myc.13079] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 03/13/2020] [Accepted: 03/15/2020] [Indexed: 11/24/2022]
Affiliation(s)
- Hailin Zheng
- Department of Medical Mycology Institute of Dermatology Chinese Academy of Medical Science and Peking Union Medical College Nanjing China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs Nanjing China
| | - Oliver Blechert
- Department of Medical Mycology Institute of Dermatology Chinese Academy of Medical Science and Peking Union Medical College Nanjing China
| | - Huan Mei
- Department of Medical Mycology Institute of Dermatology Chinese Academy of Medical Science and Peking Union Medical College Nanjing China
| | - Liyu Ge
- Department of Medical Mycology Institute of Dermatology Chinese Academy of Medical Science and Peking Union Medical College Nanjing China
| | - Jia Liu
- Department of Medical Mycology Institute of Dermatology Chinese Academy of Medical Science and Peking Union Medical College Nanjing China
| | - Ye Tao
- Shanghai Biozeron Biotechnology Co., Ltd Shanghai China
| | - Dongmei Li
- Department of Microbiology & Immunology Georgetown University Medical Center Washington DC USA
| | - G.Sybren de Hoog
- Center of Expertise in Mycology Radboud University Medical Center/Canisius Wilhelmina Hospital Nijmegen The Netherlands
| | - Weida Liu
- Department of Medical Mycology Institute of Dermatology Chinese Academy of Medical Science and Peking Union Medical College Nanjing China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs Nanjing China
- Center for Global Health School of Public Health Nanjing Medical University Nanjing China
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Shen XY, Li T, Chen S, Fan L, Gao J, Hou CL. Characterization and phylogenetic analysis of the mitochondrial genome of Shiraia bambusicola reveals special features in the order of pleosporales. PLoS One 2015; 10:e0116466. [PMID: 25790308 PMCID: PMC4366305 DOI: 10.1371/journal.pone.0116466] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 12/08/2014] [Indexed: 12/20/2022] Open
Abstract
Shiraia bambusicola P. Henn. is a pathogenic fungus of bamboo, and its fruiting bodies are regarded as folk medicine. We determined and analyzed its complete mitochondrial DNA sequence (circular DNA molecule of 39,030 bp, G + C content of 25.19%). It contains the typical genes encoding proteins involved in electron transport and coupled oxidative phosphorylation (nad1-6 and nad4L, cob and cox1-3), one ATP synthase subunit (atp6), 4 hypothetical proteins, and two genes for large and small rRNAs (rnl and rns). There is a set of 32 tRNA genes comprising all 20 amino acids, and these genes are evenly distributed on the two strands. Phylogenetic analyses based on concatenated mitochondrial proteins indicated that S. bambusicola clustered with members of the order Pleosporales, which is in agreement with previous results. The gene arrangements of Dothideomycetes species contained three regions of gene orders partitioned in their mitochondrial genomes, including block 1 (nad6-atp6), block 2 (nad1-cox3) and block 3 (genes around rns). S. bambusicola displayed unique special features that differed from the other Pleosporales species, especially in the coding regions around rns (trnR-trnY). Moreover, a comparison of gene orders in mitochondrial genomes from Pezizomycotina revealed that although all encoded regions are located on the same strand in most Pezizomycotina mtDNAs, genes from Dothideomycetes species had different orientations, as well as diverse positions and colocalization of genes (such as cox3, cox1-cox2 and nad2-nad3); these distinctions were regarded as class-specific features. Interestingly, two incomplete copies of the atp6 gene were found on different strands of the mitogenomic DNA, a finding that has not been observed in the other analyzed fungal species. In our study, mitochondrial genomes from Dothideomycetes species were comprehensively analyzed for the first time, including many species that have not appeared in previous reports.
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Affiliation(s)
- Xiao-Ye Shen
- College of Life Science, Capital Normal University, Beijing, People’s Republic of China
| | - Tong Li
- College of Life Science, Capital Normal University, Beijing, People’s Republic of China
| | - Shuang Chen
- College of Life Science, Capital Normal University, Beijing, People’s Republic of China
| | - Li Fan
- College of Life Science, Capital Normal University, Beijing, People’s Republic of China
| | - Jian Gao
- Key Laboratory of Bamboo and Rattan Science and Technology of the SFA, International Centre for Bamboo and Rattan, Beijing, People’s Republic of China
| | - Cheng-Lin Hou
- College of Life Science, Capital Normal University, Beijing, People’s Republic of China
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6
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Lin R, Liu C, Shen B, Bai M, Ling J, Chen G, Mao Z, Cheng X, Xie B. Analysis of the complete mitochondrial genome of Pochonia chlamydosporia suggests a close relationship to the invertebrate-pathogenic fungi in Hypocreales. BMC Microbiol 2015; 15:5. [PMID: 25636983 PMCID: PMC4360972 DOI: 10.1186/s12866-015-0341-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 01/08/2015] [Indexed: 11/10/2022] Open
Abstract
Background The fungus Pochonia chlamydosporia parasitizes nematode eggs and has become one of the most promising biological control agents (BCAs) for plant-parasitic nematodes, which are major agricultural pests that cause tremendous economic losses worldwide. The complete mitochondrial (mt) genome is expected to open new avenues for understanding the phylogenetic relationships and evolution of the invertebrate-pathogenic fungi in Hypocreales. Results The complete mitogenome sequence of P. chlamydosporia is 25,615 bp in size, containing the 14 typical protein-coding genes, two ribosomal RNA genes, an intronic ORF coding for a putative ribosomal protein (rps3) and a set of 23 transfer RNA genes (trn) which recognize codons for all amino acids. Sequence similarity studies and syntenic gene analyses show that 87.02% and 58.72% of P. chlamydosporia mitogenome sequences match 90.50% of Metarhizium anisopliae sequences and 61.33% of Lecanicillium muscarium sequences with 92.38% and 86.04% identities, respectively. A phylogenetic tree inferred from 14 mt proteins in Pezizomycotina fungi supports that P. chlamydosporia is most closely related to the entomopathogenic fungus M. anisopliae. The invertebrate-pathogenic fungi in Hypocreales cluster together and clearly separate from a cluster comprising plant-pathogenic fungi (Fusarium spp.) and Hypocrea jecorina. A comparison of mitogenome sizes shows that the length of the intergenic regions or the intronic regions is the major size contributor in most of mitogenomes in Sordariomycetes. Evolutionary analysis shows that rps3 is under positive selection, leading to the display of unique evolutionary characteristics in Hypocreales. Moreover, the variability of trn distribution has a clear impact on gene order in mitogenomes. Gene rearrangement analysis shows that operation of transposition drives the rearrangement events in Pezizomycotina, and most events involve in trn position changes, but no rearrangement was found in Clavicipitaceae. Conclusions We present the complete annotated mitogenome sequence of P. chlamydosporia. Based on evolutionary and phylogenetic analyses, we have determined the relationships between the invertebrate-pathogenic fungi in Hypocreales. The invertebrate-pathogenic fungi in Hypocreales referred to in this paper form a monophyletic group sharing a most recent common ancestor. Our rps3 and trn gene order results also establish a foundation for further exploration of the evolutionary trajectory of the fungi in Hypocreales. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0341-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Runmao Lin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Chichuan Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Baoming Shen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. .,College of Plant Protection, Hunan Agricultural University, Changsha, Hunan Province, 410128, China.
| | - Miao Bai
- Key Laboratory for Crop Germplasm Innovation and Utilization of Hunan Province, Hunan Agricultural University, Changsha, Hunan Province, 410128, China.
| | - Jian Ling
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Guohua Chen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Zhenchuan Mao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Xinyue Cheng
- College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Bingyan Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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7
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Cutaneous, Subcutaneous and Systemic Mycology. VETERINARY MYCOLOGY 2015. [PMCID: PMC7122059 DOI: 10.1007/978-81-322-2280-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The first description of dermatophytosis was recorded by Celsus, a Roman encyclopaedist who described a suppurative infection of scalp (‘porrigo’ or ‘kerion of Celsus’) in De Re Medicina (30 A.D.). Throughout the middle ages, several descriptions of dermatophytosis were produced where it is described as ‘tinea’. The keratin-destroying moths which made circular holes in the woollen garments are known as Tinea. Due to similarity in the structure of circular lesion of dermatophytosis on the smooth skin with the circular hole made by moth, Cassius Felix introduced the term ‘tinea’ to describe the lesions. In 1806, Alibert used the term ‘favus’ to describe the honey-like exudate in some scalp infections. However, the fungal aetiology of tinea was first detected by Robert Remak, a Polish physician who first observed the presence of hyphae in the crusts of favus. This detection is also a landmark in medical history because this is the first description of a microbe causing a human disease. He himself did not publish his work, but he permitted the reference of his observations in a dissertation by Xavier Hube in 1837. Remak gave all the credits of his discovery to his mentor Schoenlein who first published the fungal etiological report of favus in 1839. He observed the infectious nature of the favus by autoinoculation into his own hands and also successfully isolated the fungus later (1945) and named Achorion schoenleinii (Trichophyton schoenleinii) in honour of his mentor. In 1844, Gruby described the etiologic agent of tinea endothrix, later became known as Trichophyton tonsurans. The genus Trichophyton was created and described by Malmsten (1845) with its representative species T. tonsurans. Charles Robin identified T. mentagrophytes in 1847 and T. equinum was identified by Matruchot and Dassonville in 1898. Raymond Jacques Adrien Sabouraud (France) first compiled the description of Trichophyton in his book (Les Teignes) in 1910 which was based on his observation in artificial culture. The sexual state of dermatophyte was described by Nannizzi (1927). Emmons (1934) first reported the classification of dermatophytes based on vegetative structures and conidia. Gentles (1958) established the successful treatment of tinea capitis with griseofulvin.
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8
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Martins VDP, Dinamarco TM, Curti C, Uyemura SA. Classical and alternative components of the mitochondrial respiratory chain in pathogenic fungi as potential therapeutic targets. J Bioenerg Biomembr 2011; 43:81-8. [PMID: 21271279 DOI: 10.1007/s10863-011-9331-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The frequency of opportunistic fungal infection has increased drastically, mainly in patients who are immunocompromised due to organ transplant, leukemia or HIV infection. In spite of this, only a few classes of drugs with a limited array of targets, are available for antifungal therapy. Therefore, more specific and less toxic drugs with new molecular targets is desirable for the treatment of fungal infections. In this context, searching for differences between mitochondrial mammalian hosts and fungi in the classical and alternative components of the mitochondrial respiratory chain may provide new potential therapeutic targets for this purpose.
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Affiliation(s)
- Vicente de Paulo Martins
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
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9
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Evolutionary history of the mitochondrial genome in Mycosphaerella populations infecting bread wheat, durum wheat and wild grasses. Mol Phylogenet Evol 2010; 58:192-7. [PMID: 21145978 DOI: 10.1016/j.ympev.2010.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 11/10/2010] [Accepted: 12/02/2010] [Indexed: 11/20/2022]
Abstract
Plant pathogens emerge in agro-ecosystems following different evolutionary mechanisms over different time scales. Previous analyses based on sequence variation at six nuclear loci indicated that Mycosphaerella graminicola diverged from an ancestral population adapted to wild grasses during the process of wheat domestication approximately 10,500 years ago. We tested this hypothesis by conducting coalescence analyses based on four mitochondrial loci using 143 isolates that included four closely related pathogen species originating from four continents. Pathogen isolates from bread and durum wheat were included to evaluate the emergence of specificity towards these hosts in M. graminicola. Although mitochondrial and nuclear genomes differed greatly in degree of genetic variability, their coalescence was remarkably congruent, supporting the proposed origin of M. graminicola through host tracking. The coalescence analysis was unable to trace M. graminicola host specificity through recent evolutionary time, indicating that the specificity towards durum or bread wheat emerged following the domestication of the pathogen on wheat.
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10
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Salgado-Salazar C, Jones LR, Restrepo Á, McEwen JG. The human fungal pathogen Paracoccidioides brasiliensis (Onygenales: Ajellomycetaceae) is a complex of two species: phylogenetic evidence from five mitochondrial markers. Cladistics 2010; 26:613-624. [DOI: 10.1111/j.1096-0031.2010.00307.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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11
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Wu Y, Yang J, Yang F, Liu T, Leng W, Chu Y, Jin Q. Recent dermatophyte divergence revealed by comparative and phylogenetic analysis of mitochondrial genomes. BMC Genomics 2009; 10:238. [PMID: 19457268 PMCID: PMC2693141 DOI: 10.1186/1471-2164-10-238] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Accepted: 05/21/2009] [Indexed: 11/17/2022] Open
Abstract
Background Dermatophytes are fungi that cause superficial infections of the skin, hair, and nails. They are the most common agents of fungal infections worldwide. Dermatophytic fungi constitute three genera, Trichophyton, Epidermophyton, and Microsporum, and the evolutionary relationships between these genera are epidemiologically important. Mitochondria are considered to be of monophyletic origin and mitochondrial sequences offer many advantages for phylogenetic studies. However, only one complete dermatophyte mitochondrial genome (E. floccosum) has previously been determined. Results The complete mitochondrial DNA sequences of five dermatophyte species, T. rubrum (26,985 bp), T. mentagrophytes (24,297 bp), T. ajelloi (28,530 bp), M. canis (23,943 bp) and M. nanum (24,105 bp) were determined. These were compared to the E. floccosum sequence. Mitochondrial genomes of all 6 species were found to harbor the same set of genes arranged identical order indicating that these dermatophytes are closely related. Genome size differences were largely due to variable lengths of non-coding intergenic regions and the presence/absence of introns. Phylogenetic analyses based on complete mitochondrial genomes reveals that the divergence of the dermatophyte clade was later than of other groups of pathogenic fungi. Conclusion This is the first systematic comparative genomic study on dermatophytes, a highly conserved and recently-diverged lineage of ascomycota fungi. The data reported here provide a basis for further exploration of interrelationships between dermatophytes and will contribute to the study of mitochondrial evolution in higher fungi.
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Affiliation(s)
- Yuan Wu
- Department of Microbiology and Immunology, Medical School of Xi'an Jiaotong University, Shaanxi, 710061, PR China.
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12
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Pantou MP, Kouvelis VN, Typas MA. The complete mitochondrial genome of Fusarium oxysporum: Insights into fungal mitochondrial evolution. Gene 2008; 419:7-15. [DOI: 10.1016/j.gene.2008.04.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Revised: 04/21/2008] [Accepted: 04/21/2008] [Indexed: 11/26/2022]
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13
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Intraspecific comparison and annotation of two complete mitochondrial genome sequences from the plant pathogenic fungus Mycosphaerella graminicola. Fungal Genet Biol 2008; 45:628-37. [DOI: 10.1016/j.fgb.2007.12.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Revised: 12/10/2007] [Accepted: 12/10/2007] [Indexed: 11/18/2022]
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14
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Hane JK, Lowe RGT, Solomon PS, Tan KC, Schoch CL, Spatafora JW, Crous PW, Kodira C, Birren BW, Galagan JE, Torriani SFF, McDonald BA, Oliver RP. Dothideomycete plant interactions illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorum. THE PLANT CELL 2007; 19:3347-68. [PMID: 18024570 PMCID: PMC2174895 DOI: 10.1105/tpc.107.052829] [Citation(s) in RCA: 174] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Revised: 09/11/2007] [Accepted: 10/15/2007] [Indexed: 05/18/2023]
Abstract
Stagonospora nodorum is a major necrotrophic fungal pathogen of wheat (Triticum aestivum) and a member of the Dothideomycetes, a large fungal taxon that includes many important plant pathogens affecting all major crop plant families. Here, we report the acquisition and initial analysis of a draft genome sequence for this fungus. The assembly comprises 37,164,227 bp of nuclear DNA contained in 107 scaffolds. The circular mitochondrial genome comprises 49,761 bp encoding 46 genes, including four that are intron encoded. The nuclear genome assembly contains 26 classes of repetitive DNA, comprising 4.5% of the genome. Some of the repeats show evidence of repeat-induced point mutations consistent with a frequent sexual cycle. ESTs and gene prediction models support a minimum of 10,762 nuclear genes. Extensive orthology was found between the polyketide synthase family in S. nodorum and Cochliobolus heterostrophus, suggesting an ancient origin and conserved functions for these genes. A striking feature of the gene catalog was the large number of genes predicted to encode secreted proteins; the majority has no meaningful similarity to any other known genes. It is likely that genes for host-specific toxins, in addition to ToxA, will be found among this group. ESTs obtained from axenic mycelium grown on oleate (chosen to mimic early infection) and late-stage lesions sporulating on wheat leaves were obtained. Statistical analysis shows that transcripts encoding proteins involved in protein synthesis and in the production of extracellular proteases, cellulases, and xylanases predominate in the infection library. This suggests that the fungus is dependant on the degradation of wheat macromolecular constituents to provide the carbon skeletons and energy for the synthesis of proteins and other components destined for the developing pycnidiospores.
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MESH Headings
- Ascomycota/genetics
- DNA, Mitochondrial/genetics
- Expressed Sequence Tags
- Fungal Proteins/chemistry
- Fungal Proteins/genetics
- Gene Expression Regulation, Fungal
- Genes, Fungal
- Genome, Fungal/genetics
- Host-Parasite Interactions
- Multigene Family
- Phylogeny
- Protein Structure, Tertiary
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Transfer/genetics
- Repetitive Sequences, Nucleic Acid
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Triticum/microbiology
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Affiliation(s)
- James K Hane
- Australian Centre for Necrotrophic Fungal Pathogens, Murdoch University, WA 6150, Australia
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