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Cai L, Adelberg J, Naylor-Adelberg J, Schnabel G, Calle A, Li Z, Reighard G, Gasic K, Saski CA. Transcriptomics reveal the genetic coordination of early defense to Armillaria root rot (ARR) in Prunus spp. FRONTIERS IN PLANT SCIENCE 2023; 14:1181153. [PMID: 37332708 PMCID: PMC10274510 DOI: 10.3389/fpls.2023.1181153] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/09/2023] [Indexed: 06/20/2023]
Abstract
Armillaria root rot (ARR) poses a significant threat to the long-term productivity of stone-fruit and nut crops in the predominant production area of the United States. To mitigate this issue, the development of ARR-resistant and horticulturally-acceptable rootstocks is a crucial step towards the maintenance of production sustainability. To date, genetic resistance to ARR has been found in exotic plum germplasm and a peach/plum hybrid rootstock, 'MP-29'. However, the widely-used peach rootstock Guardian® is susceptible to the pathogen. To understand the molecular defense mechanisms involved in ARR resistance in Prunus rootstocks, transcriptomic analyses of one susceptible and two resistant Prunus spp. were performed using two causal agents of ARR, including Armillaria mellea and Desarmillaria tabescens. The results of in vitro co-culture experiments revealed that the two resistant genotypes showed different temporal response dynamics and fungus-specific responses, as seen in the genetic response. Gene expression analysis over time indicated an enrichment of defense-related ontologies, including glucosyltransferase activity, monooxygenase activity, glutathione transferase activity, and peroxidase activity. Differential gene expression and co-expression network analysis highlighted key hub genes involved in the sensing and enzymatic degradation of chitin, GSTs, oxidoreductases, transcription factors, and biochemical pathways likely involved in Armillaria resistance. These data provide valuable resources for the improvement of ARR resistance in Prunus rootstocks through breeding.
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Research Status and Application Prospects of the Medicinal Mushroom Armillaria mellea. Appl Biochem Biotechnol 2022; 195:3491-3507. [PMID: 36417110 DOI: 10.1007/s12010-022-04240-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2022] [Indexed: 11/24/2022]
Abstract
Armillaria is one of the most common diseases underlying chronic root rot in woody plants. Although there is no particularly effective way to prevent it, soil disinfection is a common effective protective measure. However, Armillaria itself has important medicinal value and is a symbiotic fungus in the cultivation of Gastrodia elata and Polyporus umbellatus. Therefore, researching Armillaria is of great practical significance. In this review, the biological characteristics, cultivation methods, chemical components, food and medicinal value and efficacy of Armillaria were all reviewed, and its development and utilization direction were analyzed and discussed.
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Wingfield BD, Berger DK, Coetzee MPA, Duong TA, Martin A, Pham NQ, van den Berg N, Wilken PM, Arun-Chinnappa KS, Barnes I, Buthelezi S, Dahanayaka BA, Durán A, Engelbrecht J, Feurtey A, Fourie A, Fourie G, Hartley J, Kabwe ENK, Maphosa M, Narh Mensah DL, Nsibo DL, Potgieter L, Poudel B, Stukenbrock EH, Thomas C, Vaghefi N, Welgemoed T, Wingfield MJ. IMA genome‑F17 : Draft genome sequences of an Armillaria species from Zimbabwe, Ceratocystis colombiana, Elsinoë necatrix, Rosellinia necatrix, two genomes of Sclerotinia minor, short‑read genome assemblies and annotations of four Pyrenophora teres isolates from barley grass, and a long-read genome assembly of Cercospora zeina. IMA Fungus 2022; 13:19. [PMID: 36411457 PMCID: PMC9677705 DOI: 10.1186/s43008-022-00104-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2022] [Indexed: 11/22/2022] Open
Affiliation(s)
- Brenda D. Wingfield
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Dave K. Berger
- grid.49697.350000 0001 2107 2298Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028 South Africa
| | - Martin P. A. Coetzee
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Tuan A. Duong
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Anke Martin
- grid.1048.d0000 0004 0473 0844Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350 Australia
| | - Nam Q. Pham
- grid.49697.350000 0001 2107 2298Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028 South Africa
| | - Noelani van den Berg
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - P. Markus Wilken
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Kiruba Shankari Arun-Chinnappa
- grid.1048.d0000 0004 0473 0844Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350 Australia ,PerkinElmer Pty Ltd., Level 2, Building 5, Brandon Business Park, 530‑540, Springvale Road, Glen Waverley, VIC 3150 Australia
| | - Irene Barnes
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Sikelela Buthelezi
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | | | - Alvaro Durán
- Plant Health Program, Research and Development, Asia Pacific Resources International Holdings Ltd. (APRIL), Pangkalan Kerinci, Riau 28300 Indonesia
| | - Juanita Engelbrecht
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Alice Feurtey
- grid.419520.b0000 0001 2222 4708Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany ,grid.9764.c0000 0001 2153 9986Environmental Genomics, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Arista Fourie
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Gerda Fourie
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Jesse Hartley
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Eugene N. K. Kabwe
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Centre for Bioinformatics and Computational Biology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Mkhululi Maphosa
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Deborah L. Narh Mensah
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa ,grid.423756.10000 0004 1764 1672CSIR, Food Research Institute, Accra, Ghana
| | - David L. Nsibo
- grid.49697.350000 0001 2107 2298Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028 South Africa
| | - Lizel Potgieter
- grid.419520.b0000 0001 2222 4708Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany ,grid.9764.c0000 0001 2153 9986Environmental Genomics, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Barsha Poudel
- grid.1048.d0000 0004 0473 0844Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350 Australia
| | - Eva H. Stukenbrock
- grid.419520.b0000 0001 2222 4708Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany ,grid.9764.c0000 0001 2153 9986Environmental Genomics, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Chanel Thomas
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Niloofar Vaghefi
- grid.1048.d0000 0004 0473 0844Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350 Australia ,grid.1008.90000 0001 2179 088XSchool of Agriculture and Food, University of Melbourne, Parkville, VIC 3010 Australia
| | - Tanya Welgemoed
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Centre for Bioinformatics and Computational Biology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Michael J. Wingfield
- grid.49697.350000 0001 2107 2298Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028 South Africa
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Menolli N, Sánchez-Ramírez S, Sánchez-García M, Wang C, Patev S, Ishikawa NK, Mata JL, Lenz AR, Vargas-Isla R, Liderman L, Lamb M, Nuhn M, Hughes KW, Xiao Y, Hibbett DS. Global phylogeny of the Shiitake mushroom and related Lentinula species uncovers novel diversity and suggests an origin in the Neotropics. Mol Phylogenet Evol 2022; 173:107494. [PMID: 35490968 DOI: 10.1016/j.ympev.2022.107494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 01/18/2023]
Abstract
Lentinula (Basidiomycota, Agaricales) includes the most widely cultivated mushroom in the world, Lentinula edodes, also known as shiitake (Japanese) or xiang-gu (Chinese). At present, nine species are recognized in the genus, based on morphology, mating criteria, and geographic distributions. However, analyses of internal transcribed spacers (ITS) of ribosomal RNA genes have suggested that there are cryptic lineages. We analyzed a global-scale phylogenetic dataset from 325 Lentinula individuals from 24 countries in Asia-Australasia and the Americas plus Madagascar, with 325 sequences of ITS, 80 LSU sequences, and 111 sequences of translation elongation factor (tef1-α) genes. We recovered 15 independent lineages (Groups 1-15) that may correspond to species. Lineages in Asia-Australasia (Groups 1-5) and the Americas plus Madagascar (Groups 6-15) formed sister clades. Four lineages are represented only by sequences from single individuals and require further molecular sampling, including L. aff. raphanica (Group 7), L. ixodes (Group 8), L. boryana (Group 12), and L. aff. aciculospora (Group 14). Groups 1 and 5 are here referred to L. edodes and L. aff. edodes, respectively. However, these groups most likely represent the same species and are only recognized as (unsupported) monophyletic lineages by maximum likelihood analyses of ITS alone. Other putative species resolved here include L. lateritia (Group 2), L. novae-zelandieae (Group 3), L. aff. lateritia (Group 4), L. raphanica (Group 6), L. aff. detonsa (Group 9), L. detonsa (Group 10), L. guzmanii sp. nov. (Group 11), L. aciculospora (Group 13), and L. madagasikarensis (Group 15). Groups 9-12 represent the "L. boryana complex". Molecular clock and historical biogeographic analyses suggest that the most recent common ancestor (MRCA) of Lentinula can be placed in the middle Oligocene, ca. 30 million years ago (Ma), and had a likely presence in neotropical America. The MRCA of Lentinula in the Americas and Madagascar lived ca. 22 Ma in the Neotropics and the MRCA of Lentinula in Asia-Australasia lived ca. 6 Ma in Oceania. Given the current knowledge about plate tectonics and paleoclimatic models of the last 30 Myr, our phylogenetic hypothesis suggests that the extant distribution of Lentinula is likely to have arisen, in large part, due to long-distance dispersal. Lentinula collections include at least four dubious taxa that need further taxonomic studies: L. reticeps from the USA (Ohio); L. guarapiensis from Paraguay; Lentinus puiggarii from Brazil (São Paulo); and "L. platinedodes" from Vietnam. Approximately ten of the fifteen Groups are reported on Fagaceae, which appears to be the ancestral substrate of Lentinula.
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Affiliation(s)
- Nelson Menolli
- IFungiLab, Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), Câmpus São Paulo (SPO), Departamento de Ciências da Natureza e Matemática (DCM) / Subárea de Biologia (SAB), Rua Pedro Vicente 625, São Paulo, SP 01109-010, Brazil.
| | - Santiago Sánchez-Ramírez
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario M5S 3B2, Canada
| | - Marisol Sánchez-García
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-75005, Sweden
| | - Chaoqun Wang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Science, Guangzhou 510070, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sean Patev
- Biology Department, Clark University, Worcester, MA 01610, USA
| | - Noemia Kazue Ishikawa
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo, 2936, Petrópolis, Manaus, AM 69067-375, Brazil
| | - Juan L Mata
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Alexandre Rafael Lenz
- Departamento de Ciências Exatas e da Terra, Colegiado de Sistemas de Informação, Campus I, Universidade do Estado da Bahia (UNEB), Salvador, BA, Brazil
| | - Ruby Vargas-Isla
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo, 2936, Petrópolis, Manaus, AM 69067-375, Brazil
| | - Lauren Liderman
- Biology Department, Clark University, Worcester, MA 01610, USA
| | - Meriel Lamb
- Biology Department, Clark University, Worcester, MA 01610, USA
| | - Mitchell Nuhn
- Biology Department, Clark University, Worcester, MA 01610, USA
| | - Karen W Hughes
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Yang Xiao
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - David S Hibbett
- Biology Department, Clark University, Worcester, MA 01610, USA
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Phylogenetic Relationships, Speciation, and Origin of Armillaria in the Northern Hemisphere: A Lesson Based on rRNA and Elongation Factor 1-Alpha. J Fungi (Basel) 2021; 7:jof7121088. [PMID: 34947070 PMCID: PMC8705980 DOI: 10.3390/jof7121088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/06/2021] [Accepted: 12/13/2021] [Indexed: 01/09/2023] Open
Abstract
Armillaria species have a global distribution and play various roles in the natural ecosystems, e.g., pathogens, decomposers, and mycorrhizal associates. However, their taxonomic boundaries, speciation processes, and origin are poorly understood. Here, we used a phylogenetic approach with 358 samplings from Europe, East Asia, and North America to delimit the species boundaries and to discern the evolutionary forces underpinning divergence and evolution. Three species delimitation methods indicated multiple unrecognized phylogenetic species, and biological species recognition did not reflect the natural evolutionary relationships within Armillaria; for instance, biological species of A. mellea and D. tabescens are divergent and cryptic species/lineages exist associated with their geographic distributions in Europe, North America, and East Asia. While the species-rich and divergent Gallica superclade might represent three phylogenetic species (PS I, PS II, and A. nabsnona) that undergo speciation. The PS II contained four lineages with cryptic diversity associated with the geographic distribution. The genus Armillaria likely originated from East Asia around 21.8 Mya in early Miocene when Boreotropical flora (56–33.9 Mya) and the Bering land bridge might have facilitated transcontinental dispersal of Armillaria species. The Gallica superclade arose at 9.1 Mya and the concurrent vicariance events of Bering Strait opening and the uplift of the northern Tibetan plateau might be important factors in driving the lineage divergence.
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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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Transcriptomics Reveals the Putative Mycoparasitic Strategy of the Mushroom Entoloma abortivum on Species of the Mushroom Genus Armillaria. mSystems 2021; 6:e0054421. [PMID: 34636668 PMCID: PMC8510539 DOI: 10.1128/msystems.00544-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
During mycoparasitism, a fungus—the host—is parasitized by another fungus—the mycoparasite. The genetic underpinnings of these relationships have been best characterized in ascomycete fungi. However, within basidiomycete fungi, there are rare instances of mushroom-forming species parasitizing the reproductive structures, or sporocarps, of other mushroom-forming species, which have been rarely investigated on a genetic level. One of the most enigmatic of these occurs between Entoloma abortivum and species of Armillaria, where hyphae of E. abortivum are hypothesized to disrupt the development of Armillaria sporocarps, resulting in the formation of carpophoroids. However, it remains unknown whether carpophoroids are the direct result of a mycoparasitic relationship. To address the nature of this unique interaction, we analyzed gene expression of field-collected Armillaria and E. abortivum sporocarps and carpophoroids. Transcripts in the carpophoroids are primarily from E. abortivum, supporting the hypothesis that this species is parasitizing Armillaria. Most notably, we identified differentially upregulated E. abortivum β-trefoil-type lectins in the carpophoroid, which we hypothesize bind to Armillaria cell wall galactomannoproteins, thereby mediating recognition between the mycoparasite and the host. The most differentially upregulated E. abortivum transcripts in the carpophoroid code for oxalate decarboxylases—enzymes that degrade oxalic acid. Oxalic acid is a virulence factor in many plant pathogens, including Armillaria species; however, E. abortivum has evolved a sophisticated strategy to overcome this defense mechanism. The number of gene models and genes that code for carbohydrate-active enzymes in the E. abortivum transcriptome was reduced compared to other closely related species, perhaps as a result of the specialized nature of this interaction. IMPORTANCE By studying fungi that parasitize other fungi, we can understand the basic biology of these unique interactions. Studies focused on the genetic mechanisms regulating mycoparasitism between host and parasite have thus far concentrated on a single fungal lineage within the Ascomycota. The work presented here expands our understanding of mycoparasitic relationships to the Basidiomycota and represents the first transcriptomic study to our knowledge that examines fungal-fungal relationships in their natural setting. The results presented here suggest that even distantly related mycoparasites utilize similar mechanisms to parasitize their host. Given that species of the mushroom-forming pathogen Armillaria cause plant root-rot diseases in many agroecosystems, an enhanced understanding of this interaction may contribute to better control of these diseases through biocontrol applications.
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Abstract
Species of Armillaria are distributed globally and include some of the most important pathogens of forest and ornamental trees. Some of them form large long-living clones that are considered as one of the largest organisms on earth and are capable of long-range spore-mediated transfer as well as vegetative spread by drought-resistant hyphal cords called rhizomorphs. However, the virus community infecting these species has remained unknown. In this study we used dsRNA screening and high-throughput sequencing to search for possible virus infections in a collection of Armillaria isolates representing three different species: Armillaria mellea from South Africa, A. borealis from Finland and Russia (Siberia) and A. cepistipes from Finland. Our analysis revealed the presence of both negative-sense RNA viruses and positive-sense RNA viruses, while no dsRNA viruses were detected. The viruses included putative new members of virus families Mymonaviridae, Botourmiaviridae and Virgaviridae and members of a recently discovered virus group tentatively named "ambiviruses" with ambisense bicistronic genomic organization. We demonstrated that Armillaria isolates can be cured of viruses by thermal treatment, which enables the examination of virus effects on host growth and phenotype using isogenic virus-infected and virus-free strains.
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Xu F, LoBuglio KF, Pfister DH. On the co-occurrence of species of Wynnea ( Ascomycota, Pezizales, Sarcoscyphaceae) and Armillaria ( Basidiomycota, Agaricales, Physalacriaceae). Fungal Syst Evol 2020; 4:1-12. [PMID: 32467902 PMCID: PMC7241679 DOI: 10.3114/fuse.2019.04.01] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Species of the genus Wynnea are collected in association with a subterranean mass generally referred to as a sclerotium. This is one of the few genera of the Sarcoscyphaceae not associated with plant material – wood or leaves. The sclerotium is composed of hyphae of both Armillaria species and Wynnea species. To verify the existence of Armillaria species in the sclerotia of those Wynnea species not previously examined and to fully understand the structure and nature of the sclerotium, molecular data and morphological characters were analyzed. Using nuclear ITS rDNA sequences the Armillaria species co-occurring with Wynnea species were identified from all examined material. These Armillaria symbionts fall into two main Armillaria groups – the A. gallica-nabsnona-calvescens group and the A. mellea group. Divergent time estimates of the Armillaria and Wynnea lineages support a co-evolutionary relationship between these two fungi.
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Affiliation(s)
- F Xu
- Harvard University Herbaria and Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USA
| | - K F LoBuglio
- Harvard University Herbaria and Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USA
| | - D H Pfister
- Harvard University Herbaria and Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USA
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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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Abstract
Dispersal is a fundamental biological process, operating at multiple temporal and spatial scales. Despite an increasing understanding of fungal biodiversity, most research on fungal dispersal focuses on only a small fraction of species. Thus, any discussion of the dispersal dynamics of fungi as a whole is problematic. While abundant morphological and biogeographic data are available for hundreds of species, researchers have yet to integrate this information into a unifying paradigm of fungal dispersal, especially in the context of long-distance dispersal (LDD). Fungal LDD is mediated by multiple vectors, including meteorological phenomena (e.g., wind and precipitation), plants (e.g., seeds and senesced leaves), animals (e.g., fur, feathers, and gut microbiomes), and in many cases humans. In addition, fungal LDD is shaped by both physical constraints on travel and the ability of spores to survive harsh environments. Finally, fungal LDD is commonly measured in different ways, including by direct capture of spores, genetic comparisons of disconnected populations, and statistical modeling and simulations of dispersal data. To unify perspectives on fungal LDD, we propose a synthetic three-part definition that includes (i) an identification of the source population and a measure of the concentration of source inoculum and (ii) a measured and/or modeled dispersal kernel. With this information, LDD is defined as (iii) the distance found within the dispersal kernel beyond which only 1% of spores travel.
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Heinzelmann R, Prospero S, Rigling D. Virulence and Stump Colonization Ability of Armillaria borealis on Norway Spruce Seedlings in Comparison to Sympatric Armillaria Species. PLANT DISEASE 2017; 101:470-479. [PMID: 30677340 DOI: 10.1094/pdis-06-16-0933-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Although Armillaria borealis is one of the closest relatives of the aggressive root rot pathogen A. ostoyae, little is known about its ecology. In central and northern Europe, A. borealis often co-occurs with A. ostoyae or A. cepistipes, a weak pathogen, in conifer or mixed-forest stands. In this study, the virulence of 10 A. borealis, nine A. ostoyae, and five A. cepistipes isolates toward 2- and 4-year-old potted Norway spruce (Picea abies) seedlings was assessed. In addition, the ability of all isolates to colonize fresh stumps cut from 6-year-old Norway spruce seedlings was tested. All inoculations were done by insertion of Armillaria-colonized hazelnut stem segments into the soil substrate. On the 2-year-old seedlings, A. borealis and A. ostoyae showed, overall, a similar virulence 29 months after inoculation whereas, on the 4-year-old seedlings, A. ostoyae was more virulent. The third species in the experiment, A. cepistipes, caused almost no seedling mortality. Six months after cutting, the highest percentage of stumps was colonized by A. ostoyae (94.3%), followed by A. borealis (85.2%), and A. cepistipes (78.4%). Our inoculation experiments show that A. borealis has a clear pathogenic potential toward Norway spruce seedlings. However, compared with A. ostoyae, damage caused by A. borealis may decrease more rapidly with increasing tree age. Similar to other Armillaria species, A. borealis seems to be an efficient colonizer of fresh stumps.
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Affiliation(s)
- Renate Heinzelmann
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
| | - Simone Prospero
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
| | - Daniel Rigling
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
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Klopfenstein NB, Stewart JE, Ota Y, Hanna JW, Richardson BA, Ross-Davis AL, Elías-Román RD, Korhonen K, Keča N, Iturritxa E, Alvarado-Rosales D, Solheim H, Brazee NJ, Łakomy P, Cleary MR, Hasegawa E, Kikuchi T, Garza-Ocañas F, Tsopelas P, Rigling D, Prospero S, Tsykun T, Bérubé JA, Stefani FOP, Jafarpour S, Antonín V, Tomšovský M, McDonald GI, Woodward S, Kim MS. Insights into the phylogeny of Northern Hemisphere Armillaria: Neighbor-net and Bayesian analyses of translation elongation factor 1-α gene sequences. Mycologia 2017; 109:75-91. [PMID: 28402796 DOI: 10.1080/00275514.2017.1286572] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Armillaria possesses several intriguing characteristics that have inspired wide interest in understanding phylogenetic relationships within and among species of this genus. Nuclear ribosomal DNA sequence-based analyses of Armillaria provide only limited information for phylogenetic studies among widely divergent taxa. More recent studies have shown that translation elongation factor 1-α (tef1) sequences are highly informative for phylogenetic analysis of Armillaria species within diverse global regions. This study used Neighbor-net and coalescence-based Bayesian analyses to examine phylogenetic relationships of newly determined and existing tef1 sequences derived from diverse Armillaria species from across the Northern Hemisphere, with Southern Hemisphere Armillaria species included for reference. Based on the Bayesian analysis of tef1 sequences, Armillaria species from the Northern Hemisphere are generally contained within the following four superclades, which are named according to the specific epithet of the most frequently cited species within the superclade: (i) Socialis/Tabescens (exannulate) superclade including Eurasian A. ectypa, North American A. socialis (A. tabescens), and Eurasian A. socialis (A. tabescens) clades; (ii) Mellea superclade including undescribed annulate North American Armillaria sp. (Mexico) and four separate clades of A. mellea (Europe and Iran, eastern Asia, and two groups from North America); (iii) Gallica superclade including Armillaria Nag E (Japan), multiple clades of A. gallica (Asia and Europe), A. calvescens (eastern North America), A. cepistipes (North America), A. altimontana (western USA), A. nabsnona (North America and Japan), and at least two A. gallica clades (North America); and (iv) Solidipes/Ostoyae superclade including two A. solidipes/ostoyae clades (North America), A. gemina (eastern USA), A. solidipes/ostoyae (Eurasia), A. cepistipes (Europe and Japan), A. sinapina (North America and Japan), and A. borealis (Eurasia) clade 2. Of note is that A. borealis (Eurasia) clade 1 appears basal to the Solidipes/Ostoyae and Gallica superclades. The Neighbor-net analysis showed similar phylogenetic relationships. This study further demonstrates the utility of tef1 for global phylogenetic studies of Armillaria species and provides critical insights into multiple taxonomic issues that warrant further study.
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Affiliation(s)
- Ned B Klopfenstein
- a United States Department of Agriculture Forest Service , Rocky Mountain Research Station , 1221 South Main Street, Moscow , Idaho 83843
| | - Jane E Stewart
- b Department of Bioagricultural Sciences and Pest Management , Colorado State University , 307 University Avenue, Ft. Collins , Colorado 80523
| | - Yuko Ota
- c College of Bioresource Sciences , Nihon University , 1866 Kameino, Fujisawa, Kanagawa 252-0880 , Japan
| | - John W Hanna
- a United States Department of Agriculture Forest Service , Rocky Mountain Research Station , 1221 South Main Street, Moscow , Idaho 83843
| | - Bryce A Richardson
- d United States Department of Agriculture Forest Service , Rocky Mountain Research Station , 735 North 500 East, Provo , Utah 84606
| | - Amy L Ross-Davis
- a United States Department of Agriculture Forest Service , Rocky Mountain Research Station , 1221 South Main Street, Moscow , Idaho 83843
| | - Rubén D Elías-Román
- e Departamento de Agronomía, División de Ciencias de la Vida , Campus Irapuato-Salamanca, Universidad de Guanajuato , C.P. 36824 , Apdo. Postal 311, Irapuato , Guanajuato , México
| | | | - Nenad Keča
- g Faculty of Forestry , University of Belgrade , Kneza Viseslava 1, 11030 Belgrade , Serbia
| | - Eugenia Iturritxa
- h Neiker Tecnalia, Production and Plant Protection , Granja Modelo de Arkaute , 46 Post, Vitoria-Gasteiz , 01080 , Spain
| | - Dionicio Alvarado-Rosales
- i Colegio de Postgraduados, Campus Montecillo , Instituto de Fitosanidad-Fitopatología , Texcoco 56230 , México
| | - Halvor Solheim
- j Norwegian Institute of Bioeconomy Research , Pb 115, NO-1431 Ås, Norway
| | - Nicholas J Brazee
- k UMass Extension, Center for Agriculture, Food and the Environment , University of Massachusetts , Amherst , Massachusetts 01002
| | - Piotr Łakomy
- l Department of Forest Pathology , Poznan University of Life Sciences , Wojska Polskiego 71c, 60-625 Poznań , Poland
| | - Michelle R Cleary
- m Sveriges Lantbruksuniversitet , Swedish University of Agricultural Sciences, Southern Swedish Forest Research Centre , 230 53 Alnarp , Sweden
| | - Eri Hasegawa
- n Kansai Research Center , Forestry and Forest Products Research Institute , 68 Nagai-Kyutaro, Momoyama, Fushimi , Kyoto 612-0855 , Japan
| | - Taisei Kikuchi
- o Department of Infectious Diseases, Faculty of Medicine , University of Miyazaki, Miyazaki 889-1692, Japan and Forestry and Forest Products Research Institute , Matsunosato 1, Tsukuba , Ibaraki 305-8687 , Japan
| | - Fortunato Garza-Ocañas
- p Facultad de Ciencias Forestales , Universidad Autónoma de Nuevo León , Linares , Nuevo León , Mexico
| | - Panaghiotis Tsopelas
- q NAGREF-Institute of Mediterranean Forest Ecosystems , Terma Alkmanos , 11528 Athens, B.O. 14180 , Greece
| | - Daniel Rigling
- r Swiss Federal Research Institute WSL , Zuercherstrasse 111 , CH-8903 Birmensdorf , Switzerland
| | - Simone Prospero
- r Swiss Federal Research Institute WSL , Zuercherstrasse 111 , CH-8903 Birmensdorf , Switzerland
| | - Tetyana Tsykun
- r Swiss Federal Research Institute WSL , Zuercherstrasse 111 , CH-8903 Birmensdorf , Switzerland
| | - Jean A Bérubé
- s Canadian Forest Service , Natural Resources Canada , PO Box 10380 Stn Sainte-Foy, Quebec City , Quebec G1V 4C7 , Canada
| | - Franck O P Stefani
- t Agriculture and Agri-Food Canada , KW Neatby Bldg , Ottawa , Ontario K1A 0C6 Canada
| | - Saeideh Jafarpour
- u Department of Plant Protection, Faculty of Agricultural Science and Engineering, College of Agriculture and Natural Resources , University of Tehran , Karaj , 31587-77871 , Iran
| | - Vladimír Antonín
- v Moravian Museum , Department of Botany , Zelny trh 6, 659 37 Brno , Czech Republic
| | - Michal Tomšovský
- w Faculty of Forestry and Wood Technology , Mendel University in Brno , Zemědělská 3, CZ-613 00 Brno , Czech Republic
| | - Geral I McDonald
- a United States Department of Agriculture Forest Service , Rocky Mountain Research Station , 1221 South Main Street, Moscow , Idaho 83843
| | - Stephen Woodward
- x Department of Plant and Soil Sciences, Institute of Biological and Environmental Sciences , University of Aberdeen , Aberdeen AB24 2TZ , Scotland , UK
| | - Mee-Sook Kim
- y Department of Forestry, Environment and Systems , Kookmin University , Seoul 02707 , Republic of Korea
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Koch RA, Wilson AW, Séné O, Henkel TW, Aime MC. Resolved phylogeny and biogeography of the root pathogen Armillaria and its gasteroid relative, Guyanagaster. BMC Evol Biol 2017; 17:33. [PMID: 28122504 PMCID: PMC5264464 DOI: 10.1186/s12862-017-0877-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 01/10/2017] [Indexed: 11/18/2022] Open
Abstract
Background Armillaria is a globally distributed mushroom-forming genus composed primarily of plant pathogens. Species in this genus are prolific producers of rhizomorphs, or vegetative structures, which, when found, are often associated with infection. Because of their importance as plant pathogens, understanding the evolutionary origins of this genus and how it gained a worldwide distribution is of interest. The first gasteroid fungus with close affinities to Armillaria—Guyanagaster necrorhizus—was described from the Neotropical rainforests of Guyana. In this study, we conducted phylogenetic analyses to fully resolve the relationship of G. necrorhizus with Armillaria. Data sets containing Guyanagaster from two collecting localities, along with a global sampling of 21 Armillaria species—including newly collected specimens from Guyana and Africa—at six loci (28S, EF1α, RPB2, TUB, actin-1 and gpd) were used. Three loci—28S, EF1α and RPB2—were analyzed in a partitioned nucleotide data set to infer divergence dates and ancestral range estimations for well-supported, monophyletic lineages. Results The six-locus phylogenetic analysis resolves Guyanagaster as the earliest diverging lineage in the armillarioid clade. The next lineage to diverge is that composed of species in Armillaria subgenus Desarmillaria. This subgenus is elevated to genus level to accommodate the exannulate mushroom-forming armillarioid species. The final lineage to diverge is that composed of annulate mushroom-forming armillarioid species, in what is now Armillaria sensu stricto. The molecular clock analysis and ancestral range estimation suggest the most recent common ancestor to the armillarioid lineage arose 51 million years ago in Eurasia. A new species, Guyanagaster lucianii sp. nov. from Guyana, is described. Conclusions The armillarioid lineage evolved in Eurasia during the height of tropical rainforest expansion about 51 million years ago, a time marked by a warm and wet global climate. Species of Guyanagaster and Desarmillaria represent extant taxa of these early diverging lineages. Desarmillaria represents an armillarioid lineage that was likely much more widespread in the past. Guyanagaster likely evolved from a gilled mushroom ancestor and could represent a highly specialized endemic in the Guiana Shield. Armillaria species represent those that evolved after the shift in climate from warm and tropical to cool and arid during the late Eocene. No species in either Desarmillaria or Guyanagaster are known to produce melanized rhizomorphs in nature, whereas almost all Armillaria species are known to produce them. The production of rhizomorphs is an adaptation to harsh environments, and could be a driver of diversification in Armillaria by conferring a competitive advantage to the species that produce them. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0877-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rachel A Koch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Andrew W Wilson
- Sam Mitchel Herbarium of Fungi, Denver Botanic Gardens, Denver, CO, 80206, USA
| | - Olivier Séné
- Institute of Agricultural Research for Development (IRAD), National Herbarium of Cameroon (MINRESI), PO Box 1601, Yaoundé, Cameroon
| | - Terry W Henkel
- Department of Biological Sciences, Humboldt State University, Arcata, CA, 95521, USA
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA.
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Wingfield BD, Ambler JM, Coetzee MP, de Beer ZW, Duong TA, Joubert F, Hammerbacher A, McTaggart AR, Naidoo K, Nguyen HD, Ponomareva E, Santana QS, Seifert KA, Steenkamp ET, Trollip C, van der Nest MA, Visagie CM, Wilken PM, Wingfield MJ, Yilmaz N. IMA Genome-F 6: Draft genome sequences of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E. polonica and Penicillium freii DAOMC 242723. IMA Fungus 2016; 7:217-27. [PMID: 27433447 PMCID: PMC4941685 DOI: 10.5598/imafungus.2016.07.01.11] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/15/2016] [Indexed: 10/25/2022] Open
Abstract
The genomes of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E. polonica, and Penicillium freii DAOMC 242723 are presented in this genome announcement. These six genomes are from plant pathogens and otherwise economically important fungal species. The genome sizes range from 21 Mb in the case of Ceratocystiopsis minuta to 58 Mb for the basidiomycete Armillaria fuscipes. These genomes include the first reports of genomes for the genus Endoconidiophora. The availability of these genome data will provide opportunities to resolve longstanding questions regarding the taxonomy of species in these genera. In addition these genome sequences through comparative studies with closely related organisms will increase our understanding of how these pathogens cause disease.
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Affiliation(s)
- Brenda D. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Jon M. Ambler
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Martin P.A. Coetzee
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Z. Wilhelm de Beer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Tuan A. Duong
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Fourie Joubert
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry and Genomics Research Institute, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Almuth Hammerbacher
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Alistair R. McTaggart
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Kershney Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Hai D.T. Nguyen
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
- Department of Biology, University of Ottawa, 30 Marie-Curie, Ottawa, Ontario, K1N6N5, Canada
| | - Ekaterina Ponomareva
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - Quentin S. Santana
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Keith A. Seifert
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - Emma T. Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Conrad Trollip
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Magriet A. van der Nest
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Cobus M. Visagie
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - P. Markus Wilken
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Michael J. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Neriman Yilmaz
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
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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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Smith DS, Rocheleau H, Chapados JT, Abbott C, Ribero S, Redhead SA, Lévesque CA, De Boer SH. Phylogeny of the genus Synchytrium and the development of TaqMan PCR assay for sensitive detection of Synchytrium endobioticum in soil. PHYTOPATHOLOGY 2014; 104:422-432. [PMID: 24328493 DOI: 10.1094/phyto-05-13-0144-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Potato wart, caused by the fungal pathogen Synchytrium endobioticum, is a serious disease with the potential to cause significant economic damage. The small subunit (SSU) and internal transcribed spacer (ITS) ribosomal DNA (rDNA) were sequenced for several Synchytrium spp., showing a high rate of variability for both of these markers among the different species and monophyly of the genus within phylum Chytridiomycota. The intergenic nontranscribed spacer (IGS) of rDNA was sequenced for different pathotypes and showed no intraspecific variation within S. endobioticum, similar to the other rDNA markers from this study. To facilitate screening for the pathogen in soil, three TaqMan polymerase chain reaction (PCR) assays were developed from SSU, ITS, and IGS rDNA sequences to detect S. endobioticum sporangia in the chloroform-flotation fraction of sieved soil extracts. In the screening portion of the method, a first TaqMan assay targeting the SSU rDNA was developed with positive results that were further confirmed with amplicon melt analysis. A synthetic reaction control cloned into a plasmid was incorporated into the procedure, facilitating the validation of negative results. The presence of the reaction control did not adversely affect the efficiency of the SSU target amplification. A second TaqMan assay targeting the ITS-1 region was developed as a confirmatory test. There was 100% accordance between the SSU and ITS-1 TaqMan assays. Utilizing these two assays in tandem achieved good specificity for S. endobioticum, generating negative results with the cloned SSU and ITS-1 regions from all 14 other Synchytrium spp. considered. Spike recovery experiments indicated that these assays, targeting the SSU and ITS-1 rDNA regions, developed from a phylogeny dataset of the genus, could reliably detect a single sporangium in the chloroform flotation fraction of a soil extract. Good correlation between microscopic detection of sporangia and PCR results in both positive and negative soil samples was dually demonstrated for both the SSU and ITS-1 assays.
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David-Palma M, Libkind D, Sampaio JP. Global distribution, diversity hot spots and niche transitions of an astaxanthin-producing eukaryotic microbe. Mol Ecol 2014; 23:921-32. [DOI: 10.1111/mec.12642] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 12/05/2013] [Accepted: 12/13/2013] [Indexed: 01/20/2023]
Affiliation(s)
- Márcia David-Palma
- Departamento de Ciências da Vida; Faculdade de Ciências e Tecnologia; Centro de Recursos Microbiológicos (CREM); Universidade Nova de Lisboa; 2829-516 Caparica Portugal
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada y Biotecnología; Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA); CONICET - UNComahue; Quintral 1250 (8400), Bariloche Argentina
| | - José Paulo Sampaio
- Departamento de Ciências da Vida; Faculdade de Ciências e Tecnologia; Centro de Recursos Microbiológicos (CREM); Universidade Nova de Lisboa; 2829-516 Caparica Portugal
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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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