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Hough B, Steenkamp E, Wingfield B, Read D. Fungal Viruses Unveiled: A Comprehensive Review of Mycoviruses. Viruses 2023; 15:1202. [PMID: 37243288 PMCID: PMC10224137 DOI: 10.3390/v15051202] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/07/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Mycoviruses (viruses of fungi) are ubiquitous throughout the fungal kingdom and are currently classified into 23 viral families and the genus botybirnavirus by the International Committee on the Taxonomy of Viruses (ICTV). The primary focus of mycoviral research has been on mycoviruses that infect plant pathogenic fungi, due to the ability of some to reduce the virulence of their host and thus act as potential biocontrol against these fungi. However, mycoviruses lack extracellular transmission mechanisms and rely on intercellular transmission through the hyphal anastomosis, which impedes successful transmission between different fungal strains. This review provides a comprehensive overview of mycoviruses, including their origins, host range, taxonomic classification into families, effects on their fungal counterparts, and the techniques employed in their discovery. The application of mycoviruses as biocontrol agents of plant pathogenic fungi is also discussed.
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Affiliation(s)
| | | | - Brenda Wingfield
- Forestry & Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics & Microbiology, University of Pretoria, Pretoria 0002, South Africa; (B.H.); (E.S.); (D.R.)
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Kartali T, Zsindely N, Nyilasi I, Németh O, Sávai GN, Kocsubé S, Lipinszki Z, Patai R, Spisák K, Nagy G, Bodai L, Vágvölgyi C, Papp T. Molecular Characterization of Novel Mycoviruses in Seven Umbelopsis Strains. Viruses 2022; 14:v14112343. [PMID: 36366438 PMCID: PMC9694724 DOI: 10.3390/v14112343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 02/01/2023] Open
Abstract
The presence of viruses is less explored in Mucoromycota as compared to other fungal groups such as Ascomycota and Basidiomycota. Recently, more and more mycoviruses are identified from the early-diverging lineages of fungi. We have determined the genome of 11 novel dsRNA viruses in seven different Umbelopsis strains with next-generation sequencing (NGS). The identified viruses were named Umbelopsis ramanniana virus 5 (UrV5), 6a (UrV6a); 6b (UrV6b); 7 (UrV7); 8a (UrV8a); 8b (UrV8b); Umbelopsis gibberispora virus 1 (UgV1); 2 (UgV2) and Umbelopsis dimorpha virus 1a (UdV1a), 1b (UdV1b) and 2 (UdV2). All the newly identified viruses contain two open reading frames (ORFs), which putatively encode the coat protein (CP) and the RNA-dependent RNA polymerase (RdRp), respectively. Based on the phylogeny inferred from the RdRp sequences, eight viruses (UrV7, UrV8a, UrV8b, UgV1, UgV2, UdV1a, UdV1b and UdV2) belong to the genus Totivirus, while UrV5, UrV6a and UrV6b are placed into a yet unclassified but well-defined Totiviridae-related group. In UrV5, UgV1, UgV2, UrV8b, UdV1a, UdV2 and UdV1b, ORF2 is predicted to be translated as a fusion protein via a rare +1 (or -2) ribosomal frameshift, which is not characteristic to most members of the Totivirus genus. Virus particles 31 to 32 nm in diameter could be detected in the examined fungal strains by transmission electron microscopy. Through the identification and characterization of new viruses of Mucoromycota fungi, we can gain insight into the diversity of mycoviruses, as well as into their phylogeny and genome organization.
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Affiliation(s)
- Tünde Kartali
- ELKH-SZTE Fungal Pathogenicity Mechanisms Research Group, University of Szeged, 6726 Szeged, Hungary
- Correspondence: (T.K.); (T.P.)
| | - Nóra Zsindely
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Ildikó Nyilasi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Orsolya Németh
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Gergő Norbert Sávai
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Sándor Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Zoltán Lipinszki
- MTA SZBK Lendület Laboratory of Cell Cycle Regulation, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network (ELKH), 6726 Szeged, Hungary
| | - Roland Patai
- Neuronal Plasticity Research Group, Institute of Biophysics, Biological Research Centre, 6726 Szeged, Hungary
| | - Krisztina Spisák
- Neuronal Plasticity Research Group, Institute of Biophysics, Biological Research Centre, 6726 Szeged, Hungary
- Theoretical Medicine Doctoral School, University of Szeged, 6722 Szeged, Hungary
| | - Gábor Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - László Bodai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Tamás Papp
- ELKH-SZTE Fungal Pathogenicity Mechanisms Research Group, University of Szeged, 6726 Szeged, Hungary
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
- Correspondence: (T.K.); (T.P.)
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Kartali T, Nyilasi I, Kocsubé S, Patai R, Polgár TF, Zsindely N, Nagy G, Bodai L, Lipinszki Z, Vágvölgyi C, Papp T. Characterization of Four Novel dsRNA Viruses Isolated from Mucor hiemalis Strains. Viruses 2021; 13:v13112319. [PMID: 34835124 PMCID: PMC8625083 DOI: 10.3390/v13112319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022] Open
Abstract
We previously screened the total nucleic acid extracts of 123 Mucor strains for the presence of dsRNA molecules without further molecular analyses. Here, we characterized five novel dsRNA genomes isolated from four different Mucor hiemalis strains with next-generation sequencing (NGS), namely Mucor hiemalis virus 1a (MhV1a) from WRL CN(M) 122; Mucor hiemalis virus 1b (MhV1b) from NRRL 3624; Mucor hiemalis virus 2 (MhV2) from NRRL 3616; and Mucor hiemalis virus 3 (MhV3) and Mucor hiemalis virus (MhV4) from NRRL 3617 strains. Genomes contain two open reading frames (ORF), which encode the coat protein (CP) and the RNA dependent RNA polymerase (RdRp), respectively. In MhV1a and MhV1b, it is predicted to be translated as a fusion protein via -1 ribosomal frameshift, while in MhV4 via a rare +1 (or-2) ribosomal frameshift. In MhV2 and MhV3, the presence of specific UAAUG pentanucleotide motif points to the fact for coupled translation termination and reinitialization. MhV1a, MhV2, and MhV3 are part of the clade representing the genus Victorivirus, while MhV4 is seated in Totivirus genus clade. The detected VLPs in Mucor strains were from 33 to 36 nm in diameter. Hybridization analysis revealed that the dsRNA molecules of MhV1a-MhV4 hybridized to the corresponding molecules.
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Affiliation(s)
- Tünde Kartali
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (I.N.); (S.K.); (N.Z.); (C.V.)
- Correspondence: (T.K.); (T.P.)
| | - Ildikó Nyilasi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (I.N.); (S.K.); (N.Z.); (C.V.)
| | - Sándor Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (I.N.); (S.K.); (N.Z.); (C.V.)
| | - Roland Patai
- Neuronal Plasticity Research Group, Institute of Biophysics, Biological Research Centre, 6726 Szeged, Hungary; (R.P.); (T.F.P.)
| | - Tamás F. Polgár
- Neuronal Plasticity Research Group, Institute of Biophysics, Biological Research Centre, 6726 Szeged, Hungary; (R.P.); (T.F.P.)
- Theoretical Medicine Doctoral School, University of Szeged, 6722 Szeged, Hungary
| | - Nóra Zsindely
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (I.N.); (S.K.); (N.Z.); (C.V.)
| | - Gábor Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (G.N.); (L.B.)
| | - László Bodai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (G.N.); (L.B.)
| | - Zoltán Lipinszki
- MTA SZBK Lendület Laboratory of Cell Cycle Regulation, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network (ELKH), 6726 Szeged, Hungary;
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (I.N.); (S.K.); (N.Z.); (C.V.)
| | - Tamás Papp
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (I.N.); (S.K.); (N.Z.); (C.V.)
- MTA-SZTE Fungal Pathogenicity Mechanisms Research Group, Hungarian Academy of Sciences and Department of Microbiology, University of Szeged, 6726 Szeged, Hungary
- Correspondence: (T.K.); (T.P.)
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Abstract
Viruses are key drivers of evolution and ecosystem function and are increasingly recognized as symbionts of fungi. Fungi in early-diverging lineages are widespread, ecologically important, and comprise the majority of the phylogenetic diversity of the kingdom. Viruses infecting early-diverging lineages of fungi have been almost entirely unstudied. In this study, we screened fungi for viruses by two alternative approaches: a classic culture-based method and by transcriptome-mining. The results of our large-scale survey demonstrate that early-diverging lineages have higher infection rates than have been previously reported in other fungal taxa and that laboratory strains worldwide are host to infections, the implications of which are unknown. The function and diversity of mycoviruses found in these basal fungal lineages will help guide future studies into mycovirus origins and their evolutionary ramifications and ecological impacts. Mycoviruses are widespread and purportedly common throughout the fungal kingdom, although most are known from hosts in the two most recently diverged phyla, Ascomycota and Basidiomycota, together called Dikarya. To augment our knowledge of mycovirus prevalence and diversity in underexplored fungi, we conducted a large-scale survey of fungi in the earlier-diverging lineages, using both culture-based and transcriptome-mining approaches to search for RNA viruses. In total, 21.6% of 333 isolates were positive for RNA mycoviruses. This is a greater proportion than expected based on previous taxonomically broad mycovirus surveys and is suggestive of a strong phylogenetic component to mycoviral infection. Our newly found viral sequences are diverse, composed of double-stranded RNA, positive-sense single-stranded RNA (ssRNA), and negative-sense ssRNA genomes and include novel lineages lacking representation in the public databases. These identified viruses could be classified into 2 orders, 5 families, and 5 genera; however, half of the viruses remain taxonomically unassigned. Further, we identified a lineage of virus-like sequences in the genomes of members of Phycomycetaceae and Mortierellales that appear to be novel genes derived from integration of a viral RNA-dependent RNA polymerase gene. The two screening methods largely agreed in their detection of viruses; thus, we suggest that the culture-based assay is a cost-effective means to quickly assess whether a laboratory culture is virally infected. This study used culture collections and publicly available transcriptomes to demonstrate that mycoviruses are abundant in laboratory cultures of early-diverging fungal lineages. The function and diversity of mycoviruses found here will help guide future studies into mycovirus origins and ecological functions.
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Soare AY, Watkins TN, Bruno VM. Understanding Mucormycoses in the Age of "omics". Front Genet 2020; 11:699. [PMID: 32695145 PMCID: PMC7339291 DOI: 10.3389/fgene.2020.00699] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/09/2020] [Indexed: 12/14/2022] Open
Abstract
Mucormycoses are deadly invasive infections caused by several fungal species belonging to the subphylum Mucoromycotina, order Mucorales. Hallmarks of disease progression include angioinvasion and tissue necrosis that aid in fungal dissemination through the blood stream, causing deeper infections and resulting in poor penetration of antifungal agents to the site of infection. In the absence of surgical removal of the infected focus, antifungal therapy alone is rarely curative. Even when surgical debridement is combined with high-dose antifungal therapy, the mortality associated with mucormycoses is >50%. The unacceptably high mortality rate, limited options for therapy and the extreme morbidity of highly disfiguring surgical therapy provide a clear mandate to understand the molecular mechanisms that govern pathogenesis with the hopes of developing alternative strategies to treat and prevent mucormycoses. In the absence of robust forward and reverse genetic systems available for this taxonomic group of fungi, unbiased next generation sequence (NGS)-based approaches have provided much needed insights into our understanding of many aspects of Mucormycoses, including genome structure, drug resistance, diagnostic development, and fungus-host interactions. Here, we will discuss the specific contributions that NGS-based approaches have made to the field and discuss open questions that can be addressed using similar approaches.
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Affiliation(s)
- Alexandra Y Soare
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Tonya N Watkins
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Vincent M Bruno
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
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Kartali T, Nyilasi I, Szabó B, Kocsubé S, Patai R, Polgár TF, Nagy G, Vágvölgyi C, Papp T. Detection and Molecular Characterization of Novel dsRNA Viruses Related to the Totiviridae Family in Umbelopsis ramanniana. Front Cell Infect Microbiol 2019; 9:249. [PMID: 31380294 PMCID: PMC6644447 DOI: 10.3389/fcimb.2019.00249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/26/2019] [Indexed: 11/24/2022] Open
Abstract
Umbelopsis ramanniana is an oleaginous fungus belonging to the Mucoromycotina subphylum. Our group had previously detected four double-stranded RNA (dsRNA) bands in the U. ramanniana NRRL 1296 strain by gel electrophoresis. Here we describe the molecular characterization of its dsRNA elements as well as the discovery of four novel dsRNA viruses: Umbelopsis ramanniana virus 1 (UrV1), Umbelopsis ramanniana virus 2 (UrV2), Umbelopsis ramanniana virus 3 (UrV3), and Umbelopsis ramanniana virus 4 (UrV4). Full genomes of UrV1, UrV3, and UrV4 were determined using the full-length amplification of cDNAs (FLAC) technique; they contain two open reading frames (ORF), which putatively encode the coat protein (CP) and the RNA dependent RNA polymerase (RdRp), respectively. In case of UrV2, a partial ORF encoding a partial RdRp gene could be determined. Based on the phylogeny inferred from the RdRp sequences, UrV1 and UrV4 belong to the genus Totivirus, while UrV2 may belong to the genus Victorivirus. UrV3 nested to a novel, unclassified group of Totiviridae, which is related to the genus Totivirus. Hybridization analysis revealed that the dsRNA molecules of UrV1 and UrV4 correspond to the same 5.0-kbp electrophoretic band, whilst the probe for the UrV3 hybridized to the largest, 5.3-kbp and the 3.0-kbp bands of the dsRNA pattern of U. ramanniana. Interestingly, the probe for the UrV2 sequence did not hybridized to any dsRNA bands, but it could be amplified from the isolated 3.0-kbp fragment. By transmission electron microscopy, two different isometric virus particles with about 50 and 35 nm in diameter were detected in U. ramanniana NRRL 1296 indicating that this strain harbor multiple viruses. Beside U. ramanniana, dsRNA elements were also detected in other Umbelopsis isolates with different patterns consisting of 2 to 4 discrete and different sized (0.7–5.3-kbp) dsRNA molecules. Based on a hybridization analysis with UrV1 CP and RdRp probes, the bands with the size of around 5.0-kbp, which were present in all tested Umbelopsis strains, are presumed as possible full mycovirus genomes.
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Affiliation(s)
- Tünde Kartali
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Ildikó Nyilasi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Boglárka Szabó
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Sándor Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Roland Patai
- Biological Research Centre of the Hungarian Academy of Sciences, Institute of Biophysics, Szeged, Hungary
| | - Tamás F Polgár
- Biological Research Centre of the Hungarian Academy of Sciences, Institute of Biophysics, Szeged, Hungary
| | - Gábor Nagy
- MTA-SZTE Fungal Pathogenicity Mechanisms Research Group, Department of Microbiology, University of Szeged, Hungarian Academy of Sciences, Szeged, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Tamás Papp
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary.,MTA-SZTE Fungal Pathogenicity Mechanisms Research Group, Department of Microbiology, University of Szeged, Hungarian Academy of Sciences, Szeged, Hungary
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Lima JS, Figueiredo JG, Gomes RG, Stringari D, Goulin EH, Adamoski D, Kava-Cordeiro V, Galli-Terasawa LV, Glienke C. Genetic Diversity of Colletotrichum spp. an Endophytic Fungi in a Medicinal Plant, Brazilian Pepper Tree. ISRN MICROBIOLOGY 2012; 2012:215716. [PMID: 23724319 PMCID: PMC3658576 DOI: 10.5402/2012/215716] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 03/14/2012] [Indexed: 11/23/2022]
Abstract
In this study, we reported thirty-nine endophytic fungi identified as Colletotrichum spp. associated with Brazilian pepper tree or aroeira (Schinus terebinthifolius Raddi. Anacardiaceae) in Paraná state, Brazil. These endophytes were identified by morphological and molecular methods, using PCR taxon-specific with CaInt/ITS4, CgInt/ITS4, and Col1/ITS4 primers, which amplify specific bands in C. acutatum, C. gloeosporioides lato sensu, and Colletotrichum boninensis, respectively, and by DNA sequence analysis of the nrDNA internal transcribed spacer region (ITS1, 5.8S, ITS2). We also assayed the presence of dsRNA particles in Colletotrichum spp. isolates. Combining both morphological characters and molecular data, we identified the species C. gloeosporioides, C. boninense, and C. simmondsii. However, we found a high genetic variability intraspecific in C. gloeosporioides which suggests the existence of several other species. Bands of double-stranded RNA (dsRNA) were detected in three of thirty-nine isolates. Identity of these bands was confirmed by RNAse, DNAse, and S1 nuclease treatments for the isolates LGMF633, LGMF726, and LGMF729. This is the first study reporting these particles of dsRNA in C. gloeosporioides.
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Affiliation(s)
| | | | | | | | | | | | | | | | - C. Glienke
- Department of Genetics, Centro Politécnico, Universidade Federal do Paraná (UFPR), Box 19071, 81531-990 Curitiba, PR, Brazil
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van de Sande WWJ, Lo-Ten-Foe JR, van Belkum A, Netea MG, Kullberg BJ, Vonk AG. Mycoviruses: future therapeutic agents of invasive fungal infections in humans? Eur J Clin Microbiol Infect Dis 2010; 29:755-63. [PMID: 20437251 DOI: 10.1007/s10096-010-0946-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2010] [Accepted: 04/12/2010] [Indexed: 12/22/2022]
Abstract
Invasive fungal infections are relatively common opportunistic infections in immunocompromised patients and are still associated with a high mortality rate. Furthermore, these infections are often complicated by resistance or refractoriness to current antimicrobial agents. Therefore, an urgent need exists for new therapeutic strategies based on the identification of new microbial targets and novel antimicrobial agents. One such hypothetical therapeutic strategy may involve the use of mycoviruses that are able to selectively infect fungi. Current knowledge of mycoviruses of human pathogenic fungi and the scope for using (recombinant) mycoviruses as future biological control agents are reviewed here.
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Affiliation(s)
- W W J van de Sande
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center Rotterdam, s-Gravendijkwal 230, 3015 CE, Rotterdam, The Netherlands
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Abstract
Different types of molecular markers are available for use in evolutionary and population studies of microscopic fungi. These approaches have proved their merits and have been successfully applied to a wide range of fungal species belonging in the Ascomycetes and Basidiomycetes. Species in the class Zygomycetes have been rather neglected from this aspect. This review discusses the information available from investigations of the genotypic variability in this group of fungi.
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Affiliation(s)
- M Takó
- Department of Microbiology, Faculty of Sciences, University of Szeged, P.O. Box 533, H-6701 Szeged, Hungary.
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Affiliation(s)
- J Varga
- Department of Microbiology, Faculty of Sciences, University of Szeged, P.O. Box 533, H-6701 Szeged, Hungary
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