1
|
Umata H, Gale SW, Suetsugu K, Ota Y. Variable, life stage-dependent mycorrhizal specificity and its developmental consequences in the fully myco-heterotrophic orchid Cyrtosia septentrionalis. MYCOSCIENCE 2024; 65:68-78. [PMID: 39234511 PMCID: PMC11369304 DOI: 10.47371/mycosci.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/28/2023] [Accepted: 12/06/2023] [Indexed: 09/06/2024]
Abstract
The degree of specificity between fully myco-heterotrophic (MH) orchids and mycorrhizal fungi is regarded as high, but some species undergo a mycobiont shift as they transition from juvenile to adult plant. We investigated morphological and physiological aspects of the interaction between the fully MH Cyrtosia septentrionalis and its four known mycobionts to elucidate developmental consequences of variable, life-stage-dependent specificity. Of five randomly sampled germinated seeds co-cultured with each mycobiont, Physisporinus sp. 'TK-10' colonized all, Armillaria gallica and Desarmillaria tabescens colonized one, and A. mellea subsp. nipponica colonized none. Whereas 16.2% of aseptically germinated seeds exhibited onward growth when co-cultured with TK-10, just 1.5-2.6% did so with the other species. Even so, A. gallica colonized and formed internal rhizomorphs within rhizomes established with TK-10, suggesting that this mycobiont can replace and potentially can oust the latter. We infer that the orchid can associate with Armillaria and Desarmillaria mycobionts throughout its life, but that TK-10 enhances early growth. However, because TK-10 has a higher wood-rotting capacity than A. gallica, rapid resource exhaustion may cause nutrient supply shortages. We hypothesize that secondary colonization by Armillaria or Desarmillaria species triggers TK-10 displacement and that this mycobiont shift sustains orchid growth for longer.
Collapse
Affiliation(s)
| | | | - Kenji Suetsugu
- Department of Biology, Graduate School of Science, Kobe University
| | - Yuko Ota
- College of Bioresource Sciences, Nihon University
| |
Collapse
|
2
|
Narh Mensah DL, Wingfield BD, Coetzee MPA. Two distinct non-ribosomal peptide synthetase-independent siderophore synthetase gene clusters identified in Armillaria and other species in the Physalacriaceae. G3 (BETHESDA, MD.) 2023; 13:jkad205. [PMID: 37843963 PMCID: PMC10700112 DOI: 10.1093/g3journal/jkad205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/28/2023] [Indexed: 10/18/2023]
Abstract
Siderophores are important for ferric iron solubilization, sequestration, transportation, and storage, especially under iron-limiting conditions such as aerobic conditions at high pH. Siderophores are mainly produced by non-ribosomal peptide synthetase-dependent siderophore pathway, non-ribosomal peptide synthetase-independent siderophore synthetase pathway, or the hybrid non-ribosomal peptide synthetases/non-ribosomal peptide synthetases-independent siderophore pathway. Outcompeting or inhibition of plant pathogens, alteration of host defense mechanisms, and alteration of plant-fungal interactions have been associated with fungal siderophores. To understand these mechanisms in fungi, studies have been conducted on siderophore biosynthesis by ascomycetes with limited focus on the basidiomycetes. Armillaria includes several species that are pathogens of woody plants and trees important to agriculture, horticulture, and forestry. The aim of this study was to investigate the presence of non-ribosomal peptide synthetases-independent siderophore synthetase gene cluster(s) in genomes of Armillaria species using a comparative genomics approach. Iron-dependent growth and siderophore biosynthesis in strains of selected Armillaria spp. were also evaluated in vitro. Two distinct non-ribosomal peptide synthetases-independent siderophore synthetase gene clusters were identified in all the genomes. All non-ribosomal peptide synthetases-independent siderophore synthetase genes identified putatively encode Type A' non-ribosomal peptide synthetases-independent siderophore synthetases, most of which have IucA_IucC and FhuF-like transporter domains at their N- and C-terminals, respectively. The effect of iron on culture growth varied among the strains studied. Bioassays using the CAS assay on selected Armillaria spp. revealed in vitro siderophore biosynthesis by all strains irrespective of added FeCl3 concentration. This study highlights some of the tools that Armillaria species allocate to iron homeostasis. The information generated from this study may in future aid in developing molecular based methods to control these phytopathogens.
Collapse
Affiliation(s)
- Deborah L Narh Mensah
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa
- CSIR—Food Research Institute, Microbiology and Mushroom Research Division, P. O. Box, M20, Accra, Ghana
| | - Brenda D Wingfield
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa
| | - Martin P A Coetzee
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa
| |
Collapse
|
3
|
Kim MS, Hanna JW, McDonald GI, Klopfenstein NB. Armillaria altimontana in North America: Biology and Ecology. J Fungi (Basel) 2023; 9:904. [PMID: 37755012 PMCID: PMC10532946 DOI: 10.3390/jof9090904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023] Open
Abstract
Armillaria altimontana is a fungus (Basidiomycota, Agaricomycetes, Agaricales, and Physalacriaceae) that is generally considered as a weak/opportunistic pathogen or saprophyte on many tree hosts. It widely occurs across the northwestern USA to southern British Columbia, Canada, but relatively little is known about its ecological role in the diverse forest ecosystems where it occurs. This review summarizes the biology and ecology of A. altimontana, including its identification, life cycle, distribution, host associations, and bioclimatic models under climate change.
Collapse
Affiliation(s)
- Mee-Sook Kim
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR 97331, USA
| | - John W. Hanna
- Rocky Mountain Research Station, USDA Forest Service, Moscow, ID 83843, USA; (J.W.H.)
| | - Geral I. McDonald
- Rocky Mountain Research Station, USDA Forest Service, Moscow, ID 83843, USA; (J.W.H.)
| | - Ned B. Klopfenstein
- Rocky Mountain Research Station, USDA Forest Service, Moscow, ID 83843, USA; (J.W.H.)
| |
Collapse
|
4
|
Sahu N, Indic B, Wong-Bajracharya J, Merényi Z, Ke HM, Ahrendt S, Monk TL, Kocsubé S, Drula E, Lipzen A, Bálint B, Henrissat B, Andreopoulos B, Martin FM, Bugge Harder C, Rigling D, Ford KL, Foster GD, Pangilinan J, Papanicolaou A, Barry K, LaButti K, Virágh M, Koriabine M, Yan M, Riley R, Champramary S, Plett KL, Grigoriev IV, Tsai IJ, Slot J, Sipos G, Plett J, Nagy LG. Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria. Nat Microbiol 2023; 8:1668-1681. [PMID: 37550506 PMCID: PMC7615209 DOI: 10.1038/s41564-023-01448-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 07/11/2023] [Indexed: 08/09/2023]
Abstract
The fungal genus Armillaria contains necrotrophic pathogens and some of the largest terrestrial organisms that cause tremendous losses in diverse ecosystems, yet how they evolved pathogenicity in a clade of dominantly non-pathogenic wood degraders remains elusive. Here we show that Armillaria species, in addition to gene duplications and de novo gene origins, acquired at least 1,025 genes via 124 horizontal gene transfer events, primarily from Ascomycota. Horizontal gene transfer might have affected plant biomass degrading and virulence abilities of Armillaria, and provides an explanation for their unusual, soft rot-like wood decay strategy. Combined multi-species expression data revealed extensive regulation of horizontally acquired and wood-decay related genes, putative virulence factors and two novel conserved pathogenicity-induced small secreted proteins, which induced necrosis in planta. Overall, this study details how evolution knitted together horizontally and vertically inherited genes in complex adaptive traits of plant biomass degradation and pathogenicity in important fungal pathogens.
Collapse
Affiliation(s)
- Neha Sahu
- Biological Research Center, Synthetic and Systems Biology Unit, Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Boris Indic
- Functional Genomics and Bioinformatics Group, Faculty of Forestry, Institute of Forest and Natural Resource Management, University of Sopron, Sopron, Hungary
| | - Johanna Wong-Bajracharya
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales, Australia
| | - Zsolt Merényi
- Biological Research Center, Synthetic and Systems Biology Unit, Szeged, Hungary
| | - Huei-Mien Ke
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Microbiology, Soochow University, Taipei, Taiwan
| | - Steven Ahrendt
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Tori-Lee Monk
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Sándor Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
- ELKH-SZTE Fungal Pathogenicity Mechanisms Research Group, University of Szeged, Szeged, Hungary
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Université, Marseille, France
- INRAE, UMR 1163, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Balázs Bálint
- Biological Research Center, Synthetic and Systems Biology Unit, Szeged, Hungary
| | - Bernard Henrissat
- DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Bill Andreopoulos
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Francis M Martin
- Université de Lorraine, INRAE, UMR 1136 'Interactions Arbres/Microorganismes', Centre INRAE Grand Est - Nancy, Champenoux, France
| | - Christoffer Bugge Harder
- Department of Biology, Section of Terrestrial Ecology, University of Copenhagen, København Ø, Denmark
- Department of Biosciences, University of Oslo, Blindern, Oslo, Norway
| | - Daniel Rigling
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Kathryn L Ford
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, UK
| | - Gary D Foster
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, UK
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alexie Papanicolaou
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Máté Virágh
- Biological Research Center, Synthetic and Systems Biology Unit, Szeged, Hungary
| | - Maxim Koriabine
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mi Yan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Simang Champramary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
- Functional Genomics and Bioinformatics Group, Faculty of Forestry, Institute of Forest and Natural Resource Management, University of Sopron, Sopron, Hungary
| | - Krista L Plett
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales, Australia
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | | | - Jason Slot
- Department of Plant Pathology, The Ohio State University, Columbus, OH, USA
| | - György Sipos
- Functional Genomics and Bioinformatics Group, Faculty of Forestry, Institute of Forest and Natural Resource Management, University of Sopron, Sopron, Hungary
| | - Jonathan Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - László G Nagy
- Biological Research Center, Synthetic and Systems Biology Unit, Szeged, Hungary.
| |
Collapse
|
5
|
Narh Mensah DL, Wingfield BD, Coetzee MP. A practical approach to genome assembly and annotation of Basidiomycota using the example of Armillaria. Biotechniques 2023; 75:115-128. [PMID: 37681497 DOI: 10.2144/btn-2023-0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023] Open
Abstract
Technological advancements in genome sequencing, assembly and annotation platforms and algorithms that resulted in several genomic studies have created an opportunity to further our understanding of the biology of phytopathogens, including Armillaria species. Most Armillaria species are facultative necrotrophs that cause root- and stem-rot, usually on woody plants, significantly impacting agriculture and forestry worldwide. Genome sequencing, assembly and annotation in terms of samples used and methods applied in Armillaria genome projects are evaluated in this review. Infographic guidelines and a database of resources to facilitate future Armillaria genome projects were developed. Knowledge gained from genomic studies of Armillaria species is summarized and prospects for further research are provided. This guide can be applied to other diploid and dikaryotic fungal genomics.
Collapse
Affiliation(s)
- Deborah L Narh Mensah
- Department of Biochemistry, Genetics & Microbiology, Forestry & Agricultural Biotechnology Institute (FABI), Faculty of Natural & Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa
- Council for Scientific and Industrial Research - Food Research Institute (CSIR-FRI), PO Box M20, Accra, Ghana
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics & Microbiology, Forestry & Agricultural Biotechnology Institute (FABI), Faculty of Natural & Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Martin Pa Coetzee
- Department of Biochemistry, Genetics & Microbiology, Forestry & Agricultural Biotechnology Institute (FABI), Faculty of Natural & Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa
| |
Collapse
|
6
|
Cai G, Cao Y, Tian M, Mo H, Chen X, Li Z, Ji Q, He K, Du G, Yang H. Characterization of the transcriptional responses of Armillaria gallica 012m to GA3. Arch Microbiol 2023; 205:308. [PMID: 37594611 DOI: 10.1007/s00203-023-03621-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 08/19/2023]
Abstract
Gastrodia elata needs to establish a symbiotic relationship with Armillaria strains to obtain nutrients and energy. However, the signaling cross talk between G. elata and Armillaria strains is still unclear. During our experiment, we found that the vegetative mycelium of Armillaria gallica 012m grew significantly better in the media containing gibberellic acid (GA3) than the blank control group (BK). To explore the response mechanism, we performed an RNA-sequencing experiment to profile the transcriptome changes of A. gallica 012m cultured in the medium with exogenous GA3. The transcriptome-guided differential expression genes (DEGs) analysis of GA3 and BK showed that a total of 1309 genes were differentially expressed, including 361 upregulated genes and 948 downregulated genes. Some of those DEGs correlated with the biological process, including positive regulation of chromosome segregation, mitotic metaphase/anaphase transition, attachment of mitotic spindle microtubules to kinetochore, mitotic cytokinesis, and nuclear division. These analyses explained that GA3 actively promoted the growth of A. gallica to some extent. Further analysis of protein domain features showed that the deduced polypeptide contained 41 candidate genes of GA receptor, and 27 of them were expressed in our samples. We speculate that GA receptors exist in A. gallica 012m. Comparative studies of proteins showed that the postulated GA receptor domains of A. gallica 012m have a higher homologous correlation with fungi than others based on cluster analysis.
Collapse
Affiliation(s)
- Guolei Cai
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, 2929 Yuehua Street, Chenggong District, Kunming, Yunnan, China
| | - Yapu Cao
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, 2929 Yuehua Street, Chenggong District, Kunming, Yunnan, China
| | - Menghua Tian
- Zhaotong Tianma Research Institute, Zhaotong, Yunnan, China
| | - Haiying Mo
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, 2929 Yuehua Street, Chenggong District, Kunming, Yunnan, China
| | - Xin Chen
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, 2929 Yuehua Street, Chenggong District, Kunming, Yunnan, China
| | - Zhihao Li
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, 2929 Yuehua Street, Chenggong District, Kunming, Yunnan, China
| | - Qiaolin Ji
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, 2929 Yuehua Street, Chenggong District, Kunming, Yunnan, China
| | - Kaixiang He
- School of Chemistry and Environment, Yunnan Minzu University, Kunming, China
| | - Gang Du
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, 2929 Yuehua Street, Chenggong District, Kunming, Yunnan, China.
| | - Haiying Yang
- School of Chemistry and Environment, Yunnan Minzu University, Kunming, China.
| |
Collapse
|
7
|
Oba Y, Hosaka K. The Luminous Fungi of Japan. J Fungi (Basel) 2023; 9:615. [PMID: 37367550 DOI: 10.3390/jof9060615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 06/28/2023] Open
Abstract
Luminous fungi have long attracted public attention in Japan, from old folklore and fiction to current tourism, children's toys, games, and picture books. At present, 25 species of luminous fungi have been discovered in Japan, which correspond to approximately one-fourth of the globally recognized species. This species richness is arguably due to the abundant presence of mycophiles looking to find new mushroom species and a tradition of night-time activities, such as firefly watching, in Japan. Bioluminescence, a field of bioscience focused on luminous organisms, has long been studied by many Japanese researchers, including the biochemistry and chemistry of luminous fungi. A Japanese Nobel Prize winner, Osamu Shimomura (1928-2018), primarily focused on the bioluminescence system of luminous fungi in the latter part of his life, and total elucidation of the mechanism was finally accomplished by an international research team with representatives from Russia, Brazil, and Japan in 2018. In this review, we focused on multiple aspects related to luminous fungi of Japan, including myth, taxonomy, and modern sciences.
Collapse
Affiliation(s)
- Yuichi Oba
- Department of Environmental Biology, Chubu University, Kasugai 487-8501, Aichi, Japan
| | - Kentaro Hosaka
- Department of Botany, National Museum of Nature and Science, Tsukuba 305-0005, Ibaraki, Japan
| |
Collapse
|
8
|
Zhang T, Feng J, He W, Rong X, Lv H, Li J, Li X, Wang H, Wang L, Zhang L, Yu L. Genomic and Transcriptomic Approaches Provide a Predictive Framework for Sesquiterpenes Biosynthesis in Desarmillaria tabescens CPCC 401429. J Fungi (Basel) 2023; 9:jof9040481. [PMID: 37108935 PMCID: PMC10146329 DOI: 10.3390/jof9040481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/08/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Terpenoids constitute a structurally diverse class of secondary metabolites with wide applications in the pharmaceutical, fragrance and flavor industries. Desarmillaria tabescens CPCC 401429 is a basidiomycetous mushroom that could produce anti-tumor melleolides. To date, no studies have been conducted to thoroughly investigate the sesquiterpenes biosynthetic potential in Desarmillaria or related genus. This study aims to unravel the phylogeny, terpenome, and functional characterization of unique sesquiterpene biosynthetic genes of the strain CPCC 401429. Herein, we report the genome of the fungus containing 15,145 protein-encoding genes. MLST-based phylogeny and comparative genomic analyses shed light on the precise reclassification of D. tabescens suggesting that it belongs to the genus Desarmillaria. Gene ontology enrichment and pathway analyses uncover the hidden capacity for producing polyketides and terpenoids. Genome mining directed predictive framework reveals a diverse network of sesquiterpene synthases (STSs). Among twelve putative STSs encoded in the genome, six ones are belonging to the novel minor group: diverse Clade IV. In addition, RNA-sequencing based transcriptomic profiling revealed differentially expressed genes (DEGs) of the fungus CPCC 401429 in three different fermentation conditions, that of which enable us to identify noteworthy genes exemplified as STSs coding genes. Among the ten sesquiterpene biosynthetic DEGs, two genes including DtSTS9 and DtSTS10 were selected for functional characterization. Yeast cells expressing DtSTS9 and DtSTS10 could produce diverse sesquiterpene compounds, reinforced that STSs in the group Clade IV might be highly promiscuous producers. This highlights the potential of Desarmillaria in generating novel terpenoids. To summarize, our analyses will facilitate our understanding of phylogeny, STSs diversity and functional significance of Desarmillaria species. These results will encourage the scientific community for further research on uncharacterized STSs of Basidiomycota phylum, biological functions, and potential application of this vast source of secondary metabolites.
Collapse
Affiliation(s)
- Tao Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jianjv Feng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Wenni He
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xiaoting Rong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Hui Lv
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jun Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xinxin Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Hao Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Lu Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai 200237, China
| | - Liyan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| |
Collapse
|
9
|
Narh Mensah DL, Wingfield BD, Coetzee MPA. Nonribosomal peptide synthetase gene clusters and characteristics of predicted NRPS-dependent siderophore synthetases in Armillaria and other species in the Physalacriaceae. Curr Genet 2023; 69:7-24. [PMID: 36369495 DOI: 10.1007/s00294-022-01256-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/13/2022]
Abstract
Fungal secondary metabolites are often pathogenicity or virulence factors synthesized by genes contained in secondary metabolite gene clusters (SMGCs). Nonribosomal polypeptide synthetase (NRPS) clusters are SMGCs which produce peptides such as siderophores, the high affinity ferric iron chelating compounds required for iron uptake under aerobic conditions. Armillaria spp. are mostly facultative necrotrophs of woody plants. NRPS-dependent siderophore synthetase (NDSS) clusters of Armillaria spp. and selected Physalacriaceae were investigated using a comparative genomics approach. Siderophore biosynthesis by strains of selected Armillaria spp. was evaluated using CAS and split-CAS assays. At least one NRPS cluster and other clusters were detected in the genomes studied. No correlation was observed between the number and types of SMGCs and reported pathogenicity of the species studied. The genomes contained one NDSS cluster each. All NDSSs were multi-modular with the domain architecture (ATC)3(TC)2. NDSS clusters of the Armillaria spp. showed a high degree of microsynteny. In the genomes of Desarmillaria spp. and Guyanagaster necrorhizus, NDSS clusters were more syntenic with NDSS clusters of Armillaria spp. than to those of the other Physalacriaceae species studied. Three A-domain orthologous groups were identified in the NDSSs, and atypical Stachelhaus codes were predicted for the A3 orthologous group. In vitro biosynthesis of mainly hydroxamate and some catecholate siderophores was observed. Hence, Armillaria spp. generally contain one highly conserved, NDSS cluster although some interspecific variations in the products of these clusters is expected. Results from this study lays the groundwork for future studies to elucidate the molecular biology of fungal phyto-pathogenicity.
Collapse
Affiliation(s)
- Deborah L Narh Mensah
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.,Council for Scientific and Industrial Research-Food Research Institute (CSIR-FRI), P. O. Box M20, Accra, Ghana
| | - Brenda D Wingfield
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Martin P A Coetzee
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.
| |
Collapse
|
10
|
Caballero JRI, Lalande BM, Hanna JW, Klopfenstein NB, Kim MS, Stewart JE. Genomic Comparisons of Two Armillaria Species with Different Ecological Behaviors and Their Associated Soil Microbial Communities. MICROBIAL ECOLOGY 2023; 85:708-729. [PMID: 35312808 DOI: 10.1007/s00248-022-01989-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 03/06/2022] [Indexed: 06/14/2023]
Abstract
Armillaria species show considerable variation in ecological roles and virulence, from mycorrhizae and saprophytes to important root pathogens of trees and horticultural crops. We studied two Armillaria species that can be found in coniferous forests of northwestern USA and southwestern Canada. Armillaria altimontana not only is considered as a weak, opportunistic pathogen of coniferous trees, but it also appears to exhibit in situ biological control against A. solidipes, formerly North American A. ostoyae, which is considered a virulent pathogen of coniferous trees. Here, we describe their genome assemblies and present a functional annotation of the predicted genes and proteins for the two Armillaria species that exhibit contrasting ecological roles. In addition, the soil microbial communities were examined in association with the two Armillaria species within a 45-year-old plantation of western white pine (Pinus monticola) in northern Idaho, USA, where A. altimontana was associated with improved tree growth and survival, while A. solidipes was associated with reduced growth and survival. The results from this study reveal a high similarity between the genomes of the beneficial/non-pathogenic A. altimontana and pathogenic A. solidipes; however, many relatively small differences in gene content were identified that could contribute to differences in ecological lifestyles and interactions with woody hosts and soil microbial communities.
Collapse
Affiliation(s)
| | - Bradley M Lalande
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
- Forest Health Protection, USDA Forest Service, Gunnison, CO, 81230, USA
| | - John W Hanna
- Rocky Mountain Research Station, USDA Forest Service, Moscow, ID, 83843, USA
| | - Ned B Klopfenstein
- Rocky Mountain Research Station, USDA Forest Service, Moscow, ID, 83843, USA.
| | - Mee-Sook Kim
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, 97331, USA.
| | - Jane E Stewart
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| |
Collapse
|
11
|
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
| |
Collapse
|
12
|
Dos Reis JBA, do Vale HMM, Lorenzi AS. Insights into taxonomic diversity and bioprospecting potential of Cerrado endophytic fungi: a review exploring an unique Brazilian biome and methodological limitations. World J Microbiol Biotechnol 2022; 38:202. [PMID: 35999403 DOI: 10.1007/s11274-022-03386-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/10/2022] [Indexed: 11/26/2022]
Abstract
Cerrado is the second largest biome in Brazil, and it is known for harboring a wide variety of endemic plant and microbial species, among which are endophytic fungi. Endophytic fungi are microorganisms capable of colonizing the interior of plant tissues without causing disease in host plants. Especially in the Cerrado biome, this group of microorganisms is still poorly studied and information on species estimation, ecological and evolutionary importance is not accurate and remains unknown. Also, it is extremely important to emphasize that great part of studies available on Cerrado endophytic fungi are national literature, including master's dissertations, course conclusion works or unpublished doctoral theses. The majority of these studies has highlighted that the endemic plant species are an important habitat for fungal endophytes, and new species have increasingly been described. Due to the lack of international literature on Cerrado endophytic fungi, the present review brings a bibliographic survey on taxonomic diversity and bioprospecting potential of fungal endophytes from a unique environment. This review also emphasizes the importance of studying Brazilian endophytic fungi from Cerrado as a source of new technologies (biofertilizer and biocontroller), since they are secondary metabolite-producing organisms with different biological activities for biotechnological, agricultural and pharmaceutical applications.
Collapse
Affiliation(s)
| | - Helson Mário Martins do Vale
- Department of Phytopathology, Institute of Biological Sciences, University of Brasília-UnB, Brasília, DF, Brazil
| | - Adriana Sturion Lorenzi
- Department of Cellular Biology, Institute of Biological Sciences, University of Brasília-UnB, Brasília, DF, Brazil.
| |
Collapse
|
13
|
Bach RAK, Brann M, Aime MC. Viability of fungal rhizomorphs used in bird nest construction in tropical rainforests. Symbiosis 2022. [DOI: 10.1007/s13199-022-00856-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Patil SR, Yadav SV. Photographic record of Armillaria mellea a bioluminescent fungi from Lonavala in Western Ghats, India. JOURNAL OF THREATENED TAXA 2022. [DOI: 10.11609/jott.7677.14.2.20692-20694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Armillaria mellea is a bioluminescent fungus from the Basidiomycota division. The previous known record of the fungus is from Bhimashankar Wildlife Sanctuary. This paper provides data and photographic evidence of Armillaria mellea in Lonavala.
Collapse
|
16
|
Liang J, Pecoraro L, Cai L, Yuan Z, Zhao P, Tsui CKM, Zhang Z. 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; 7:1088. [PMID: 34947070 PMCID: PMC8705980 DOI: 10.3390/jof7121088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [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.
Collapse
Affiliation(s)
- Junmin Liang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.P.); (L.C.); (P.Z.); (Z.Z.)
| | - Lorenzo Pecoraro
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.P.); (L.C.); (P.Z.); (Z.Z.)
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.P.); (L.C.); (P.Z.); (Z.Z.)
| | - Zhilin Yuan
- Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 310029, China;
| | - Peng Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.P.); (L.C.); (P.Z.); (Z.Z.)
| | - Clement K. M. Tsui
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada;
- Department of Pathology, Sidra Medicine, Doha 2713, Qatar
| | - Zhifeng Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.P.); (L.C.); (P.Z.); (Z.Z.)
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| |
Collapse
|
17
|
Hurel A, de Miguel M, Dutech C, Desprez‐Loustau M, Plomion C, Rodríguez‐Quilón I, Cyrille A, Guzman T, Alía R, González‐Martínez SC, Budde KB. Genetic basis of growth, spring phenology, and susceptibility to biotic stressors in maritime pine. Evol Appl 2021; 14:2750-2772. [PMID: 34950227 PMCID: PMC8674897 DOI: 10.1111/eva.13309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 10/03/2021] [Indexed: 11/30/2022] Open
Abstract
Forest ecosystems are increasingly challenged by extreme events, for example, drought, storms, pest attacks, and fungal pathogen outbreaks, causing severe ecological and economic losses. Understanding the genetic basis of adaptive traits in tree species is of key importance to preserve forest ecosystems, as genetic variation in a trait (i.e., heritability) determines its potential for human-mediated or evolutionary change. Maritime pine (Pinus pinaster Aiton), a conifer widely distributed in southwestern Europe and northwestern Africa, grows under contrasted environmental conditions promoting local adaptation. Genetic variation at adaptive phenotypes, including height, spring phenology, and susceptibility to two fungal pathogens (Diplodia sapinea and Armillaria ostoyae) and an insect pest (Thaumetopoea pityocampa), was assessed in a range-wide clonal common garden of maritime pine. Broad-sense heritability was significant for height (0.219), spring phenology (0.165-0.310), and pathogen susceptibility (necrosis length caused by D. sapinea, 0.152; and by A. ostoyae, 0.021, measured on inoculated, excised branches under controlled conditions), but not for pine processionary moth incidence in the common garden. The correlations of trait variation among populations revealed contrasting trends for pathogen susceptibility to D. sapinea and A. ostoyae with respect to height. Taller trees showed longer necrosis length caused by D. sapinea while shorter trees were more affected by A. ostoyae. Moreover, maritime pine populations from areas with high summer temperatures and frequent droughts were less susceptible to D. sapinea but more susceptible to A. ostoyae. Finally, an association study using 4227 genome-wide SNPs revealed several loci significantly associated with each trait (range of 3-26), including a possibly disease-induced translation initiation factor, eIF-5, associated with needle discoloration caused by D. sapinea. This study provides important insights to develop genetic conservation and breeding strategies integrating species responses to biotic stressors.
Collapse
Affiliation(s)
- Agathe Hurel
- BIOGECO, INRAEUniversity of BordeauxCestasFrance
| | - Marina de Miguel
- BIOGECO, INRAEUniversity of BordeauxCestasFrance
- EGFV, INRAEUniversity of BordeauxVillenave‐d'OrnonFrance
| | - Cyril Dutech
- BIOGECO, INRAEUniversity of BordeauxCestasFrance
| | | | | | | | | | | | | | | | - Katharina B. Budde
- BIOGECO, INRAEUniversity of BordeauxCestasFrance
- Büsgen‐InstituteGeorg‐August University GöttingenGöttingenGermany
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Porter DL, Bradshaw AJ, Nielsen RH, Newell P, Dentinger BTM, Naleway SE. The melanized layer of Armillaria ostoyae rhizomorphs: Its protective role and functions. J Mech Behav Biomed Mater 2021; 125:104934. [PMID: 34773913 DOI: 10.1016/j.jmbbm.2021.104934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 10/20/2022]
Abstract
Armillaria ostoyae (Romagn.) Herink is a highly pathogenic fungus that uses exploratory, cordlike structures called rhizomorphs to seek out new sources of nutrition, posing a parasitic threat to natural stands of trees, orchards, and vineyards. Rhizomorphs are notoriously difficult to destroy, and this resilience is due in large part to a melanized layer that protects the rhizomorph. While this structure has been previously observed, its structural and chemical defenses are yet to be discerned. Research was conducted on both lab-cultured and wild-harvested rhizomorph samples. While both environments produce rhizomorphs, only the wild-harvested rhizomorphs produced the melanized layer, allowing for direct investigation of its structure and properties. Imaging, chemical analysis, mechanical testing, and finite element modeling were used to understand the defense mechanisms provided by the melanized layer. Imaging showed a porous outer layer in both types of rhizomorphs, though the pores were smaller in the harvested melanized layer. This melanized layer contained calcium, which provides chemical defense against both human and natural control methods, but was absent from cultured samples. Nanoindentation resulted in a larger variance of hardness values for cultured rhizomorphs than for wild-harvested. Finite element analysis proved that the smaller pore structure of the melanized porous layer had the best balance between maximum deformation and resulting permanent deformation. These results allow for a better understanding of the defenses of this pathogenic fungus, which may lead to better control methods.
Collapse
Affiliation(s)
| | - Alexander J Bradshaw
- Natural History Museum of Utah & School of Biological Sciences, University of Utah, USA
| | - Ryan H Nielsen
- The University of Utah Department of Mechanical Engineering, USA
| | - Pania Newell
- The University of Utah Department of Mechanical Engineering, USA
| | - Bryn T M Dentinger
- Natural History Museum of Utah & School of Biological Sciences, University of Utah, USA
| | - Steven E Naleway
- The University of Utah Department of Mechanical Engineering, USA
| |
Collapse
|
20
|
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.
Collapse
|
21
|
Koch RA, Yoon GM, Aryal UK, Lail K, Amirebrahimi M, LaButti K, Lipzen A, Riley R, Barry K, Henrissat B, Grigoriev IV, Herr JR, Aime MC. Symbiotic nitrogen fixation in the reproductive structures of a basidiomycete fungus. Curr Biol 2021; 31:3905-3914.e6. [PMID: 34245690 DOI: 10.1016/j.cub.2021.06.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/09/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022]
Abstract
Nitrogen (N) fixation is a driving force for the formation of symbiotic associations between N2-fixing bacteria and eukaryotes.1 Limited examples of these associations are known in fungi, and none with sexual structures of non-lichenized species.2-6 The basidiomycete Guyanagaster necrorhizus is a sequestrate fungus endemic to the Guiana Shield.7 Like the root rot-causing species in its sister genera Armillaria and Desarmillaria, G. necrorhizus sporocarps fruit from roots of decaying trees (Figures 1A-1C),8 and genome sequencing is consistent with observations that G. necrorhizus is a white-rotting decomposer. This species also represents the first documentation of an arthropod-dispersed sequestrate fungus. Numerous species of distantly related wood-feeding termites, which scavenge for N-rich food, feed on the mature spore-bearing tissue, or gleba, of G. necrorhizus. During feeding, mature spores adhere to termites for subsequent dispersal.9 Using chemical assays, isotope analysis, and high-throughput sequencing, we show that the sporocarps harbor actively N2-fixing Enterobacteriaceae species and that the N content within fungal tissue increases with maturation. Untargeted proteomic profiling suggests that ATP generation in the gleba is accomplished via fermentation. The use of fermentation-an anaerobic process-indicates that the sporocarp environment is anoxic, likely an adaptation to protect the oxygen-sensitive nitrogenase enzyme. Sporocarps also have a thick outer covering, possibly to limit oxygen diffusion. The enriched N content within mature sporocarps may offer a dietary inducement for termites in exchange for spore dispersal. These results show that the flexible metabolic capacity of fungi may facilitate N2-fixing associations, as well as higher-level organismal associations.
Collapse
Affiliation(s)
- Rachel A Koch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA; Department of Plant Pathology, University of Nebraska, Lincoln, NE 68520, USA.
| | - Gyeong Mee Yoon
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Uma K Aryal
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA; Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
| | - Kathleen Lail
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mojgan Amirebrahimi
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille 13288, France; Institut National de la Recherche Agronomique, USC1408 Architecture et Fonction des Macromolécules Biologiques, Marseille 13288, France; Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Joshua R Herr
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68520, USA; Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68520, USA
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA.
| |
Collapse
|
22
|
Antonín V, Stewart JE, Ortiz RM, Kim MS, Bonello PE, Tomšovský M, Klopfenstein NB. Desarmillaria caespitosa, a North American vicariant of D. tabescens. Mycologia 2021; 113:776-790. [PMID: 33914673 DOI: 10.1080/00275514.2021.1890969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Desarmillaria caespitosa, a North American vicariant species of European D. tabescens, is redescribed in detail based on recent collections from the USA and Mexico. This species is characterized by morphological features and multilocus phylogenetic analyses using portions of nuc rDNA 28S (28S), translation elongation factor 1-alpha (tef1), the second largest subunit of RNA polymerase II (rpb2), actin (act), and glyceraldehyde-3-phosphate dehydrogenase (gpd). A neotype of D. caespitosa is designated here. Morphological and genetic differences between D. caespitosa and D. tabescens were identified. Morphologically, D. caespitosa differs from D. tabescens by having wider basidiospores, narrower cheilocystidia, which are often irregular or mixed (regular, irregular, or coralloid), and narrower caulocystidia. Phylogenetic analyses of five independent gene regions show that D. caespitosa and D. tabescens are separated by nodes with strong support. The new combination, D. caespitosa, is proposed.
Collapse
Affiliation(s)
- Vladimír Antonín
- Department of Botany, Moravian Museum, Zelný trh 6, 659 37 Brno, Czech Republic
| | - Jane E Stewart
- Department of Agricultural Biology, Colorado State University, 307 University Avenue, Ft. Collins, Colorado 80523
| | - Rosario Medel Ortiz
- Centro de Investigación en Micología Aplicada/Universidad Veracruzana, Médicos 5, Col. Unidad del Bosque, Xalapa, 91010, Veracruz, Mexico
| | - Mee-Sook Kim
- United States Department of Agriculture, Forest Service, Pacific Northwest Research Station, 3200 SW Jefferson Way, Corvallis, Oregon 97331
| | - Pierluigi Enrico Bonello
- Department of Plant Pathology, The Ohio State University, 201 Kottman Hall, 2021 Coffey Road, Columbus, Ohio 43210
| | - Michal Tomšovský
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemedelska 3, 613 00 Brno, Czech Republic
| | - Ned B Klopfenstein
- United States Department of Agriculture, Forest Service, Rocky Mountain Research Station, 1221 South Main Street, Moscow, Idaho 83843
| |
Collapse
|
23
|
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.
Collapse
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.)
| |
Collapse
|
24
|
Lücking R, Aime MC, Robbertse B, Miller AN, Ariyawansa HA, Aoki T, Cardinali G, Crous PW, Druzhinina IS, Geiser DM, Hawksworth DL, Hyde KD, Irinyi L, Jeewon R, Johnston PR, Kirk PM, Malosso E, May TW, Meyer W, Öpik M, Robert V, Stadler M, Thines M, Vu D, Yurkov AM, Zhang N, Schoch CL. Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus 2020; 11:14. [PMID: 32714773 PMCID: PMC7353689 DOI: 10.1186/s43008-020-00033-z] [Citation(s) in RCA: 185] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
Collapse
Affiliation(s)
- Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, Germany
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
| | - M. Catherine Aime
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
| | - Andrew N. Miller
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820-6970 USA
| | - Hiran A. Ariyawansa
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, Taipe City, Taiwan
| | - Takayuki Aoki
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Agriculture and Food Research Organization, Genetic Resources Center, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Gianluigi Cardinali
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
| | - Pedro W. Crous
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Irina S. Druzhinina
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - David M. Geiser
- Department of Plant Pathology & Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802 USA
| | - David L. Hawksworth
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Surrey, TW9 3DS UK
- Geography and Environment, University of Southampton, Southampton, SO17 1BJ UK
- Jilin Agricultural University, Changchun, 130118 Jilin Province China
| | - Kevin D. Hyde
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- World Agroforestry Centre, East and Central Asia, Kunming, 650201 Yunnan China
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Rai, 50150 Thailand
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Rajesh Jeewon
- Department of Health Sciences, Faculty of Science, University of Mauritius, Reduit, Mauritius
| | - Peter R. Johnston
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Manaaki Whenua – Landcare Research, Private Bag 92170, Auckland, 1142 New Zealand
| | | | - Elaine Malosso
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Universidade Federal de Pernambuco, Centro de Biociências, Departamento de Micologia, Laboratório de Hifomicetos de Folhedo, Avenida da Engenharia, s/n Cidade Universitária, Recife, PE 50.740-600 Brazil
| | - Tom W. May
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, Victoria 3004 Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Maarja Öpik
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- University of Tartu, 40 Lai Street, 51 005 Tartu, Estonia
| | - Vincent Robert
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Marc Stadler
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department Microbial Drugs, Helmholtz Centre for Infection Research, and German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Marco Thines
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60439 Frankfurt (Main); Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Andrey M. Yurkov
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Ning Zhang
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901 USA
| | - Conrad L. Schoch
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
| |
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
Miller SB, Gasic K, Reighard GL, Henderson WG, Rollins PA, Vassalos M, Schnabel G. Preventative Root-Collar Excavation Reduces Peach Tree Mortality Caused By Armillaria Root Rot On Replant Sites. PLANT DISEASE 2020; 104:1274-1279. [PMID: 32213125 DOI: 10.1094/pdis-09-19-1831-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In the southeastern United States, Armillaria root rot (ARR) is caused by Desarmillaria tabescens and has become the primary cause of premature mortality in peach orchards. Most rootstocks used in commercial orchards are susceptible and management options are limited. A postinfection practice known as root-collar excavation (RCE), which involves permanent removal of the soil from the base of the trunk, has been shown to improve yields and prolong the productive life of symptomatic trees. However, symptomatic trees already have an advanced infection at the base of the trunk. This study evaluated the efficacy of preventative RCE on the progression of tree mortality in two orchards that were planted in infested replant sites. To provide convincing data for growers, the study was carried out in a commercial orchard and an experimental orchard for 8 years. Furthermore, representative enterprise budgets and net present value (NPV) analysis were utilized to compare the profitability of the two approaches. Trees were planted shallow on berms (45 by 90 cm) to facilitate RCE with hoes and AirSpade 2 years later. Tree mortality in the RCE treatment of the experimental orchard was first observed in year 6 and increased 8% on average per year thereafter. In contrast, tree mortality in the "Grower Standard" treatment was first observed in year 4 and increased 12.7% on average per year thereafter. At the commercial orchard, tree mortality in the RCE treatment was first observed in year 7 and increased 1.9% on average thereafter, while tree mortality in the Grower Standard treatment first appeared in year 5 and increased 4.3% on average thereafter. The delayed onset of ARR-associated tree mortality and the lower annual tree mortality rate in the RCE treatment led to higher NPVs in both locations. There were no negative effects on yield or fruit quality. However, the new planting system can create horticultural challenges, including the formation of a proper berm, uneven ground around the tree interfering with tree care and harvest, increased erosion due to channeling of rainwater, and increased rootstock suckering. The RCE is a valid option for southeastern growers needing to manage high ARR disease pressure on replant sites or on sites only recently cleared from ARR-infected forest land.
Collapse
Affiliation(s)
- Sarah B Miller
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, U.S.A
| | - Ksenija Gasic
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, U.S.A
| | - Gregory L Reighard
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, U.S.A
| | | | - Phillip A Rollins
- Cooperative Extension Service, Clemson University, Clemson, SC 29634, U.S.A
| | - Michael Vassalos
- Department of Agricultural Science, Clemson University, Clemson, SC 29634, U.S.A
| | - Guido Schnabel
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, U.S.A
| |
Collapse
|
27
|
Abstract
One of the main aims of the University of Pavia mycology laboratory was to collect wood decay fungal (WDF) strains in order to deepen taxonomic studies, species distribution, officinal properties or to investigate potential applications such as biocomposite material production based on fungi. The Italian Alps, Apennines and wood plains were investigated to collect Basidiomycota basidiomata from living or dead trees. The purpose of this study was to investigate the wood decay strains of the Mediterranean area, selecting sampling sites in North and Central Italy, including forests near the Ligurian and Adriatic seas, or near the Lombardy lakes. The isolation of mycelia in pure culture was performed according to the current methodology and the identity of the strains was confirmed by molecular analyses. The strains are maintained in the Research Culture Collection MicUNIPV of Pavia University (Italy). Among the 500 WDF strains in the collection, the most interesting isolates from the Mediterranean area are: Dichomitus squalens (basidioma collected from Pinus pinea), Hericium erinaceus (medicinal mushroom), Inocutis tamaricis (white-rot agent on Tamarix trees), Perenniporia meridionalis (wood degrader through Mn peroxidase) and P. ochroleuca. In addition, strains of species related to the Mediterranean climate (e.g., Fomitiporia mediterranea and Cellulariella warnieri) were obtained from sites with a continental-temperate climate.
Collapse
|
28
|
Ramzi AB, Che Me ML, Ruslan US, Baharum SN, Nor Muhammad NA. Insight into plant cell wall degradation and pathogenesis of Ganoderma boninense via comparative genome analysis. PeerJ 2019; 7:e8065. [PMID: 31879570 PMCID: PMC6927665 DOI: 10.7717/peerj.8065] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 10/20/2019] [Indexed: 12/20/2022] Open
Abstract
Background G. boninense is a hemibiotrophic fungus that infects oil palms (Elaeis guineensis Jacq.) causing basal stem rot (BSR) disease and consequent massive economic losses to the oil palm industry. The pathogenicity of this white-rot fungus has been associated with cell wall degrading enzymes (CWDEs) released during saprophytic and necrotrophic stage of infection of the oil palm host. However, there is a lack of information available on the essentiality of CWDEs in wood-decaying process and pathogenesis of this oil palm pathogen especially at molecular and genome levels. Methods In this study, comparative genome analysis was carried out using the G. boninense NJ3 genome to identify and characterize carbohydrate-active enzyme (CAZymes) including CWDE in the fungal genome. Augustus pipeline was employed for gene identification in G. boninense NJ3 and the produced protein sequences were analyzed via dbCAN pipeline and PhiBase 4.5 database annotation for CAZymes and plant-host interaction (PHI) gene analysis, respectively. Comparison of CAZymes from G. boninense NJ3 was made against G. lucidum, a well-studied model Ganoderma sp. and five selected pathogenic fungi for CAZymes characterization. Functional annotation of PHI genes was carried out using Web Gene Ontology Annotation Plot (WEGO) and was used for selecting candidate PHI genes related to cell wall degradation of G. boninense NJ3. Results G. boninense was enriched with CAZymes and CWDEs in a similar fashion to G. lucidum that corroborate with the lignocellulolytic abilities of both closely-related fungal strains. The role of polysaccharide and cell wall degrading enzymes in the hemibiotrophic mode of infection of G. boninense was investigated by analyzing the fungal CAZymes with necrotrophic Armillaria solidipes, A. mellea, biotrophic Ustilago maydis, Melampsora larici-populina and hemibiotrophic Moniliophthora perniciosa. Profiles of the selected pathogenic fungi demonstrated that necrotizing pathogens including G. boninense NJ3 exhibited an extensive set of CAZymes as compared to the more CAZymes-limited biotrophic pathogens. Following PHI analysis, several candidate genes including polygalacturonase, endo β-1,3-xylanase, β-glucanase and laccase were identified as potential CWDEs that contribute to the plant host interaction and pathogenesis. Discussion This study employed bioinformatics tools for providing a greater understanding of the biological mechanisms underlying the production of CAZymes in G. boninense NJ3. Identification and profiling of the fungal polysaccharide- and lignocellulosic-degrading enzymes would further facilitate in elucidating the infection mechanisms through the production of CWDEs by G. boninense. Identification of CAZymes and CWDE-related PHI genes in G. boninense would serve as the basis for functional studies of genes associated with the fungal virulence and pathogenicity using systems biology and genetic engineering approaches.
Collapse
Affiliation(s)
- Ahmad Bazli Ramzi
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Muhammad Lutfi Che Me
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Ummul Syafiqah Ruslan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | | | | |
Collapse
|
29
|
He MQ, Zhao RL, Hyde KD, Begerow D, Kemler M, Yurkov A, McKenzie EHC, Raspé O, Kakishima M, Sánchez-Ramírez S, Vellinga EC, Halling R, Papp V, Zmitrovich IV, Buyck B, Ertz D, Wijayawardene NN, Cui BK, Schoutteten N, Liu XZ, Li TH, Yao YJ, Zhu XY, Liu AQ, Li GJ, Zhang MZ, Ling ZL, Cao B, Antonín V, Boekhout T, da Silva BDB, De Crop E, Decock C, Dima B, Dutta AK, Fell JW, Geml J, Ghobad-Nejhad M, Giachini AJ, Gibertoni TB, Gorjón SP, Haelewaters D, He SH, Hodkinson BP, Horak E, Hoshino T, Justo A, Lim YW, Menolli N, Mešić A, Moncalvo JM, Mueller GM, Nagy LG, Nilsson RH, Noordeloos M, Nuytinck J, Orihara T, Ratchadawan C, Rajchenberg M, Silva-Filho AGS, Sulzbacher MA, Tkalčec Z, Valenzuela R, Verbeken A, Vizzini A, Wartchow F, Wei TZ, Weiß M, Zhao CL, Kirk PM. Notes, outline and divergence times of Basidiomycota. FUNGAL DIVERS 2019. [DOI: 10.1007/s13225-019-00435-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AbstractThe Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.
Collapse
|
30
|
Abstract
Lingering in forests around the world, some of the largest and oldest terrestrial organisms on earth hide in plain sight. In this Quick Guide, Sipos et al. shed light on the biology of the Armillaria fungi.
Collapse
Affiliation(s)
- György Sipos
- Fungal Genomics and Bioinformatics Group, Research Center for Forestry and Wood Industry, University of Sopron, Sopron, 9400 Hungary.
| | - James B Anderson
- Department of Biology, University of Toronto, Mississauga, ON L5L 1C6 Canada.
| | - László G Nagy
- Synthetic and Systems Biology Unit, Biological Research Center, Hungarian Academy of Sciences, Szeged, 6726, Hungary.
| |
Collapse
|
31
|
|
32
|
Kolesnikova AI, Putintseva YA, Simonov EP, Biriukov VV, Oreshkova NV, Pavlov IN, Sharov VV, Kuzmin DA, Anderson JB, Krutovsky KV. Mobile genetic elements explain size variation in the mitochondrial genomes of four closely-related Armillaria species. BMC Genomics 2019; 20:351. [PMID: 31068137 PMCID: PMC6506933 DOI: 10.1186/s12864-019-5732-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 04/24/2019] [Indexed: 12/03/2022] Open
Abstract
Background Species in the genus Armillaria (fungi, basidiomycota) are well-known as saprophytes and pathogens on plants. Many of them cause white-rot root disease in diverse woody plants worldwide. Mitochondrial genomes (mitogenomes) are widely used in evolutionary and population studies, but despite the importance and wide distribution of Armillaria, the complete mitogenomes have not previously been reported for this genus. Meanwhile, the well-supported phylogeny of Armillaria species provides an excellent framework in which to study variation in mitogenomes and how they have evolved over time. Results Here we completely sequenced, assembled, and annotated the circular mitogenomes of four species: A. borealis, A. gallica, A. sinapina, and A. solidipes (116,443, 98,896, 103,563, and 122,167 bp, respectively). The variation in mitogenome size can be explained by variable numbers of mobile genetic elements, introns, and plasmid-related sequences. Most Armillaria introns contained open reading frames (ORFs) that are related to homing endonucleases of the LAGLIDADG and GIY-YIG families. Insertions of mobile elements were also evident as fragments of plasmid-related sequences in Armillaria mitogenomes. We also found several truncated gene duplications in all four mitogenomes. Conclusions Our study showed that fungal mitogenomes have a high degree of variation in size, gene content, and genomic organization even among closely related species of Armillara. We suggest that mobile genetic elements invading introns and intergenic sequences in the Armillaria mitogenomes have played a significant role in shaping their genome structure. The mitogenome changes we describe here are consistent with widely accepted phylogenetic relationships among the four species. Electronic supplementary material The online version of this article (10.1186/s12864-019-5732-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Anna I Kolesnikova
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia.,Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk, 660036, Russia
| | - Yuliya A Putintseva
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia
| | - Evgeniy P Simonov
- Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk, 660036, Russia.,Institute of Animal Systematics and Ecology, Siberian Branch of Russian Academy of Sciences, 630091, Novosibirsk, Russia
| | - Vladislav V Biriukov
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia.,Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk, 660036, Russia
| | - Natalya V Oreshkova
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia.,Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk, 660036, Russia.,Laboratory of Forest Genetics and Selection, V. N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, Krasnoyarsk, 660036, Russia
| | - Igor N Pavlov
- Laboratory of Reforestation, Mycology and Plant Pathology, V. N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, Krasnoyarsk, 660036, Russia
| | - Vadim V Sharov
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia.,Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk, 660036, Russia.,Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, Krasnoyarsk, 660074, Russia
| | - Dmitry A Kuzmin
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia.,Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, Krasnoyarsk, 660074, Russia
| | - James B Anderson
- Department of Biology, University of Toronto, Mississauga, ON, l5L 1C6, Canada
| | - Konstantin V Krutovsky
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia. .,Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, 37077, Göttingen, Germany. .,Laboratory of Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia. .,Department of Ecosystem Science and Management, Texas A&M University, College Station, TX, 77843-2138, USA.
| |
Collapse
|
33
|
Mujic AB, Zheng N, Kim K, Spatafora JW, Castellano MA, Smith ME. The Cedrus-associated truffle Trappeindia himalayensis is a morphologically unique and phylogenetically divergent species of Rhizopogon. Mycologia 2019; 111:225-234. [PMID: 30753119 DOI: 10.1080/00275514.2018.1542864] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In the northwestern Himalayan mountains of India, the hypogeous sequestrate fungus Trappeindia himalayensis is harvested from forests dominated by the ectomycorrhizal tree Cedrus deodara (Himalayan cedar). This truffle has basidiospores that are ornamented with raised reticulation. The original description of Trappeindia himalayensis suggested that the gleba of this species is similar to young specimens of Scleroderma (Boletales), whereas its basidiospores are ornamented with raised reticulation, suggesting a morphological affinity to Leucogaster (Russulales) or Strobilomyces (Boletales). Given this systematic ambiguity, we have generated DNA sequence data from type material and other herbarium specimens and present the first molecular phylogenetic analysis of this unusual Cedrus-associated truffle. Despite the irregular ornamented basidiospore morphology, T. himalayensis is resolved within the genus Rhizopogon (Suillineae, Boletales) and represents a unique lineage that has not been previously detected. All known Rhizopogon species possess an ectomycorrhizal trophic mode, and because of its placement in this lineage, it is likely that Trappeindia himalayensis is an ectomycorrhizal partner of Cedrus deodara. This study highlights the importance of generating sequence data from herbarium specimens in order to identify fungal biodiversity and clarify the systematic relationships of poorly documented fungi.
Collapse
Affiliation(s)
- Alija B Mujic
- a Department of Plant Pathology , University of Florida , Gainesville , Florida 32611
| | - Nan Zheng
- a Department of Plant Pathology , University of Florida , Gainesville , Florida 32611
| | - Kristy Kim
- a Department of Plant Pathology , University of Florida , Gainesville , Florida 32611
| | - Joseph W Spatafora
- b Department of Botany and Plant Pathology , Oregon State University , Corvallis , Oregon 97331
| | - Michael A Castellano
- c US Department of Agriculture, Forest Service , Northern Research Station , 3200 SW Jefferson Way, Corvallis , Oregon 97331
| | - Matthew E Smith
- a Department of Plant Pathology , University of Florida , Gainesville , Florida 32611
| |
Collapse
|
34
|
Lee HY, Moon S, Koo CD, Chung JW, Ryu H. The complete mitochondrial genome of the edible and phytopathogenic fungus Desarmillaria tabescens. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 4:33-34. [PMID: 33365409 PMCID: PMC7510627 DOI: 10.1080/23802359.2018.1535861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 09/20/2018] [Indexed: 10/27/2022]
Abstract
Desarmillaria tabescens is one of the most important edible, medicinal, and phytopathogenic basidiomycetes. The complete mitochondrial genome of this species was determined using next-generation sequencing technology. This mitogenome is a circular molecule of 93,439 bp with a GC content of 29.28% and contains 15 protein-coding, two rRNA (rnl and rns), and 24 tRNA genes. Phylogenetic analysis revealed that D. tabescens is genetically closest to Agrocybe aegerita. Desarmillaria tabescens mitogenome can contribute to our understanding of the phylogeny and evolution of this species.
Collapse
Affiliation(s)
- Hwa-Yong Lee
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea.,Department of Forest Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Suyun Moon
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea
| | - Chang-Duck Koo
- Department of Forest Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea
| |
Collapse
|
35
|
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.
Collapse
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.
| |
Collapse
|
36
|
Bioluminescence expression during the transition from mycelium to mushroom in three North American Armillaria and Desarmillaria species. Fungal Biol 2018; 122:1064-1068. [PMID: 30342622 DOI: 10.1016/j.funbio.2018.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/19/2018] [Accepted: 08/28/2018] [Indexed: 11/23/2022]
Abstract
Unlike most bioluminescent fungi, mycelia of Armillaria and Desarmillaria are constitutively bioluminescent while mature mushrooms are not. The absence of the luciferin, 3-hydroxyhispidin, and its precursor hispidin in mature mushrooms have been proposed to explain the lack of bioluminescence from Armillaria mushrooms. Using three North American species, A. gallica, A. mellea and D. tabescens (syn., Armillaria tabescens), we documented a decline in luminescence of ten fold during the transition from mycelia to, immature mushrooms (i.e., pins) for the two Armillaria species. As pins matured, luminescence declined by an additional two or three orders of magnitude. Lower initial luminescence of D. tabescens mycelia declined to negligible levels during mushroom development. Further, light production was localized in the gills and lower stipe of A. mellea mushrooms. The decline in luminescence during mushroom formation was reversed by addition of hispidin to stipe or gills which significantly enhanced luminescence by one and three orders of magnitude, respectively. We conclude that the modulation of Armillaria and Desarmillaria luminescence is achieved by luciferin availability early in mushroom development. However, since the temporal regulation of bioluminescence differs between Armillaria species and other genera, we conclude that bioluminescence in Armillaria is under unique selective pressures.
Collapse
|
37
|
Tying up loose threads: revised taxonomy and phylogeny of an avian-dispersed Neotropical rhizomorph-forming fungus. Mycol Prog 2018. [DOI: 10.1007/s11557-018-1411-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
38
|
Koch RA, Aime MC. Population structure of
Guyanagaster necrorhizus
supports termite dispersal for this enigmatic fungus. Mol Ecol 2018; 27:2667-2679. [PMID: 29729049 DOI: 10.1111/mec.14710] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 04/07/2018] [Indexed: 02/02/2023]
Affiliation(s)
- Rachel A. Koch
- Department of Botany and Plant Pathology Purdue University West Lafayette Indiana
| | - M. Catherine Aime
- Department of Botany and Plant Pathology Purdue University West Lafayette Indiana
| |
Collapse
|
39
|
Elías-Román RD, Medel-Ortiz R, Alvarado-Rosales D, Hanna JW, Ross-Davis AL, Kim MS, Klopfenstein NB. Armillaria mexicana, a newly described species from Mexico. Mycologia 2018; 110:347-360. [PMID: 29608410 DOI: 10.1080/00275514.2017.1419031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Armillaria mexicana (Agaricales, Physalacriaceae) is described as a new species based on morphology, DNA sequence data, and phylogenetic analyses. It clearly differs from previously reported Armillaria species in North, Central, and South America. It is characterized by the absence of fibulae in the basidioma, abundant cheilocystidia, and ellipsoidal, hyaline basidiospores that are apparently smooth under light microscope, but slightly to moderately rugulose under scanning electron microscope. It is differentiated from other Armillaria species by macromorphological characters, including annulus structure, pileus and stipe coloration, and other structures. DNA sequence data (nuc rDNA internal transcribed spacers [ITS1-5.8S-ITS2 = ITS], 28S D-domain, 3' end of 28S intergenic spacer 1, and translation elongation factor 1-α [TEF1]) show that A. mexicana sequences are quite distinct from sequences of analogous Armillaria species in GenBank. In addition, sequences of ITS of the A. mexicana ex-type culture reveal an ITS1 of 1299 bp and an ITS2 of 582 bp, the longest ITS regions reported thus far in fungi. Phylogenetic analysis based on TEF1 sequences place A. mexicana in a well-separated, monophyletic clade basal to the polyphyletic A. mellea complex.
Collapse
Affiliation(s)
- Rubén Damián Elías-Román
- a Departamento de Agronomía, División de Ciencias de la Vida (DICIVA) , Campus Irapuato-Salamanca, Universidad de Guanajuato, C.P. 36824 , Irapuato , Guanajuato , México
| | - Rosario Medel-Ortiz
- b Instituto de Investigaciones Forestales, Universidad Veracruzana , Xalapa , Veracruz , México
| | | | - John W Hanna
- d US Department of Agriculture Forest Service , Rocky Mountain Research Station, 1221 S. Main Street, Moscow , Idaho 83843
| | - Amy L Ross-Davis
- d US Department of Agriculture Forest Service , Rocky Mountain Research Station, 1221 S. Main Street, Moscow , Idaho 83843
| | - Mee-Sook Kim
- e U.S. Department of Agriculture Forest Service, Pacific Northwest Research Station , 3200 SW Jefferson Way , Corvallis , Oregon 97331
| | - Ned B Klopfenstein
- d US Department of Agriculture Forest Service , Rocky Mountain Research Station, 1221 S. Main Street, Moscow , Idaho 83843
| |
Collapse
|
40
|
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.
Collapse
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
| |
Collapse
|