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Koch RA, Herr JR. Global Distribution and Richness of Armillaria and Related Species Inferred From Public Databases and Amplicon Sequencing Datasets. Front Microbiol 2021; 12:733159. [PMID: 34803949 PMCID: PMC8602889 DOI: 10.3389/fmicb.2021.733159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/14/2021] [Indexed: 01/30/2023] Open
Abstract
Armillaria is a globally distributed fungal genus most notably composed of economically important plant pathogens that are found predominantly in forest and agronomic systems. The genus sensu lato has more recently received attention for its role in woody plant decomposition and in mycorrhizal symbiosis with specific plants. Previous phylogenetic analyses suggest that around 50 species are recognized globally. Despite this previous work, no studies have analyzed the global species richness and distribution of the genus using data derived from fungal community sequencing datasets or barcoding initiatives. To assess the global diversity and species richness of Armillaria, we mined publicly available sequencing datasets derived from numerous primer regions for the ribosomal operon, as well as ITS sequences deposited on Genbank, and clustered them akin to metabarcoding studies. Our estimates reveal that species richness ranges from 50 to 60 species, depending on whether the ITS1 or ITS2 marker is used. Eastern Asia represents the biogeographic region with the highest species richness. We also assess the overlap of species across geographic regions and propose some hypotheses regarding the drivers of variability in species diversity and richness between different biogeographic regions.
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Affiliation(s)
- Rachel A. Koch
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, United States
| | - Joshua R. Herr
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, United States
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, United States
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Kedves O, Shahab D, Champramary S, Chen L, Indic B, Bóka B, Nagy VD, Vágvölgyi C, Kredics L, Sipos G. Epidemiology, Biotic Interactions and Biological Control of Armillarioids in the Northern Hemisphere. Pathogens 2021; 10:pathogens10010076. [PMID: 33467216 PMCID: PMC7830283 DOI: 10.3390/pathogens10010076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 12/11/2022] Open
Abstract
Armillarioids, including the genera Armillaria, Desarmillaria and Guyanagaster, represent white-rot specific fungal saprotrophs with soilborne pathogenic potentials on woody hosts. They propagate in the soil by root-like rhizomorphs, connecting between susceptible root sections of their hosts, and often forming extended colonies in native forests. Pathogenic abilities of Armillaria and Desarmillaria genets can readily manifest in compromised hosts, or hosts with full vigour can be invaded by virulent mycelia when exposed to a larger number of newly formed genets. Armillaria root rot-related symptoms are indicators of ecological imbalances in native forests and plantations at the rhizosphere levels, often related to abiotic environmental threats, and most likely unfavourable changes in the microbiome compositions in the interactive zone of the roots. The less-studied biotic impacts that contribute to armillarioid host infection include fungi and insects, as well as forest conditions. On the other hand, negative biotic impactors, like bacterial communities, antagonistic fungi, nematodes and plant-derived substances may find applications in the environment-friendly, biological control of armillarioid root diseases, which can be used instead of, or in combination with the classical, but frequently problematic silvicultural and chemical control measures.
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Affiliation(s)
- Orsolya Kedves
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (O.K.); (D.S.); (S.C.); (L.C.); (B.B.); (V.D.N.); (C.V.)
| | - Danish Shahab
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (O.K.); (D.S.); (S.C.); (L.C.); (B.B.); (V.D.N.); (C.V.)
| | - Simang Champramary
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (O.K.); (D.S.); (S.C.); (L.C.); (B.B.); (V.D.N.); (C.V.)
- Functional Genomics and Bioinformatics Group, Research Center for Forestry and Wood Industry, University of Sopron, Bajcsy-Zsilinszky str. 4., H-9400 Sopron, Hungary;
| | - Liqiong Chen
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (O.K.); (D.S.); (S.C.); (L.C.); (B.B.); (V.D.N.); (C.V.)
| | - Boris Indic
- Functional Genomics and Bioinformatics Group, Research Center for Forestry and Wood Industry, University of Sopron, Bajcsy-Zsilinszky str. 4., H-9400 Sopron, Hungary;
| | - Bettina Bóka
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (O.K.); (D.S.); (S.C.); (L.C.); (B.B.); (V.D.N.); (C.V.)
| | - Viktor Dávid Nagy
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (O.K.); (D.S.); (S.C.); (L.C.); (B.B.); (V.D.N.); (C.V.)
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (O.K.); (D.S.); (S.C.); (L.C.); (B.B.); (V.D.N.); (C.V.)
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (O.K.); (D.S.); (S.C.); (L.C.); (B.B.); (V.D.N.); (C.V.)
- Correspondence: (L.K.); (G.S.); Tel.: +36-62-544516 (L.K.); +36-99-518769 (G.S.)
| | - György Sipos
- Functional Genomics and Bioinformatics Group, Research Center for Forestry and Wood Industry, University of Sopron, Bajcsy-Zsilinszky str. 4., H-9400 Sopron, Hungary;
- Correspondence: (L.K.); (G.S.); Tel.: +36-62-544516 (L.K.); +36-99-518769 (G.S.)
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Heinzelmann R, Rigling D, Sipos G, Münsterkötter M, Croll D. Chromosomal assembly and analyses of genome-wide recombination rates in the forest pathogenic fungus Armillaria ostoyae. Heredity (Edinb) 2020; 124:699-713. [PMID: 32203246 DOI: 10.1038/s41437-020-0306-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 03/02/2020] [Accepted: 03/02/2020] [Indexed: 02/08/2023] Open
Abstract
Recombination shapes the evolutionary trajectory of populations and plays an important role in the faithful transmission of chromosomes during meiosis. Levels of sexual reproduction and recombination are important properties of host-pathogen interactions because the speed of antagonistic co-evolution depends on the ability of hosts and pathogens to generate genetic variation. However, our understanding of the importance of recombination is limited because large taxonomic groups remain poorly investigated. Here, we analyze recombination rate variation in the basidiomycete fungus Armillaria ostoyae, which is an aggressive pathogen on a broad range of conifers and other trees. We analyzed a previously constructed, dense genetic map based on 198 single basidiospore progeny from a cross. Progeny were genotyped at a genome-wide set of single-nucleotide polymorphism (SNP) markers using double digest restriction site associated DNA sequencing. Based on a linkage map of on 11,700 SNPs spanning 1007.5 cM, we assembled genomic scaffolds into 11 putative chromosomes of a total genome size of 56.6 Mb. We identified 1984 crossover events among all progeny and found that recombination rates were highly variable along chromosomes. Recombination hotspots tended to be in regions close to the telomeres and were more gene-poor than the genomic background. Genes in proximity to recombination hotspots were encoding on average shorter proteins and were enriched for pectin degrading enzymes. Our analyses enable more powerful population and genome-scale studies of a major tree pathogen.
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Affiliation(s)
- Renate Heinzelmann
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland. .,Department of Forest and Conservation Sciences, The University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
| | - Daniel Rigling
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - György Sipos
- Functional Genomics and Bioinformatics Group, Research Center for Forestry and Wood Industry, University of Sopron, Bajcsy-Zsilinszky. u. 4, Sopron, H-9400, Hungary
| | - Martin Münsterkötter
- Functional Genomics and Bioinformatics Group, Research Center for Forestry and Wood Industry, University of Sopron, Bajcsy-Zsilinszky. u. 4, Sopron, H-9400, Hungary.,Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München (GmbH), Ingolstädter Landstrasse 1, D-85764, Neuherberg, Germany
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000, Neuchâtel, Switzerland
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Coetzee MPA, Wingfield BD, Wingfield MJ. Armillaria Root-Rot Pathogens: Species Boundaries and Global Distribution. Pathogens 2018; 7:E83. [PMID: 30356027 PMCID: PMC6313743 DOI: 10.3390/pathogens7040083] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/21/2018] [Accepted: 10/21/2018] [Indexed: 11/16/2022] Open
Abstract
This review considers current knowledge surrounding species boundaries of the Armillaria root-rot pathogens and their distribution. In addition, a phylogenetic tree using translation elongation factor subunit 1-alpha (tef-1α) from isolates across the globe are used to present a global phylogenetic framework for the genus. Defining species boundaries based on DNA sequence-inferred phylogenies has been a central focus of contemporary mycology. The results of such studies have in many cases resolved the biogeographic history of species, mechanisms involved in dispersal, the taxonomy of species and how certain phenotypic characteristics have evolved throughout lineage diversification. Such advances have also occurred in the case of Armillaria spp. that include important causal agents of tree root rots. This commenced with the first phylogeny for Armillaria that was based on IGS-1 (intergenic spacer region one) DNA sequence data, published in 1992. Since then phylogenies were produced using alternative loci, either as single gene phylogenies or based on concatenated data. Collectively these phylogenies revealed species clusters in Armillaria linked to their geographic distributions and importantly species complexes that warrant further research.
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Affiliation(s)
- Martin P A Coetzee
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.
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Xing X, Men J, Guo S. Phylogenetic constrains on Polyporus umbellatus-Armillaria associations. Sci Rep 2017; 7:4226. [PMID: 28652610 PMCID: PMC5484660 DOI: 10.1038/s41598-017-04578-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/23/2017] [Indexed: 11/29/2022] Open
Abstract
It has been well established that some Armillaria species are symbionts of Polyporus umbellatus, However, little is known about the evolutionary history of P. umbellatus-Armillaria associations. In this research, we used an analysis based on the strength of the phylogenetic signal to investigate P. umbellatus-Armillaria associations in 57 sclerotial samples across 11 provinces of China. We isolated Armillaria strains from the invasion cavity inside the sclerotia of P. umbellatus and then phylogenetically analyzed these Armillaria isolates. We also tested the effect of P. umbellatus and Armillaria phylogenies on the P. umbellatus-Armillaria associations. We isolated forty-seven Armillaria strains from 26 P. umbellatus sclerotial samples. All Armillaria isolates were classified into the 5 phylogenetic lineages found in China except for one singleton. Among the 5 phylogenetic lineages, one lineage (lineage 8) was recognized by delimitation of an uncertain phylogenetic lineage in previous study. Results of simple Mantel test implied that phylogenetically related P. umbellatus populations tend to interact with phylogenetically related Armillaria species. Phylogenetic network analyses revealed that the interaction between P. umbellatus and Armillaria is significantly influenced by the phylogenetic relationships between the Armillaria species.
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Affiliation(s)
- Xiaoke Xing
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China.
| | - Jinxin Men
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Shunxing Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China.
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Guo T, Wang HC, Xue WQ, Zhao J, Yang ZL. Phylogenetic Analyses of Armillaria Reveal at Least 15 Phylogenetic Lineages in China, Seven of Which Are Associated with Cultivated Gastrodia elata. PLoS One 2016; 11:e0154794. [PMID: 27138686 PMCID: PMC4854404 DOI: 10.1371/journal.pone.0154794] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 04/19/2016] [Indexed: 11/18/2022] Open
Abstract
Fungal species of Armillaria, which can act as plant pathogens and/or symbionts of the Chinese traditional medicinal herb Gastrodia elata ("Tianma"), are ecologically and economically important and have consequently attracted the attention of mycologists. However, their taxonomy has been highly dependent on morphological characterization and mating tests. In this study, we phylogenetically analyzed Chinese Armillaria samples using the sequences of the internal transcribed spacer region, translation elongation factor-1 alpha gene and beta-tubulin gene. Our data revealed at least 15 phylogenetic lineages of Armillaria from China, of which seven were newly discovered and two were recorded from China for the first time. Fourteen Chinese biological species of Armillaria, which were previously defined based on mating tests, could be assigned to the 15 phylogenetic lineages identified herein. Seven of the 15 phylogenetic lineages were found to be disjunctively distributed in different continents of the Northern Hemisphere, while eight were revealed to be endemic to certain continents. In addition, we found that seven phylogenetic lineages of Armillaria were used for the cultivation of Tianma, only two of which had been recorded to be associated with Tianma previously. We also illustrated that G. elata f. glauca ("Brown Tianma") and G. elata f. elata ("Red Tianma"), two cultivars of Tianma grown in different regions of China, form symbiotic relationships with different phylogenetic lineages of Armillaria. These findings should aid the development of Tianma cultivation in China.
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Affiliation(s)
- Ting Guo
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Heilongtan, Kunming 650201, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Han Chen Wang
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China
| | - Wan Qiu Xue
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China
| | - Jun Zhao
- General Station of Forest Pest Control, State Forestry Administration, Shenyang 110034, China
| | - Zhu L. Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Heilongtan, Kunming 650201, China
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Coetzee MP, Wingfield BD, Zhao J, van Coller SJ, Wingfield MJ. Phylogenetic relationships among biological species of Armillaria from China. MYCOSCIENCE 2015. [DOI: 10.1016/j.myc.2015.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Umata H, Ota Y, Yamada M, Watanabe Y, Gale SW. Germination of the fully myco-heterotrophic orchid Cyrtosia septentrionalis is characterized by low fungal specificity and does not require direct seed-mycobiont contact. MYCOSCIENCE 2013. [DOI: 10.1016/j.myc.2012.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Baumgartner K, Baker BR, Korhonen K, Zhao J, Hughes KW, Bruhn J, Bowman TS, Bergemann SE. Evidence of natural hybridization among homothallic members of the basidiomycete Armillaria mellea sensu stricto. Fungal Biol 2012; 116:677-91. [DOI: 10.1016/j.funbio.2012.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 02/24/2012] [Accepted: 03/30/2012] [Indexed: 01/09/2023]
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Baumgartner K, Coetzee MPA, Hoffmeister D. Secrets of the subterranean pathosystem of Armillaria. MOLECULAR PLANT PATHOLOGY 2011; 12:515-34. [PMID: 21722292 PMCID: PMC6640247 DOI: 10.1111/j.1364-3703.2010.00693.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
UNLABELLED Armillaria root disease affects fruit and nut crops, timber trees and ornamentals in boreal, temperate and tropical regions of the world. The causal pathogens are members of the genus Armillaria (Basidiomycota, Physalacriaceae). This review summarizes the state of knowledge and highlights recent advances in Armillaria research. TAXONOMY Armillaria includes more than 40 morphological species. However, the identification and delineation of species on the basis of morphological characters are problematic, resulting in many species being undetected. Implementation of the biological species' concept and DNA sequence comparisons in the contemporary taxonomy of Armillaria have led to the discovery of a number of new species that are not linked to described morphological species. HOST RANGE Armillaria exhibits a range of symbioses with both plants and fungi. As plant pathogens, Armillaria species have broad host ranges, infecting mostly woody species. Armillaria can also colonize orchids Galeola and Gastrodia but, in this case, the fungus is the host and the plant is the parasite. Similar to its contrasting relationships with plants, Armillaria acts as either host or parasite in its interactions with other fungi. Disease control: Recent research on post-infection controls has revealed promising alternatives to the former pre-plant eradication attempts with soil fumigants, which are now being regulated more heavily or banned outright because of their negative effects on the environment. New study tools for genetic manipulation of the pathogen and characterization of the molecular basis of the host response will greatly advance the development of resistant rootstocks in a new stage of research. The depth of the research, regardless of whether traditional or genomic approaches are used, will depend on a clear understanding of where the different propagules of Armillaria attack a root system, which of the pathogen's diverse biolymer-degrading enzymes and secondary metabolites facilitate infection, and how the course of infection differs between resistant and susceptible hosts.
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Affiliation(s)
- Kendra Baumgartner
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), University of California, Davis, USA.
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Wingfield MJ, Coetzee MP, Crous PW, Six D, Wingfield BD. Fungal phoenix rising from the ashes? IMA Fungus 2010; 1:149-53. [PMID: 22679573 PMCID: PMC3348778 DOI: 10.5598/imafungus.2010.01.02.06] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2010] [Accepted: 11/04/2010] [Indexed: 12/02/2022] Open
Abstract
During May 2010, sporocarps of what appeared to be an Armillaria sp. were found in large clumps in historic Kirstenbosch Botanical Gardens on the foot of Table Mountain, Cape Town, South Africa. These sporocarps could be physically linked to the roots of unidentified dead trees and Protea spp. The aim of this study was to identify the Armillaria sp. found fruiting in Kirstenbosch. To achieve this goal isolates were made from the mycelium under the bark of dead roots linked to sporocarps. The ITS and IGS-1 regions were sequenced and compared to sequences of Armillaria spp. available on GenBank. Cladograms were generated using ITS sequences to determine the phylogenetic relationship of the isolates with other Armillaria spp. Sequence comparisons and phylogenetic analyses showed that the isolates represented A. mellea. They were also identical to isolates of this species previously discovered in the Company Gardens in South Africa and introduced from Europe apparently by the early Dutch Settlers. Armillaria mellea is alien and apparently invasive in Cape Town, fruits profusely and has the potential to spread to sensitive native forests on the foothills of the City.
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Affiliation(s)
- Michael J. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Martin P.A. Coetzee
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Pedro W. Crous
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Diana Six
- Department of Ecosystem and Conservation Sciences, College of Forestry and Conservation, University of Montana, Missoula, MT 59812, USA
| | - Brenda D. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
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