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Sumampong G, Feau N, Bernier L, Hamelin RC, Liu JJ, Shamoun SF. Genome sequence of Heterobasidion occidentale, a fungus that causes annosus root and butt rot among conifer trees in North America. Microbiol Resour Announc 2024:e0041924. [PMID: 39177369 DOI: 10.1128/mra.00419-24] [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: 05/07/2024] [Accepted: 07/29/2024] [Indexed: 08/24/2024] Open
Abstract
We report an annotated draft genome of Heterobasidion occidentale, a fungus (Basidiomycota, Agaricomycetes) that has pathogenic and saprophytic lifestyles. This fungus belongs to the H. annosum (Fr.) Bref. sensu lato species complex that comprises several root rot pathogens. Heterobasidion occidentale causes annosus root and butt rot primarily in true fir (Abies spp.) and spruce (Picea spp.) species throughout western North America.
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Affiliation(s)
- Grace Sumampong
- Département des Sciences du bois et de la Forêt, Faculté de Foresterie et Géographie, Université Laval, Québec, Canada
- Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, Victoria, British Columbia, Canada
| | - Nicolas Feau
- Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, Victoria, British Columbia, Canada
| | - Louis Bernier
- Département des Sciences du bois et de la Forêt, Faculté de Foresterie et Géographie, Université Laval, Québec, Canada
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jun-Jun Liu
- Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, Victoria, British Columbia, Canada
| | - Simon F Shamoun
- Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, Victoria, British Columbia, Canada
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Ren W, Penttilä R, Kasanen R, Asiegbu FO. Interkingdom and intrakingdom interactions in the microbiome of Heterobasidion fruiting body and associated decayed woody tissues. Appl Environ Microbiol 2023; 89:e0140623. [PMID: 38014962 PMCID: PMC10734517 DOI: 10.1128/aem.01406-23] [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: 08/19/2023] [Accepted: 10/06/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE We applied macro- (forest stand and forest management) and micro-scale (bacterial and fungal community) analyses for a better understanding of the Heterobasidion pathosystem and associated wood decay process. The core microbiome, as defined by hierarchy analysis and a consistent model, and environmental factors correlation with the community assembly were found to be novel.
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Affiliation(s)
- Wenzi Ren
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Reijo Penttilä
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Risto Kasanen
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Fred O. Asiegbu
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
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Yuan Y, Bian LS, Wu YD, Chen JJ, Wu F, Liu HG, Zeng GY, Dai YC. Species diversity of pathogenic wood-rotting fungi (Agaricomycetes, Basidiomycota) in China. Mycology 2023; 14:204-226. [PMID: 37583455 PMCID: PMC10424591 DOI: 10.1080/21501203.2023.2238779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/14/2023] [Indexed: 08/17/2023] Open
Abstract
Wood-rotting basidiomycetes have been investigated in the Chinese forest ecosystem for the past 30 years. Two hundred and five pathogenic wood-decayers belonging to 9 orders, 30 families, and 74 genera have been found in Chinese native forests, plantations, and gardens. Seventy-two species (accounting for 35% of the total pathogenic species) are reported as pathogenic fungi in China for the first time. Among these pathogens, 184 species are polypores, nine are corticioid fungi, eight are agarics and five are hydnoid basidiomycetes. One hundred and seventy-seven species (accounting for 86%) cause white rot, while 28 species (accounting for 14%) result in brown rot; 157 species grow on angiosperm trees (accounting for 76.5%) and 44 species occur on gymnosperm trees (accounting for 21.5%), only four species inhabit both angiosperms and gymnosperms (accounting for 2%); 95 species are distributed in boreal to temperate forests and 110 in subtropical to tropical forests. In addition, 17 species, including Fomitopsis pinicola, Heterobasidion parviporum, and Phellinidium weirii etc. which were previously treated as pathogenic species in China, do not occur in China according to recent studies. In this paper, the host(s), type of forest, rot type, and distribution of each pathogenic species in China are given.
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Affiliation(s)
- Yuan Yuan
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Lu-Sen Bian
- Experimental Centre of Forestry in North China, Warm Temperate Zone Forestry Jiulong Mountain National Permanent Scientific Research Base, Chinese Academy of Forestry, Beijing, China
| | - Ying-Da Wu
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- Key Laboratory of Forest and Grassland Fire Risk Prevention, Ministry of Emergency Management, China Fire and Rescue Institute, Beijing, China
| | - Jia-Jia Chen
- College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang, China
| | - Fang Wu
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Hong-Gao Liu
- Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong, China
| | - Guang-Yu Zeng
- Guangxi Forestry Science Research Institute, Nanning, China
| | - Yu-Cheng Dai
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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Ecological speciation of Japanese hedgehog mushroom: Hydnum subalpinum sp. nov. is distinguished from its sister species H. repando-orientale by means of integrative taxonomy. Mycol Prog 2022. [DOI: 10.1007/s11557-022-01844-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Liu JJ, Zamany A, Cartwright C, Xiang Y, Shamoun SF, Rancourt B. Transcriptomic Reprogramming and Genetic Variations Contribute to Western Hemlock Defense and Resistance Against Annosus Root and Butt Rot Disease. FRONTIERS IN PLANT SCIENCE 2022; 13:908680. [PMID: 35845706 PMCID: PMC9279933 DOI: 10.3389/fpls.2022.908680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Western hemlock (Tsuga heterophylla) is highly susceptible to Annosus root and butt rot disease, caused by Heterobasidion occidentale across its native range in western North America. Understanding molecular mechanisms of tree defense and dissecting genetic components underlying disease resistance will facilitate forest breeding and disease control management. The aim of this study was to profile host transcriptome reprogramming in response to pathogen infection using RNA-seq analysis. Inoculated seedlings were clearly grouped into three types: quantitative resistant (QR), susceptible (Sus), and un-infected (Uif), based on profiles of H. occidentale genes expressed in host tissues. Following de novo assembly of a western hemlock reference transcriptome with more than 33,000 expressed genes, the defensive transcriptome reprogramming was characterized and a set of differentially expressed genes (DEGs) were identified with gene ontology (GO) annotation. The QR seedlings showed controlled and coordinated molecular defenses against biotic stressors with enhanced biosynthesis of terpenoids, cinnamic acids, and other secondary metabolites. The Sus seedlings showed defense responses to abiotic stimuli with a few biological processes enhanced (such as DNA replication and cell wall organization), while others were suppressed (such as killing of cells of other organism). Furthermore, non-synonymous single nucleotide polymorphisms (ns-SNPs) of the defense- and resistance-related genes were characterized with high genetic variability. Both phylogenetic analysis and principal coordinate analysis (PCoA) revealed distinct evolutionary distances among the samples. The QR and Sus seedlings were well separated and grouped into different phylogenetic clades. This study provides initial insight into molecular defense and genetic components of western hemlock resistance against the Annosus root and butt rot disease. Identification of a large number of genes and their DNA variations with annotated functions in plant resistance and defense promotes the development of genomics-based breeding strategies for improved western hemlock resistance to H. occidentale.
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Affiliation(s)
- Jun-Jun Liu
- Natural Resources Canada, Canadian Forest Service, Victoria, BC, Canada
| | - Arezoo Zamany
- Natural Resources Canada, Canadian Forest Service, Victoria, BC, Canada
| | - Charlie Cartwright
- British Columbia Ministry of Forests, Cowichan Lake Research Station, Mesachie Lake, BC, Canada
| | - Yu Xiang
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC, Canada
| | - Simon F. Shamoun
- Natural Resources Canada, Canadian Forest Service, Victoria, BC, Canada
| | - Benjamin Rancourt
- Natural Resources Canada, Canadian Forest Service, Victoria, BC, Canada
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Kashif M, Jurvansuu J, Hyder R, Vainio EJ, Hantula J. Phenotypic Recovery of a Heterobasidion Isolate Infected by a Debilitation-Associated Virus Is Related to Altered Host Gene Expression and Reduced Virus Titer. Front Microbiol 2022; 12:661554. [PMID: 35310390 PMCID: PMC8930199 DOI: 10.3389/fmicb.2021.661554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Abstract
The fungal genus Heterobasidion includes forest pathogenic species hosting a diverse group of partitiviruses. They include the host debilitating Heterobasidion partitivirus 13 strain an1 (HetPV13-an1), which was originally observed in a slowly growing H. annosum strain 94233. In this study, a relatively fast-growing sector strain 94233-RC3 was isolated from a highly debilitated mycelial culture of 94233, and its gene expression and virus transcript quantities as well as the genomic sequence of HetPV13-an1 were examined. The sequence of HetPV13-an1 genome in 94233-RC3 was identical to that in the original 94233, and thus not the reason for the partial phenotypic recovery. According to RNA-seq analysis, the HetPV13-an1 infected 94233-RC3 transcribed eight genes differently from the partitivirus-free 94233-32D. Three of these genes were downregulated and five upregulated. The number of differentially expressed genes was considerably lower and the changes in their expression were small compared to those of the highly debilitated original strain 94233 with the exception of the most highly upregulated ones, and therefore viral effects on the host transcriptome correlated with the degree of the virus-caused debilitation. The amounts of RdRp and CP transcripts of HetPV13-an1 were considerably lower in 94233-RC3 and also in 94233 strain infected by a closely related mildly debilitating virus HetPV13-an2, suggesting that the virus titer would have a role in determining the effect of HetPV13 viruses on their hosts.
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Affiliation(s)
| | | | - Rafiqul Hyder
- Natural Resources Institute Finland, Helsinki, Finland
| | - Eeva J Vainio
- Natural Resources Institute Finland, Helsinki, Finland
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Efficacy of Chemical and Biological Stump Treatments for the Control of Heterobasidion occidentale Infection of California Abies concolor. Pathogens 2021; 10:pathogens10111390. [PMID: 34832546 PMCID: PMC8621004 DOI: 10.3390/pathogens10111390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/16/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022] Open
Abstract
We conducted an experimental evaluation of treatments to limit Heterobasidion occidentale infection of white fir (Abies concolor) stumps and wounds in California mixed conifer forests. We tested the efficacy of urea, borate, and a mixture of two locally collected Phlebiopsis gigantea strains in preventing pathogen colonization of fir stumps and separately, urea and borate as infection controls on experimental stem wounds. These were paired with a laboratory test on ~100 g wood blocks with and without a one-week delay between inoculation and treatment. Urea, borates, and Phlebiopsis treatments all significantly reduced the stump surface area that was colonized by H. occidentale at 84%, 91%, and 68%, respectively, relative to the controls. However, only the borate treatments significantly lowered the number of stumps that were infected by the pathogen. The laboratory study matched the patterns that were found in the stump experiment with a reduced area of colonization for urea, borates, or P. gigantea treatments relative to the controls; delaying the treatment did not affect efficacy. The field wound experiment did not result in any Heterobasidion colonization, even in positive control treatments, rendering the experiment uninformative. Our study suggests treatments that are known to limit Heterobasidion establishment on pine or spruce stumps elsewhere in the world may also be effective on true firs in California.
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Stalpers JA, Redhead SA, May TW, Rossman AY, Crouch JA, Cubeta MA, Dai YC, Kirschner R, Langer GJ, Larsson KH, Mack J, Norvell LL, Oberwinkler F, Papp V, Roberts P, Rajchenberg M, Seifert KA, Thorn RG. Competing sexual-asexual generic names in Agaricomycotina (Basidiomycota) with recommendations for use. IMA Fungus 2021; 12:22. [PMID: 34380577 PMCID: PMC8359032 DOI: 10.1186/s43008-021-00061-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 04/03/2021] [Indexed: 11/10/2022] Open
Abstract
With the change to one scientific name for fungal taxa, generic names typified by species with sexual or asexual morph types are being evaluated to determine which names represent the same genus and thus compete for use. In this paper generic names of the Agaricomycotina (Basidiomycota) were evaluated to determine synonymy based on their type. Forty-seven sets of sexually and asexually typified names were determined to be congeneric and recommendations are made for which generic name to use. In most cases the principle of priority is followed. However, 16 generic names are recommended for use that do not have priority and thus need to be protected: Aleurocystis over Matula; Armillaria over Acurtis and Rhizomorpha; Asterophora over Ugola; Botryobasidium over Acladium, Allescheriella, Alysidium, Haplotrichum, Physospora, and Sporocephalium; Coprinellus over Ozonium; Coprinopsis over Rhacophyllus; Dendrocollybia over Sclerostilbum and Tilachlidiopsis; Diacanthodes over Bornetina; Echinoporia over Echinodia; Neolentinus over Digitellus; Postia over Ptychogaster; Riopa over Sporotrichum; Scytinostroma over Artocreas, Michenera, and Stereofomes; Tulasnella over Hormomyces; Typhula over Sclerotium; and Wolfiporia over Gemmularia and Pachyma. Nine species names are proposed for protection: Botryobasidium aureum, B. conspersum, B. croceum, B. simile, Pellicularia lembosporum (syn. B. lembosporum), Phanerochaete chrysosporium, Polyporus metamorphosus (syn. Riopa metamorphosa), Polyporus mylittae (syn. Laccocephalum mylittae), and Polyporus ptychogaster (syn. Postia ptychogaster). Two families are proposed for protection: Psathyrellaceae and Typhulaceae. Three new species names and 30 new combinations are established, and one lectotype is designated.
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Affiliation(s)
| | - Scott A Redhead
- Ottawa Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, CEF, Ottawa, Ontario, K1A OC6, Canada
| | - Tom W May
- Royal Botanic Gardens Victoria, 100 Birdwood Avenue, Melbourne, Victoria, 3004, Australia
| | - Amy Y Rossman
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA.
| | - Jo Anne Crouch
- USDA-ARS, Mycology & Nematology Genetic Diversity & Biology Laboratory, Beltsville, MD, 20705, USA
| | - Marc A Cubeta
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27606, USA
| | - Yu-Cheng Dai
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Roland Kirschner
- Department of Biomedical Sciences and Engineering, National Central University, Zhongli District, Taoyuan City, 320, Taiwan, Republic of China
| | - Gitta Jutta Langer
- Department of Forest Protection, Northwest German Forest Research Institute (NW-FVA), 37079, Goettingen, Lower Saxony, Germany
| | | | - Jonathan Mack
- Ottawa Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, CEF, Ottawa, Ontario, K1A OC6, Canada
| | | | - Franz Oberwinkler
- Lehrstuhl für Spezielle Botanik und Mykologie, Botanisches Institut, Universität, Auf der Morgenstelle 1, 72076, Tübingen, Germany
| | - Viktor Papp
- Department of Botany, Institute of Agronomy, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| | | | - Mario Rajchenberg
- Centro Forestal CIEFAP, C.C. 14, 9200, Esquel, Chubut, Argentina.,National Research Council of Argentina (CONICET), Buenos Aires, Argentina
| | - Keith A Seifert
- Department of Biology, Carlton University, Ottawa, Ontario, K1S 5B6, Canada
| | - R Greg Thorn
- Department of Biology, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
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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.
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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
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Yuan Y, Chen JJ, Korhonen K, Martin F, Dai YC. An Updated Global Species Diversity and Phylogeny in the Forest Pathogenic Genus Heterobasidion (Basidiomycota, Russulales). Front Microbiol 2021; 11:596393. [PMID: 33488542 PMCID: PMC7817714 DOI: 10.3389/fmicb.2020.596393] [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] [Received: 08/19/2020] [Accepted: 11/30/2020] [Indexed: 11/28/2022] Open
Abstract
Heterobasidion species are amongst the most intensively studied polypores because several species are aggressive white rot pathogens of managed coniferous forests mainly in Europe and North America. In the present study, both morphological and multilocus phylogenetic analyses were carried out on Heterobasidion samples from Asia, Oceania, Europe and North America. Three new taxa were found, i.e., H. armandii, H. subinsulare, and H. subparviporum are from Asia and are described as new species. H. ecrustosum is treated as a synonym of H. insulare. So far, six taxa in the H. annosum species complex are recognized. Heterobasidion abietinum, H. annosum, and H. parviporum occur in Europe, H. irregulare, and H. occidentale in North America, and H. subparviporum in East Asia. The North American H. irregulare was introduced to Italy during the Second World War. Species in the H. annosum complex are pathogens of coniferous trees, except H. subparviporum that seems to be a saprotroph. Ten species are found in the H. insulare species complex, all of them are saprotrophs. The pathogenic species are distributed in Europe and North America; the Asian countries should consider the European and North American species as entry plant quarantine fungi. Parallelly, European countries should consider the American H. occidentale and H. irregulare as entry plant quarantine fungi although the latter species is already in Italy, while North America should treat H. abietinum, H. annosum s.s., and H. parviporum as entry plant quarantine fungi. Eight Heterobasidion species found in the Himalayas suggest that the ancestral Heterobasidion species may have occurred in Asia.
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Affiliation(s)
- Yuan Yuan
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Jia-Jia Chen
- Permanent Research Base of National Forestry and Grassland Administration, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang, China
| | - Kari Korhonen
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Francis Martin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,University of Lorraine, INRAE, Tree-Microbes Interaction Department, Champenoux, France
| | - Yu-Cheng Dai
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
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11
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Seierstad KS, Fossdal R, Miettinen O, Carlsen T, Skrede I, Kauserud H. Contrasting genetic structuring in the closely related basidiomycetes Trichaptum abietinum and Trichaptum fuscoviolaceum (Hymenochaetales). Fungal Biol 2020; 125:269-275. [PMID: 33766305 DOI: 10.1016/j.funbio.2020.11.001] [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: 05/04/2020] [Revised: 11/09/2020] [Accepted: 11/13/2020] [Indexed: 10/23/2022]
Abstract
Trichaptum abietinum and Trichaptum fuscoviolaceum (Hymenochaetales, Basidiomycota) are closely related saprotrophic fungi, widely distributed on coniferous wood in temperate regions worldwide. Three intersterility groups have previously been detected in T. abietinum, while no prezygotic barriers have been proven within T. fuscoviolaceum. The aim of this study was to reveal the phylogeography and genetic relationship between these two closely related species and to explore whether the previously observed intersterility groups in T. abietinum are reflected in the genetic data. We assembled worldwide fruit body collections of both species (N = 314) and generated DNA sequences from three nuclear (ITS2, LSU, IGS) and one mitochondrial rDNA region (mtLSU). The two species are genetically well separated in all analyses. In correspondence with observations from earlier mating studies, our results revealed that T. fuscoviolaceum is genetically more uniform than T. abietinum. Multiple genetic sub-groups exist in T. abietinum that may correspond to the previously observed intersterility groups. However, there is low consistency across the investigated loci in delimiting the different sub-groups, except for a consistent North American group. As for many other widespread fungi, a complex phylogeographic pattern is found in T. abietinum which may have been formed by geographic, as well as multiple genetic intersterility barriers.
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Affiliation(s)
- Kristian Skaven Seierstad
- Integrative Systematics of Plant and Fungi, Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, NO-0318, Oslo, Norway; Evogene, Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway.
| | - Renate Fossdal
- Evogene, Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway
| | - Otto Miettinen
- Botanical Museum, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, Finland
| | - Tor Carlsen
- Evogene, Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway
| | - Inger Skrede
- Evogene, Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway
| | - Håvard Kauserud
- Evogene, Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway
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Jayawardena RS, Hyde KD, Chen YJ, Papp V, Palla B, Papp D, Bhunjun CS, Hurdeal VG, Senwanna C, Manawasinghe IS, Harischandra DL, Gautam AK, Avasthi S, Chuankid B, Goonasekara ID, Hongsanan S, Zeng X, Liyanage KK, Liu N, Karunarathna A, Hapuarachchi KK, Luangharn T, Raspé O, Brahmanage R, Doilom M, Lee HB, Mei L, Jeewon R, Huanraluek N, Chaiwan N, Stadler M, Wang Y. One stop shop IV: taxonomic update with molecular phylogeny for important phytopathogenic genera: 76–100 (2020). FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00460-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractThis is a continuation of a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi and fungus-like organisms. This paper focuses on one family: Erysiphaceae and 24 phytopathogenic genera: Armillaria, Barriopsis, Cercospora, Cladosporium, Clinoconidium, Colletotrichum, Cylindrocladiella, Dothidotthia,, Fomitopsis, Ganoderma, Golovinomyces, Heterobasidium, Meliola, Mucor, Neoerysiphe, Nothophoma, Phellinus, Phytophthora, Pseudoseptoria, Pythium, Rhizopus, Stemphylium, Thyrostroma and Wojnowiciella. Each genus is provided with a taxonomic background, distribution, hosts, disease symptoms, and updated backbone trees. Species confirmed with pathogenicity studies are denoted when data are available. Six of the genera are updated from previous entries as many new species have been described.
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Sadowska A, Zapora E, Sawicka D, Niemirowicz-Laskowska K, Surażyński A, Sułkowska-Ziaja K, Kała K, Stocki M, Wołkowycki M, Bakier S, Pawlik A, Jaszek M, Muszyńska B, Car H. Heterobasidion annosum Induces Apoptosis in DLD-1 Cells and Decreases Colon Cancer Growth in In Vivo Model. Int J Mol Sci 2020; 21:ijms21103447. [PMID: 32414138 PMCID: PMC7279362 DOI: 10.3390/ijms21103447] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/07/2020] [Accepted: 05/09/2020] [Indexed: 12/20/2022] Open
Abstract
Application of substances from medicinal mushrooms is one of the interesting approaches to improve cancer therapy. In this study, we commenced a new attempt in the field of Heterobasidion annosum (Fr.) Bref. sensu lato to further extend our knowledge on this basidiomycete fungus. For this purpose, analysis of the active substances of Heterobasidion annosum methanolic extract and also its influence on colorectal cancer in terms of in vitro and in vivo experiments were performed. In vivo studies on mice were conducted to verify its acute toxicity and to further affirm its anticancer potential. Results indicated that all the most common substances of best known medicinal mushrooms that are also responsible for their biological activity are present in tested extracts. In vitro tests showed a high hemocompatibility and a significant decrease in viability and proliferation of DLD-1 cells in a concentration-dependent manner of Heterobasidion annosum extract. The studies performed on xenograft model of mice showed lower tendency of tumor growth in the group of mice receiving Heterobasidion annosum extract as well as mild or moderate toxicity. Obtained results suggest beneficial potential of Heterobasidion annosum against colon cancer as cytotoxic agent or as adjuvant anticancer therapy.
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Affiliation(s)
- Anna Sadowska
- Department of Experimental Pharmacology, Medical University of Białystok, Szpitalna 37, 15-295 Bialystok, Poland; (D.S.); (K.N.-L.); (H.C.)
- Correspondence: ; Tel.: +48-85-748-5554
| | - Ewa Zapora
- Institute of Forest Sciences, Bialystok University of Technology, Wiejska 45E, 15-351 Bialystok, Poland; (E.Z.); (M.S.); (M.W.); (S.B.)
| | - Diana Sawicka
- Department of Experimental Pharmacology, Medical University of Białystok, Szpitalna 37, 15-295 Bialystok, Poland; (D.S.); (K.N.-L.); (H.C.)
| | - Katarzyna Niemirowicz-Laskowska
- Department of Experimental Pharmacology, Medical University of Białystok, Szpitalna 37, 15-295 Bialystok, Poland; (D.S.); (K.N.-L.); (H.C.)
| | - Arkadiusz Surażyński
- Department of Medicinal Chemistry, Medical University of Bialystok, Mickiewicza 2D, 15-222 Bialystok, Poland;
| | - Katarzyna Sułkowska-Ziaja
- Department of Pharmaceutical Botany, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland; (K.S.-Z.); (K.K.); (B.M.)
| | - Katarzyna Kała
- Department of Pharmaceutical Botany, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland; (K.S.-Z.); (K.K.); (B.M.)
| | - Marcin Stocki
- Institute of Forest Sciences, Bialystok University of Technology, Wiejska 45E, 15-351 Bialystok, Poland; (E.Z.); (M.S.); (M.W.); (S.B.)
| | - Marek Wołkowycki
- Institute of Forest Sciences, Bialystok University of Technology, Wiejska 45E, 15-351 Bialystok, Poland; (E.Z.); (M.S.); (M.W.); (S.B.)
| | - Sławomir Bakier
- Institute of Forest Sciences, Bialystok University of Technology, Wiejska 45E, 15-351 Bialystok, Poland; (E.Z.); (M.S.); (M.W.); (S.B.)
| | - Anna Pawlik
- Department of Biochemistry and Biotechnology, Maria Curie Sklodowska University, Akademicka 19, 20-033 Lublin, Poland; (A.P.); (M.J.)
| | - Magdalena Jaszek
- Department of Biochemistry and Biotechnology, Maria Curie Sklodowska University, Akademicka 19, 20-033 Lublin, Poland; (A.P.); (M.J.)
| | - Bożena Muszyńska
- Department of Pharmaceutical Botany, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland; (K.S.-Z.); (K.K.); (B.M.)
| | - Halina Car
- Department of Experimental Pharmacology, Medical University of Białystok, Szpitalna 37, 15-295 Bialystok, Poland; (D.S.); (K.N.-L.); (H.C.)
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Hu Y, Elfstrand M, Stenlid J, Durling MB, Olson Å. The conifer root rot pathogens Heterobasidion irregulare and Heterobasidion occidentale employ different strategies to infect Norway spruce. Sci Rep 2020; 10:5884. [PMID: 32246017 PMCID: PMC7125170 DOI: 10.1038/s41598-020-62521-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 03/10/2020] [Indexed: 11/16/2022] Open
Abstract
Heterobasidion irregulare and H. occidentale are two closely related conifer root rot pathogens in the H. annosum sensu lato (s.l.) species complex. The two species H. irregulare and H. occidentale have different host preference with pine and non-pine tree species favored, respectively. The comparison of transcriptomes of H. irregulare and H. occidentale growing in Norway spruce bark, a susceptible host non-native to North America, showed large differences in gene expression. Heterobasidion irregulare induced more genes involved in detoxification of host compounds and in production of secondary metabolites, while the transcriptome induced in H. occidentale was more oriented towards carbohydrate degradation. Along with their separated evolutionary history, the difference might be driven by their host preferences as indicated by the differentially expressed genes enriched in particular Gene Ontology terms.
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Affiliation(s)
- Yang Hu
- Zhejiang Academy of Forestry, Liuhe Road, 310023, Hangzhou, China.,Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 05, Uppsala, Sweden
| | - Malin Elfstrand
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 05, Uppsala, Sweden
| | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 05, Uppsala, Sweden
| | - Mikael Brandström Durling
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 05, Uppsala, Sweden
| | - Åke Olson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 05, Uppsala, Sweden.
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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.
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New Taxon-Specific Heterobasidion PCR Primers Detect and Differentiate North American Heterobasidion spp. in Various Substrates and Led to the Discovery of Heterobasidion irregulare in British Columbia, Canada. Pathogens 2019; 8:pathogens8030156. [PMID: 31540403 PMCID: PMC6789490 DOI: 10.3390/pathogens8030156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/10/2019] [Accepted: 09/13/2019] [Indexed: 11/16/2022] Open
Abstract
Heterobasidion annosum sensu lato is a species complex of pathogenic white-rot wood decay fungi which cause root and butt rot in conifer and hardwood species across the Northern hemisphere. Annual losses to forest managers are valued in the billions of dollars, due to tree mortality, reduction in timber yield, and wood decay. In North America, H. irregulare and H. occidentale have a partially overlapping host and geographic range, cause similar disease symptoms and produce similar fruiting bodies, making discrimination between the two of them often difficult. We developed two sets of primers that bind specifically to conserved, but species-specific portions of glyceraldehyde 3-phosphate dehydrogenase and elongation factor 1α alleles. The method is sensitive enough to detect either species from infected wood. Analysis of North American isolates has further clarified the distribution of both species on this continent, including the detection of H. irregulare for the first time on ponderosa pine (Pinus ponderosa) and eastern white pine (Pinus strobus) in British Columbia. This method has the potential to be a valuable tool for the detection of the pathogen in exported/imported wood products, as well as for the further identification and assessment of the distribution of North American Heterobasidion species.
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17
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Sillo F, Gonthier P, Lockman B, Kasuga T, Garbelotto M. Molecular analyses identify hybridization-mediated nuclear evolution in newly discovered fungal hybrids. Ecol Evol 2019; 9:6588-6605. [PMID: 31236246 PMCID: PMC6580273 DOI: 10.1002/ece3.5238] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/14/2019] [Accepted: 04/23/2019] [Indexed: 12/14/2022] Open
Abstract
Hybridization may be a major driver in the evolution of plant pathogens. In a high elevation Alpine larch stand in Montana, a novel hybrid fungal pathogen of trees originating from the mating of Heterobasidion irregulare with H. occidentale has been recently discovered. In this study, sequence analyses of one mitochondrial and four nuclear loci from 11 Heterobasidion genotypes collected in the same Alpine larch stand indicated that hybridization has increased allelic diversity by generating novel polymorphisms unreported in either parental species. Sequence data and ploidy analysis through flow cytometry confirmed that heterokaryotic (n + n) genotypes were not first-generation hybrids, but were the result of multiple backcrosses, indicating hybrids are fertile. Additionally, all admixed genotypes possessed the H. occidentale mitochondrion, indicating that the hybrid progeny may have been backcrossing mostly with H. occidentale. Based on reticulate phylogenetic network analysis by PhyloNet, Bayesian assignment, and ordination tests, alleles can be defined as H. irregulare-like or H. occidentale-like. H. irregulare-like alleles are clearly distinct from all known H. irregulare alleles and are derived from the admixing of both Heterobasidion species. Instead, all but one H. occidentale alleles found in hybrids, although novel, were not clearly distinct from alleles found in the parental H. occidentale population. This discovery demonstrates that Alpine larch can be a universal host favouring the interspecific hybridization between H. irregulare and H. occidentale and the hybridization-mediated evolution of a nucleus, derived from H. irregulare parental species but clearly distinct from it.
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Affiliation(s)
- Fabiano Sillo
- Department of Agricultural, Forest and Food Sciences (DISAFA)University of TorinoGrugliasco (TO)Italy
| | - Paolo Gonthier
- Department of Agricultural, Forest and Food Sciences (DISAFA)University of TorinoGrugliasco (TO)Italy
| | - Blakey Lockman
- Pacific Northwest Region, State and Private ForestryUSDA Forest ServicePortlandOregon
| | - Takao Kasuga
- Crops Pathology and Genetics Research UnitUSDA Agricultural Research ServiceDavisCalifornia
| | - Matteo Garbelotto
- Department of Agricultural, Forest and Food Sciences (DISAFA)University of TorinoGrugliasco (TO)Italy
- Department of Environmental Science, Policy and Management, Forest Pathology and Mycology LaboratoryUniversity of California, BerkeleyBerkeleyCalifornia
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Wen Z, Raffaello T, Zeng Z, Pavicic M, Asiegbu FO. Chlorophyll fluorescence imaging for monitoring effects of Heterobasidion parviporum small secreted protein induced cell death and in planta defense gene expression. Fungal Genet Biol 2019; 126:37-49. [PMID: 30763724 DOI: 10.1016/j.fgb.2019.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 01/31/2019] [Accepted: 02/08/2019] [Indexed: 02/01/2023]
Abstract
Heterobasidion parviporum Niemelä & Korhonen is a necrotrophic fungal pathogen of Norway spruce (Picea abies). The H. parviporum genome encodes numerous necrotrophic small secreted proteins (SSP) which might be important for promoting and sustaining the disease development. However, their transcriptional dynamics and plant defense response during infection are largely unknown. In this study, we identified a necrotrophic SSP named HpSSP35.8 and its coding gene was highly expressed in the pre-symptomatic phase of the host (Norway spruce) infection. We explored the impact of HpSSP35.8 on non-host Nicotiana benthamiana using Agrobacterium-mediated transient expression system under visible spectrum RGB imaging and chlorophyll fluorescence imaging. The results showed that HpSSP35.8 triggered a form of SSP-associated programmed cell death, accompanied by a decrease in the plant photosynthetic activity. Defense-related genes including WRKY12, ethylene response factor (ERF1α) and a chitinase gene PR4 were up-regulated in both HpSSP35.8-N. benthamiana interaction and H. parviporum-Norway spruce pathosystem. This study also highlighted the potential to use the chlorophyll fluorescence imaging approach to monitor both the indirect effects of SSP and also for the selection of other potential effector-like protein candidates.
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Affiliation(s)
- Zilan Wen
- Faculty of Agriculture and Forestry, P. O. Box 27, Latokartanonkaari 7, 00014, University of Helsinki, Helsinki, Finland; Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Tommaso Raffaello
- Faculty of Agriculture and Forestry, P. O. Box 27, Latokartanonkaari 7, 00014, University of Helsinki, Helsinki, Finland
| | - Zhen Zeng
- Faculty of Agriculture and Forestry, P. O. Box 27, Latokartanonkaari 7, 00014, University of Helsinki, Helsinki, Finland; Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Mirko Pavicic
- Faculty of Agriculture and Forestry, P. O. Box 27, Latokartanonkaari 7, 00014, University of Helsinki, Helsinki, Finland; Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Fred O Asiegbu
- Faculty of Agriculture and Forestry, P. O. Box 27, Latokartanonkaari 7, 00014, University of Helsinki, Helsinki, Finland; Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
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19
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Pepori AL, Michelozzi M, Santini A, Cencetti G, Bonello P, Gonthier P, Sebastiani F, Luchi N. Comparative transcriptional and metabolic responses of Pinus pinea to a native and a non-native Heterobasidion species. TREE PHYSIOLOGY 2019; 39:31-44. [PMID: 30137615 DOI: 10.1093/treephys/tpy086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 07/31/2018] [Indexed: 05/28/2023]
Abstract
Heterobasidion irregulare is a causal agent of root and butt-rot disease in conifers, and is native to North America. In 1944 it was introduced in central Italy in a Pinus pinea stand, where it shares the same niche with the native species Heterobasidion annosum. The introduction of a non-native pathogen may have significant negative effects on a naïve host tree and the ecosystem in which it resides, requiring a better understanding of the system. We compared the spatio-temporal phenotypic, transcriptional and metabolic host responses to inoculation with the two Heterobasidion species in a large experiment with P. pinea seedlings. Differences in length of lesions at the inoculation site (IS), expression of host genes involved in lignin pathway and in cell rescue and defence, and analysis of terpenes at both IS and 12 cm above the IS (distal site, DS), were assessed at 3, 14 and 35 days post inoculation (dpi). Results clearly showed that both species elicit similar physiological and biochemical responses in P. pinea seedlings. The analysis of host transcripts and total terpenes showed differences between inoculation sites and between pathogen and mock inoculated plants. Both pathogen and mock inoculations induced antimicrobial peptide and phenylalanine ammonia-lyase overexpression at IS beginning at 3 dpi; while at DS all the analysed genes, except for peroxidase, were overexpressed at 14 dpi. A significantly higher accumulation of terpenoids was observed at 14 dpi at IS, and at 35 dpi at DS. The terpene blend at IS showed significant variation among treatments and sampling times, while no significant differences were ever observed in DS tissues. Based on our results, H. irregulare does not seem to have competitive advantages over the native species H. annosum in terms of pathogenicity towards P. pinea trees; this may explain why the non-native species has not widely spread over the 73 years since its putative year of introduction into central Italy.
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Affiliation(s)
- Alessia Lucia Pepori
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano, Sesto Fiorentino (FI), Italy
| | - Marco Michelozzi
- Institute of Biosciences and Bioresources, National Research Council (IBBR-CNR), Via Madonna del Piano, Sesto Fiorentino (FI), Italy
| | - Alberto Santini
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano, Sesto Fiorentino (FI), Italy
| | - Gabriele Cencetti
- Institute of Biosciences and Bioresources, National Research Council (IBBR-CNR), Via Madonna del Piano, Sesto Fiorentino (FI), Italy
| | - Pierluigi Bonello
- Department of Plant Pathology, The Ohio State University, 201 Kottman Hall, 2021 Coffey Rd, Columbus, OH, USA
| | - Paolo Gonthier
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Largo Paolo Braccini 2, Grugliasco, TO, Italy
| | - Federico Sebastiani
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano, Sesto Fiorentino (FI), Italy
| | - Nicola Luchi
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano, Sesto Fiorentino (FI), Italy
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Liu B, Krishnaswamyreddy S, Muraleedharan MN, Olson Å, Broberg A, Ståhlberg J, Sandgren M. Side-by-side biochemical comparison of two lytic polysaccharide monooxygenases from the white-rot fungus Heterobasidion irregulare on their activity against crystalline cellulose and glucomannan. PLoS One 2018; 13:e0203430. [PMID: 30183773 PMCID: PMC6124812 DOI: 10.1371/journal.pone.0203430] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 08/21/2018] [Indexed: 11/18/2022] Open
Abstract
Our comparative studies reveal that the two lytic polysaccharide monooxygenases HiLPMO9B and HiLPMO9I from the white-rot conifer pathogen Heterobasidion irregulare display clear difference with respect to their activity against crystalline cellulose and glucomannan. HiLPMO9I produced very little soluble sugar on bacterial microcrystalline cellulose (BMCC). In contrast, HiLPMO9B was much more active against BMCC and even released more soluble sugar than the H. irregulare cellobiohydrolase I, HiCel7A. Furthermore, HiLPMO9B was shown to cooperate with and stimulate the activity of HiCel7A, both when the BMCC was first pretreated with HiLPMO9B, as well as when HiLPMO9B and HiCel7A were added together. No such stimulation was shown by HiLPMO9I. On the other hand, HiLPMO9I was shown to degrade glucomannan, using a C4-oxidizing mechanism, whereas no oxidative cleavage activity of glucomannan was detected for HiLPMO9B. Structural modeling and comparison with other glucomannan-active LPMOs suggest that conserved sugar-interacting residues on the L2, L3 and LC loops may be essential for glucomannan binding, where 4 out of 7 residues are shared by HiLPMO9I, but only one is found in HiLPMO9B. The difference shown between these two H. irregulare LPMOs may reflect distinct biological roles of these enzymes within deconstruction of different plant cell wall polysaccharides during fungal colonization of softwood.
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Affiliation(s)
- Bing Liu
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Madhu Nair Muraleedharan
- Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
| | - Åke Olson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders Broberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
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Korhonen A, Seelan JSS, Miettinen O. Cryptic species diversity in polypores: the Skeletocutis nivea species complex. MycoKeys 2018; 36:45-82. [PMID: 30057481 PMCID: PMC6060227 DOI: 10.3897/mycokeys.36.27002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 07/07/2018] [Indexed: 11/12/2022] Open
Abstract
We propose a taxonomic revision of the two closely related white-rot polypore species, Skeletocutis nivea (Jungh.) Jean Keller and S. ochroalba Niemelä (Incrustoporiaceae, Basidiomycota), based on phylogenetic analyses of nuclear ribosomal internal transcribed spacer (ITS) and translation elongation factor EF-1α sequences. We show that prevailing morphological species concepts of S. nivea and S. ochroalba are non-monophyletic and we delineate new species boundaries based on phylogenetic inference. We recognise eleven species within the prevailing species concept of S. nivea (S. calidasp. nov., S. coprosmae comb. nov., S. futilissp. nov., S. imperviasp. nov., S. ipuletiisp. nov., S. lepidasp. nov., S. nemoralissp. nov., S. nivea sensu typi, S. semipileata comb. nov., S. unguinasp. nov. and S. yuchengiisp. nov.) and assign new sequenced epitypes for S. nivea and S. semipileata. The traditional concept of S. ochroalba comprises two independent lineages embedded within the S. nivea species complex. The Eurasian conifer-dwelling species S. cummatasp. nov. is recognised as separate from the North American S. ochroalba sensu stricto. Despite comprehensive microscopic examination, the majority of the recognised species are left without stable diagnostic character combinations that would enable species identification based solely on morphology and ecology.
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Affiliation(s)
- Aku Korhonen
- Finnish Museum of Natural History, University of Helsinki, PO Box 7, 00014 University of Helsinki, Finland
- Natural Resources Institute Finland (Luke), PO Box 2 (Latokartanonkaari 9), FI-00791, Helsinki, Finland
| | - Jaya Seelan Sathiya Seelan
- Mycology and Pathology Laboratory, Institute for Tropical Biology and Conservation (ITBC), Universiti Malaysia Sabah, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Otto Miettinen
- Finnish Museum of Natural History, University of Helsinki, PO Box 7, 00014 University of Helsinki, Finland
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Liu J, Shamoun SF, Leal I, Kowbel R, Sumampong G, Zamany A. Characterization of Heterobasidion occidentale transcriptomes reveals candidate genes and DNA polymorphisms for virulence variations. Microb Biotechnol 2018; 11:537-550. [PMID: 29611344 PMCID: PMC5954486 DOI: 10.1111/1751-7915.13259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/09/2018] [Accepted: 02/13/2018] [Indexed: 11/29/2022] Open
Abstract
Characterization of genes involved in differentiation of pathogen species and isolates with variations of virulence traits provides valuable information to control tree diseases for meeting the challenges of sustainable forest health and phytosanitary trade issues. Lack of genetic knowledge and genomic resources hinders novel gene discovery, molecular mechanism studies and development of diagnostic tools in the management of forest pathogens. Here, we report on transcriptome profiling of Heterobasidion occidentale isolates with contrasting virulence levels. Comparative transcriptomic analysis identified orthologous groups exclusive to H. occidentale and its isolates, revealing biological processes involved in the differentiation of isolates. Further bioinformatics analyses identified an H. occidentale secretome, CYPome and other candidate effectors, from which genes with species- and isolate-specific expression were characterized. A large proportion of differentially expressed genes were revealed to have putative activities as cell wall modification enzymes and transcription factors, suggesting their potential roles in virulence and fungal pathogenesis. Next, large numbers of simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were detected, including more than 14 000 interisolate non-synonymous SNPs. These polymorphic loci and species/isolate-specific genes may contribute to virulence variations and provide ideal DNA markers for development of diagnostic tools and investigation of genetic diversity.
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Affiliation(s)
- Jun‐Jun Liu
- Natural Resources CanadaCanadian Forest ServicePacific Forestry Centre506 West Burnside RoadVictoriaBCV8Z 1M5Canada
| | - Simon Francis Shamoun
- Natural Resources CanadaCanadian Forest ServicePacific Forestry Centre506 West Burnside RoadVictoriaBCV8Z 1M5Canada
| | - Isabel Leal
- Natural Resources CanadaCanadian Forest ServicePacific Forestry Centre506 West Burnside RoadVictoriaBCV8Z 1M5Canada
| | - Robert Kowbel
- Natural Resources CanadaCanadian Forest ServicePacific Forestry Centre506 West Burnside RoadVictoriaBCV8Z 1M5Canada
| | - Grace Sumampong
- Natural Resources CanadaCanadian Forest ServicePacific Forestry Centre506 West Burnside RoadVictoriaBCV8Z 1M5Canada
| | - Arezoo Zamany
- Natural Resources CanadaCanadian Forest ServicePacific Forestry Centre506 West Burnside RoadVictoriaBCV8Z 1M5Canada
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Liu B, Olson Å, Wu M, Broberg A, Sandgren M. Biochemical studies of two lytic polysaccharide monooxygenases from the white-rot fungus Heterobasidion irregulare and their roles in lignocellulose degradation. PLoS One 2017; 12:e0189479. [PMID: 29228039 PMCID: PMC5724852 DOI: 10.1371/journal.pone.0189479] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 11/27/2017] [Indexed: 12/05/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMO) are important redox enzymes produced by microorganisms for the degradation of recalcitrant natural polysaccharides. Heterobasidion irregulare is a white-rot phytopathogenic fungus that causes wood decay in conifers. The genome of this fungus encodes 10 putative Auxiliary Activity family 9 (AA9) LPMOs. We describe the first biochemical characterization of H. irregulare LPMOs through heterologous expression of two CBM-containing LPMOs from this fungus (HiLPMO9H, HiLPMO9I) in Pichia pastoris. The oxidization preferences and substrate specificities of these two enzymes were determined. The two LPMOs were shown to cleave different carbohydrate components of plant cell walls. HiLPMO9H was active on cellulose and oxidized the substrate at the C1 carbon of the pyranose ring at β-1,4-glycosidic linkages, whereas HiLPMO9I cleaved cellulose with strict oxidization at the C4 carbon of glucose unit at internal bonds, and also showed activity against glucomannan. We propose that the two LPMOs play different roles in the plant-cell-wall degrading system of H. irregulare for degradation of softwood and that the lignocellulose degradation mediated by this white-rot fungus may require collective efforts from multi-types of LPMOs.
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Affiliation(s)
- Bing Liu
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Åke Olson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Miao Wu
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders Broberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
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Choi J, Lee GW, Kim KT, Jeon J, Détry N, Kuo HC, Sun H, Asiegbu FO, Lee YH. Comparative analysis of genome sequences of the conifer tree pathogen, Heterobasidion annosum s.s. GENOMICS DATA 2017; 14:106-113. [PMID: 29085779 PMCID: PMC5654758 DOI: 10.1016/j.gdata.2017.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/21/2017] [Accepted: 10/15/2017] [Indexed: 01/09/2023]
Abstract
The causal agent of root and butt rot of conifer trees, Heterobasidion annosum, is widespread in boreal forests and economically responsible for annual loss of approximately 50 million euros to forest industries in Finland alone and much more at European level. In order to further understand the pathobiology of this fungus at the genome level, a Finnish isolate of H. annosum sensu stricto (isolate 03012) was sequenced and analyzed with the genome sequences of 23 white-rot and 13 brown-rot fungi. The draft genome assembly of H. annosum has a size of 31.01 Mb, containing 11,453 predicted genes. Whole genome alignment showed that 84.38% of H. annosum genome sequences were aligned with those of previously sequenced H. irregulare TC 32-1 counterparts. The result is further supported by the protein sequence clustering analysis which revealed that the two genomes share 6719 out of 8647 clusters. When sequencing reads of H. annosum were aligned against the genome sequences of H. irregulare, six single nucleotide polymorphisms were found in every 1 kb, on average. In addition, 98.68% of SNPs were found to be homo-variants, suggesting that the two species have long evolved from different niches. Gene family analysis revealed that most of the white-rot fungi investigated had more gene families involved in lignin degradation or modification, including laccases and peroxidase. Comparative analysis of the two Heterobasidion spp. as well as white-/brown-rot fungi would provide new insights for understanding the pathobiology of the conifer tree pathogen.
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Affiliation(s)
- Jaeyoung Choi
- Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Gir-Won Lee
- National Instrumentation Center for Environmental Management, Seoul National University, Seoul 08826, Republic of Korea
| | - Ki-Tae Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Jongbum Jeon
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Nicolas Détry
- Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Hsiao-Che Kuo
- Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Hui Sun
- Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Fred O Asiegbu
- Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Yong-Hwan Lee
- Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland.,Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea.,Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
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25
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Raffaello T, Asiegbu FO. Small secreted proteins from the necrotrophic conifer pathogen Heterobasidion annosum s.l. (HaSSPs) induce cell death in Nicotiana benthamiana. Sci Rep 2017; 7:8000. [PMID: 28801666 PMCID: PMC5554239 DOI: 10.1038/s41598-017-08010-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 07/05/2017] [Indexed: 01/07/2023] Open
Abstract
The basidiomycete Heterobasidion annosum sensu lato (s.l.) is considered to be one of the most destructive conifer pathogens in the temperate forests of the northern hemisphere. H. annosum is characterized by a dual fungal lifestyle. The fungus grows necrotrophically on living plant cells and saprotrophically on dead wood material. In this study, we screened the H. annosum genome for small secreted proteins (HaSSPs) that could potentially be involved in promoting necrotrophic growth during the fungal infection process. The final list included 58 HaSSPs that lacked predictable protein domains. The transient expression of HaSSP encoding genes revealed the ability of 8 HaSSPs to induce cell chlorosis and cell death in Nicotiana benthamiana. In particular, one protein (HaSSP30) could induce a rapid, strong, and consistent cell death within 2 days post-infiltration. HaSSP30 also increased the transcription of host-defence-related genes in N. benthamiana, which suggested a necrotrophic-specific immune response. This is the first line of evidence demonstrating that the H. annosum genome encodes HaSSPs with the capability to induce plant cell death in a non-host plant.
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Affiliation(s)
- Tommaso Raffaello
- Department of Forest Sciences, University of Helsinki, Faculty of Agriculture and Forestry, Latokartanonkaari 7, 00014, Helsinki, Finland
| | - Fred O Asiegbu
- Department of Forest Sciences, University of Helsinki, Faculty of Agriculture and Forestry, Latokartanonkaari 7, 00014, Helsinki, Finland.
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26
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Dalman K, Wind JJ, Nemesio-Gorriz M, Hammerbacher A, Lundén K, Ezcurra I, Elfstrand M. Overexpression of PaNAC03, a stress induced NAC gene family transcription factor in Norway spruce leads to reduced flavonol biosynthesis and aberrant embryo development. BMC PLANT BIOLOGY 2017; 17:6. [PMID: 28061815 PMCID: PMC5219727 DOI: 10.1186/s12870-016-0952-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 12/15/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND The NAC family of transcription factors is one of the largest gene families of transcription factors in plants and the conifer NAC gene family is at least as large, or possibly larger, as in Arabidopsis. These transcription factors control both developmental and stress induced processes in plants. Yet, conifer NACs controlling stress induced processes has received relatively little attention. This study investigates NAC family transcription factors involved in the responses to the pathogen Heterobasidion annosum (Fr.) Bref. sensu lato. RESULTS The phylogeny and domain structure in the NAC proteins can be used to organize functional specificities, several well characterized stress-related NAC proteins are found in III-3 in Arabidopsis (Jensen et al. Biochem J 426:183-196, 2010). The Norway spruce genome contain seven genes with similarity to subgroup III-3 NACs. Based on the expression pattern PaNAC03 was selected for detailed analyses. Norway spruce lines overexpressing PaNAC03 exhibited aberrant embryo development in response to maturation initiation and 482 misregulated genes were identified in proliferating cultures. Three key genes in the flavonoid biosynthesis pathway: a CHS, a F3'H and PaLAR3 were consistently down regulated in the overexpression lines. In accordance, the overexpression lines showed reduced levels of specific flavonoids, suggesting that PaNAC03 act as a repressor of this pathway, possibly by directly interacting with the promoter of the repressed genes. However, transactivation studies of PaNAC03 and PaLAR3 in Nicotiana benthamiana showed that PaNAC03 activated PaLAR3A, suggesting that PaNAC03 does not act as an independent negative regulator of flavan-3-ol production through direct interaction with the target flavonoid biosynthetic genes. CONCLUSIONS PaNAC03 and its orthologs form a sister group to well characterized stress-related angiosperm NAC genes and at least PaNAC03 is responsive to biotic stress and appear to act in the control of defence associated secondary metabolite production.
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Affiliation(s)
- Kerstin Dalman
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Chemistry and Biotechnology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Julia Johanna Wind
- KTH Biotechnology, Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Miguel Nemesio-Gorriz
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Almuth Hammerbacher
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
- Department of Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Karl Lundén
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ines Ezcurra
- KTH Biotechnology, Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Malin Elfstrand
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Forest Mycology and Plant Pathology, SLU, PO. Box 7026, Uppsala, 75007 Sweden
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27
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Mgbeahuruike AC, Kovalchuk A, Ubhayasekera W, Nelson DR, Yadav JS. CYPome of the conifer pathogen Heterobasidion irregulare: Inventory, phylogeny, and transcriptional analysis of the response to biocontrol. Fungal Biol 2016; 121:158-171. [PMID: 28089047 DOI: 10.1016/j.funbio.2016.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 10/25/2016] [Accepted: 11/26/2016] [Indexed: 01/16/2023]
Abstract
The molecular mechanisms underlying the interaction of the pathogen, Heterobasidion annosum s.l., the conifer tree and the biocontrol fungus, Phlebiopsis gigantea have not been fully elucidated. Members of the cytochrome P450 (CYP) protein family may contribute to the detoxification of components of chemical defence of conifer trees by H. annosum during infection. Additionally, they may also be involved in the interaction between H. annosum and P. gigantea. A genome-wide analysis of CYPs in Heterobasidion irregulare was carried out alongside gene expression studies. According to the Standardized CYP Nomenclature criteria, the H. irregulare genome has 121 CYP genes and 17 CYP pseudogenes classified into 11 clans, 35 families, and 64 subfamilies. Tandem CYP arrays originating from gene duplications and belonging to the same family and subfamily were found. Phylogenetic analysis showed that all the families of H. irregulare CYPs were monophyletic groups except for the family CYP5144. Microarray analysis revealed the transcriptional pattern for 130 transcripts of CYP-encoding genes during growth on culture filtrate produced by P. gigantea. The high level of P450 gene diversity identified in this study could result from extensive gene duplications presumably caused by the high metabolic demands of H. irregulare in its ecological niches.
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Affiliation(s)
- Anthony C Mgbeahuruike
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, PMB, 420001, Enugu State, Nigeria; Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, University of Nigeria, Nsukka, PMB, 420001, Enugu State, Nigeria.
| | - Andriy Kovalchuk
- Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014 Helsinki, Finland
| | - Wimal Ubhayasekera
- Structure and Molecular Biology Program, Department of Cell and Molecular Biology, Uppsala University, Box 596, Biomedical Center, SE-751 24, Uppsala, Sweden
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee, Memphis, TN 38163, USA
| | - Jagjit S Yadav
- Environmental Genetics and Molecular Toxicology Division, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, USA
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28
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Zhou LW, Nakasone KK, Burdsall HH, Ginns J, Vlasák J, Miettinen O, Spirin V, Niemelä T, Yuan HS, He SH, Cui BK, Xing JH, Dai YC. Polypore diversity in North America with an annotated checklist. Mycol Prog 2016. [DOI: 10.1007/s11557-016-1207-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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29
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Matusick G, Nadel RL, Walker DM, Hossain MJ, Eckhardt LG. Comparative behavior of root pathogens in stems and roots of southeastern Pinus species. Fungal Biol 2016; 120:471-480. [PMID: 27020149 DOI: 10.1016/j.funbio.2015.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 12/05/2015] [Accepted: 12/26/2015] [Indexed: 10/22/2022]
Abstract
Root diseases are expected to become a greater threat to trees in the future due to accidental pathogen introductions and predicted climate changes, thus there is a need for accurate and efficient pathogenicity tests. For many root pathogens, these tests have been conducted in stems instead of roots. It, however, remains unclear whether stem and root inoculations are comparable for most fungal species. In this study we compared the growth and damage caused by five root pathogens (Grosmannia huntii, Grosmannia alacris, Leptographium procerum, Leptographium terebrantis, and Heterobasidion irregulare) in root and stem tissue of two Pinus species by inoculating mature trees and tissue amended agar in the laboratory. Most fungal species tested caused greater damage in roots of both pine hosts following inoculation. The relationship between root and stem damage was, however, similar when most combinations of pathogens were compared. These results suggest that although stem inoculations are not suitable for determining the actual damage potential of a given species, they may be viewed as a useful surrogate for root inoculations when comparing the relative pathogenicity of multiple species. When grown on amended agar, fungal species generally had greater growth in stem tissue, contrasting with the findings from tree inoculations.
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Affiliation(s)
- George Matusick
- School of Forestry and Wildlife Sciences, Auburn University, 602 Duncan Drive, Auburn, AL 36849-5418, USA.
| | - Ryan L Nadel
- School of Forestry and Wildlife Sciences, Auburn University, 602 Duncan Drive, Auburn, AL 36849-5418, USA
| | - David M Walker
- Department of Forest Resources and Environmental Conservation, Virginia Tech University, 4800 Phillips Rd., Hiwassee, VA 24347, USA
| | - Mohammad J Hossain
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences, Auburn, AL 36849, USA
| | - Lori G Eckhardt
- School of Forestry and Wildlife Sciences, Auburn University, 602 Duncan Drive, Auburn, AL 36849-5418, USA
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30
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Baral B, Kovalchuk A, Asiegbu FO. Genome organisation and expression profiling of ABC protein-encoding genes in Heterobasidion annosum s.l. complex. Fungal Biol 2016; 120:376-84. [DOI: 10.1016/j.funbio.2015.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 11/05/2015] [Accepted: 11/12/2015] [Indexed: 11/29/2022]
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31
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Sillo F, Garbelotto M, Friedman M, Gonthier P. Comparative Genomics of Sibling Fungal Pathogenic Taxa Identifies Adaptive Evolution without Divergence in Pathogenicity Genes or Genomic Structure. Genome Biol Evol 2015; 7:3190-206. [PMID: 26527650 PMCID: PMC4700942 DOI: 10.1093/gbe/evv209] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2015] [Indexed: 12/27/2022] Open
Abstract
It has been estimated that the sister plant pathogenic fungal species Heterobasidion irregulare and Heterobasidion annosum may have been allopatrically isolated for 34-41 Myr. They are now sympatric due to the introduction of the first species from North America into Italy, where they freely hybridize. We used a comparative genomic approach to 1) confirm that the two species are distinct at the genomic level; 2) determine which gene groups have diverged the most and the least between species; 3) show that their overall genomic structures are similar, as predicted by the viability of hybrids, and identify genomic regions that instead are incongruent; and 4) test the previously formulated hypothesis that genes involved in pathogenicity may be less divergent between the two species than genes involved in saprobic decay and sporulation. Results based on the sequencing of three genomes per species identified a high level of interspecific similarity, but clearly confirmed the status of the two as distinct taxa. Genes involved in pathogenicity were more conserved between species than genes involved in saprobic growth and sporulation, corroborating at the genomic level that invasiveness may be determined by the two latter traits, as documented by field and inoculation studies. Additionally, the majority of genes under positive selection and the majority of genes bearing interspecific structural variations were involved either in transcriptional or in mitochondrial functions. This study provides genomic-level evidence that invasiveness of pathogenic microbes can be attained without the high levels of pathogenicity presumed to exist for pathogens challenging naïve hosts.
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Affiliation(s)
- Fabiano Sillo
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
| | - Matteo Garbelotto
- Department of Environmental Science, Policy and Management, University of California, Berkeley
| | - Maria Friedman
- Department of Environmental Science, Policy and Management, University of California, Berkeley
| | - Paolo Gonthier
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
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32
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Lundén K, Danielsson M, Durling MB, Ihrmark K, Gorriz MN, Stenlid J, Asiegbu FO, Elfstrand M. Transcriptional Responses Associated with Virulence and Defence in the Interaction between Heterobasidion annosum s.s. and Norway Spruce. PLoS One 2015; 10:e0131182. [PMID: 26151363 PMCID: PMC4495060 DOI: 10.1371/journal.pone.0131182] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 05/31/2015] [Indexed: 01/13/2023] Open
Abstract
Heterobasidion annosum sensu lato is a serious pathogen causing root and stem rot to conifers in the northern hemisphere and rendering the timber defective for sawing and pulping. In this study we applied next-generation sequencing to i) identify transcriptional responses unique to Heterobasidion-inoculated Norway spruce and ii) investigate the H. annosum transcripts to identify putative virulence factors. To address these objectives we wounded or inoculated 30-year-old Norway spruce clones with H. annosum and 454-sequenced the transcriptome of the interaction at 0, 5 and 15 days post inoculation. The 491860 high-quality reads were de novo assembled and the relative expression was analysed. Overall, very few H. annosum transcripts were represented in our dataset. Three delta-12 fatty acid desaturase transcripts and one Clavaminate synthase-like transcript, both associated with virulence in other pathosystems, were found among the significantly induced transcripts. The analysis of the Norway spruce transcriptional responses produced a handful of differentially expressed transcripts. Most of these transcripts originated from genes known to respond to H. annosum. However, three genes that had not previously been reported to respond to H. annosum showed specific induction to inoculation: an oxophytodienoic acid–reductase (OPR), a beta–glucosidase and a germin-like protein (GLP2) gene. Even in a small data set like ours, five novel highly expressed Norway spruce transcripts without significant alignment to any previously annotated protein in Genbank but present in the P. abies (v1.0) gene catalogue were identified. Their expression pattern suggests a role in defence. Therefore a more complete survey of the transcriptional responses in the interactions between Norway spruce and its major pathogen H. annosum would probably provide a better understanding of gymnosperm defence than accumulated until now.
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Affiliation(s)
- Karl Lundén
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marie Danielsson
- Chemistry, School of Chemical Science and Engineering, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Mikael Brandström Durling
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Katarina Ihrmark
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Miguel Nemesio Gorriz
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Malin Elfstrand
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
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33
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Chen JJ, Cui BK, Zhou LW, Korhonen K, Dai YC. Phylogeny, divergence time estimation, and biogeography of the genus Heterobasidion (Basidiomycota, Russulales). FUNGAL DIVERS 2015. [DOI: 10.1007/s13225-014-0317-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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34
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Kashif M, Hyder R, De Vega Perez D, Hantula J, Vainio E. Heterobasidion wood decay fungi host diverse and globally distributed viruses related to Helicobasidium mompa partitivirus V70. Virus Res 2015; 195:119-23. [DOI: 10.1016/j.virusres.2014.09.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/05/2014] [Accepted: 09/06/2014] [Indexed: 10/24/2022]
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35
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Rytioja J, Hildén K, Yuzon J, Hatakka A, de Vries RP, Mäkelä MR. Plant-polysaccharide-degrading enzymes from Basidiomycetes. Microbiol Mol Biol Rev 2014; 78:614-49. [PMID: 25428937 PMCID: PMC4248655 DOI: 10.1128/mmbr.00035-14] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
SUMMARY Basidiomycete fungi subsist on various types of plant material in diverse environments, from living and dead trees and forest litter to crops and grasses and to decaying plant matter in soils. Due to the variation in their natural carbon sources, basidiomycetes have highly varied plant-polysaccharide-degrading capabilities. This topic is not as well studied for basidiomycetes as for ascomycete fungi, which are the main sources of knowledge on fungal plant polysaccharide degradation. Research on plant-biomass-decaying fungi has focused on isolating enzymes for current and future applications, such as for the production of fuels, the food industry, and waste treatment. More recently, genomic studies of basidiomycete fungi have provided a profound view of the plant-biomass-degrading potential of wood-rotting, litter-decomposing, plant-pathogenic, and ectomycorrhizal (ECM) basidiomycetes. This review summarizes the current knowledge on plant polysaccharide depolymerization by basidiomycete species from diverse habitats. In addition, these data are compared to those for the most broadly studied ascomycete genus, Aspergillus, to provide insight into specific features of basidiomycetes with respect to plant polysaccharide degradation.
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Affiliation(s)
- Johanna Rytioja
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | - Kristiina Hildén
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jennifer Yuzon
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Annele Hatakka
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Miia R Mäkelä
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
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36
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Gene expression associated with intersterility in Heterobasidion. Fungal Genet Biol 2014; 73:104-19. [PMID: 25459536 DOI: 10.1016/j.fgb.2014.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 09/10/2014] [Accepted: 10/08/2014] [Indexed: 12/18/2022]
Abstract
Intersterility (IS) is thought to prevent mating compatibility between homokaryons that belong to different species. Although IS in Heterobasidion is regulated by the genes located at the IS loci, it is not yet known how the IS genes influence sexual compatibility and heterokaryon formation. To increase our understanding of the molecular events underlying IS, we studied mRNA abundance changes during IS compatible and incompatible interactions over time. The clustering of the transcripts into expression profiles, followed by the application of Gene Ontology (GO) enrichment pathway analysis of each of the clusters, allowed inference of biological processes participating in IS. These analyses identified events involved in mating and sexual development (i.e., linked with IS compatibility), which included processes associated with cell-cell adhesion and recognition, cell cycle control and signal transduction. We also identified events potentially involved in overriding mating between individuals belonging to different species (i.e., linked with IS incompatibility), which included reactive oxygen species (ROS) production, responses to stress (especially to oxidative stress), signal transduction and metabolic biosynthesis. Our findings thus enabled detection and characterization of gene expression changes associated with IS in Heterobasidion, as well as identification of important processes and pathways associated with this phenomenon. Overall, the results of this study increase current knowledge regarding the molecular mechanisms underpinning IS in Heterobasidion and allowed for the establishment of a vital baseline for further studies.
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37
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Intronic and plasmid-derived regions contribute to the large mitochondrial genome sizes of Agaricomycetes. Curr Genet 2014; 60:303-13. [PMID: 25011705 PMCID: PMC4201751 DOI: 10.1007/s00294-014-0436-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 05/30/2014] [Accepted: 06/21/2014] [Indexed: 01/13/2023]
Abstract
Sizes of mitochondrial genomes vary extensively between fungal species although they typically contain a conserved set of core genes. We have characterised the mitochondrial genome of the conifer root rot pathogen Heterobasidion irregulare and compared the size, gene content and structure of 20 Basidiomycete mitochondrial genomes. The mitochondrial genome of H. irregulare was 114, 193 bp and contained a core set of 15 protein coding genes, two rRNA genes and 26 tRNA genes. In addition, we found six non-conserved open reading frames (ORFs) and four putative plasmid genes clustered in three separate regions together with 24 introns and 14 intronic homing endonuclease genes, unequally spread across seven of the core genes. The size differences among the 20 Basidiomycetes can largely be explained by length variation of intergenic regions and introns. The Agaricomycetes contained the nine largest mitochondrial genomes in the Basidiomycete group and Agaricomycete genomes are significantly (p < 0.001) larger than the other Basidiomycetes. A feature of the Agaricomycete mitochondrial genomes in this study was the simultaneous occurrence of putative plasmid genes and non-conserved ORFs, with Cantharellus cibarius as only exception, where no non-conserved ORF was identified. This indicates a mitochondrial plasmid origin of the non-conserved ORFs or increased mitochondrial genome dynamics of species harbouring mitochondrial plasmids. We hypothesise that two independent factors are the driving forces for large mitochondrial genomes: the homing endonuclease genes in introns and integration of plasmid DNA.
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38
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Two new species of the Heterobasidion insulare complex based on morphology and molecular data. MYCOSCIENCE 2014. [DOI: 10.1016/j.myc.2013.11.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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39
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Comparative analysis of secretomes in basidiomycete fungi. J Proteomics 2014; 102:28-43. [DOI: 10.1016/j.jprot.2014.03.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/19/2014] [Accepted: 03/03/2014] [Indexed: 12/29/2022]
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40
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Garbelotto M, Guglielmo F, Mascheretti S, Croucher PJP, Gonthier P. Population genetic analyses provide insights on the introduction pathway and spread patterns of the North American forest pathogen Heterobasidion irregulare in Italy. Mol Ecol 2013; 22:4855-69. [PMID: 24033583 DOI: 10.1111/mec.12452] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 07/12/2013] [Accepted: 07/15/2013] [Indexed: 11/26/2022]
Abstract
A population genetics approach is used to identify the most likely introduction site and introduction pathway for the North American forest pathogen Heterobasidion irregulare using 101 isolates from six sites in Italy and 34 isolates from five sites in North America. Diversity indices based on sequences from ten loci indicate the highest diversity in Italy is found in Castelfusano/Castelporziano and that diversity progressively decreases with increasing distance from that site. AMOVA, Bayesian clustering and principal coordinates analyses based on 12 SSR loci indicate high levels of gene flow among sites, high frequency of admixing, and fail to identify groups of genotypes exclusive to single locations. Cumulatively, these analyses suggest the current infestation is the result of multiple genotypes expanding their range from a single site. Based on two sequenced loci, a single source site in North America could provide enough variability to explain the variability observed in Italy. These results support the notion that H. irregulare was introduced originally in Castelporziano: because Castelporziano has been sealed off from the rest of the world for centuries except for a camp set up by the US military in 1944, we conclude the fungus may have been transported in infected wood used by the military. Finally, spatial autocorrelation analyses using SSR data indicate a significant under-dispersion of alleles up to 0.5-10 km, while a significant overdispersion of alleles was detected at distances over 80 km: these ranges can be used to make predictions on the likely dispersal potential of the invasive pathogen.
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Affiliation(s)
- M Garbelotto
- Department of Environmental Science, Policy and Management, University of California at Berkeley, 37 Mulford Hall, Berkeley, CA, 94720, USA
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41
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The saprobic and fruiting abilities of the exotic forest pathogen Heterobasidion irregulare may explain its invasiveness. Biol Invasions 2013. [DOI: 10.1007/s10530-013-0538-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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42
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van Diepen LTA, Olson A, Ihrmark K, Stenlid J, James TY. Extensive trans-specific polymorphism at the mating type locus of the root decay fungus Heterobasidion. Mol Biol Evol 2013; 30:2286-301. [PMID: 23864721 DOI: 10.1093/molbev/mst126] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Incompatibility systems in which individuals bearing identical alleles reject each other favor the maintenance of a diversity of alleles. Mushroom mating type loci (MAT) encode for dozens or hundreds of incompatibility alleles whose loss from the population is greatly restricted through negative frequency selection, leading to a system of alleles with highly divergent sequences. Here, we use DNA sequences of homeodomain (HD) encoding genes at the MAT locus of five closely related species of the root rot basidiomycete Heterobasidion annosum sensu lato to show that the extended coalescence time of MAT alleles greatly predates speciation in the group, contrasting loci outside of MAT that show allele divergences largely consistent with the species phylogeny with those of MAT, which show rampant trans-species polymorphism. We observe a roughly 6-fold greater genealogical depth and polymorphism of MAT compared with non-MAT that argues for the maintenance of balanced polymorphism for a minimum duration of 24 My based on a molecular-clock calibrated species phylogeny. As with other basidiomycete HD genes, balancing selection appears to be concentrated at the specificity-determining region in the N-terminus of the protein based on identification of codons under selection and the absence of recombination within the region. However, the elevated polymorphism extends into the nonspecificity determining regions as well as a neighboring non-MAT gene, the mitochondrial intermediate peptidase (MIP). In doing so, increased divergence should decrease recombination among alleles and as a by-product create incompatibilities in the functional domains not involved in allele recognition but in regulating sexual development.
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43
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Yakovlev IA, Hietala AM, Courty PE, Lundell T, Solheim H, Fossdal CG. Genes associated with lignin degradation in the polyphagous white-rot pathogen Heterobasidion irregulare show substrate-specific regulation. Fungal Genet Biol 2013; 56:17-24. [PMID: 23665189 DOI: 10.1016/j.fgb.2013.04.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 04/26/2013] [Accepted: 04/29/2013] [Indexed: 11/15/2022]
Abstract
The pathogenic white-rot basidiomycete Heterobasidion irregulare is able to remove lignin and hemicellulose prior to cellulose during the colonization of root and stem xylem of conifer and broadleaf trees. We identified and followed the regulation of expression of genes belonging to families encoding ligninolytic enzymes. In comparison with typical white-rot fungi, the H. irregulare genome has exclusively the short-manganese peroxidase type encoding genes (6 short-MnPs) and thereby a slight contraction in the pool of class II heme-containing peroxidases, but an expansion of the MCO laccases with 17 gene models. Furthermore, the genome shows a versatile set of other oxidoreductase genes putatively involved in lignin oxidation and conversion, including 5 glyoxal oxidases, 19 quinone-oxidoreductases and 12 aryl-alcohol oxidases. Their genetic multiplicity and gene-specific regulation patterns on cultures based on defined lignin, cellulose or Norway spruce lignocellulose substrates suggest divergent specificities and physiological roles for these enzymes. While the short-MnP encoding genes showed similar transcript levels upon fungal growth on heartwood and reaction zone (RZ), a xylem defense tissue rich in phenolic compounds unique to trees, a subset of laccases showed higher gene expression in the RZ cultures. In contrast, other oxidoreductases depending on initial MnP activity showed generally lower transcript levels on RZ than on heartwood. These data suggest that the rate of fungal oxidative conversion of xylem lignin differs between spruce RZ and heartwood. It is conceivable that in RZ part of the oxidoreductase activities of laccases are related to the detoxification of phenolic compounds involved in host-defense. Expression of the several short-MnP enzymes indicated an important role for these enzymes in effective delignification of wood by H. irregulare.
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Affiliation(s)
- Igor A Yakovlev
- Norwegian Forest and Landscape Institute, PO Box 115, N-1431 Ås, Norway
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44
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Vainio EJ, Capretti P, Motta E, Hantula J. Molecular characterization of HetRV8-ir1, a partitivirus of the invasive conifer pathogenic fungus Heterobasidion irregulare. Arch Virol 2013; 158:1613-5. [PMID: 23456423 DOI: 10.1007/s00705-013-1643-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 01/11/2013] [Indexed: 10/27/2022]
Abstract
The Heterobasidion annosum (Fr.) Bref. complex includes some of the most destructive conifer pathogenic fungi in the Boreal forest region. H. irregulare, formerly known as the North American pine type of H. annosum, was introduced from North America into Italy during the Second World War and occurs as an invasive pathogen in Pinus pinea stands together with the native European species H. annosum sensu stricto. We describe the complete nucleotide sequence of a new putative partitivirus from an Italian strain of H. irregulare. The bisegmented genome of HetRV8-ir1 encodes an RNA-dependent RNA polymerase of 704 aa and a capsid protein of 638 aa. The polymerase and capsid aa sequences are relatively similar (59-78 %) to those of Fusarium poae virus 1, Pleurotus ostreatus virus 1, and grapevine-associated partitivirus 1. HetRV8-ir1 is the first virus described from H. irregulare, and it is distantly related to previously known partitiviruses of Heterobasidion species.
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Affiliation(s)
- Eeva J Vainio
- Finnish Forest Research Institute, Vantaa Research Unit, Vantaa, Finland.
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45
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Dalman K, Himmelstrand K, Olson Å, Lind M, Brandström-Durling M, Stenlid J. A genome-wide association study identifies genomic regions for virulence in the non-model organism Heterobasidion annosum s.s. PLoS One 2013; 8:e53525. [PMID: 23341945 PMCID: PMC3547014 DOI: 10.1371/journal.pone.0053525] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 12/03/2012] [Indexed: 12/02/2022] Open
Abstract
The dense single nucleotide polymorphisms (SNP) panels needed for genome wide association (GWA) studies have hitherto been expensive to establish and use on non-model organisms. To overcome this, we used a next generation sequencing approach to both establish SNPs and to determine genotypes. We conducted a GWA study on a fungal species, analysing the virulence of Heterobasidion annosum s.s., a necrotrophic pathogen, on its hosts Picea abies and Pinus sylvestris. From a set of 33,018 single nucleotide polymorphisms (SNP) in 23 haploid isolates, twelve SNP markers distributed on seven contigs were associated with virulence (P<0.0001). Four of the contigs harbour known virulence genes from other fungal pathogens and the remaining three harbour novel candidate genes. Two contigs link closely to virulence regions recognized previously by QTL mapping in the congeneric hybrid H. irregulare × H. occidentale. Our study demonstrates the efficiency of GWA studies for dissecting important complex traits of small populations of non-model haploid organisms with small genomes.
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Affiliation(s)
- Kerstin Dalman
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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46
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Garbelotto M, Gonthier P. Biology, epidemiology, and control of Heterobasidion species worldwide. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:39-59. [PMID: 23642002 DOI: 10.1146/annurev-phyto-082712-102225] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Heterobasidion annosum sensu lato is a species complex comprising five species that are widely distributed in coniferous forests of the Northern Hemisphere and are each characterized by a distinct host preference. More than 1,700 papers have been published on these fungi in the past four decades, making them perhaps the most widely studied forest fungi. Heterobasidion species are at different levels on the saprotroph-necrotroph gradient, and the same individual can switch from one mode to the other. This offers a unique opportunity to study how genomic structure, gene expression, and genetic trade-offs may all interact with environmental factors to determine the life mode of the organism. The abilities of Heterobasidion spp. to infect stumps as saprotrophs and to spread to neighboring trees as pathogens have resulted in significant damages to timber production in managed forests. This review focuses on the current knowledge of the biology, ecology, evolution, and management of these species and is based on classical and modern studies.
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Affiliation(s)
- Matteo Garbelotto
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720, USA.
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47
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Vainio EJ, Piri T, Hantula J. Virus community dynamics in the conifer pathogenic fungus Heterobasidion parviporum following an artificial introduction of a partitivirus. MICROBIAL ECOLOGY 2013; 65:28-38. [PMID: 22961364 DOI: 10.1007/s00248-012-0118-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 08/20/2012] [Indexed: 06/01/2023]
Abstract
Viruses infecting the conifer pathogenic fungus Heterobasidion annosum sensu lato are intracellular and spread via anastomosis contacts. In the laboratory, these viruses transmit readily even between somatically incompatible isolates, but their dispersal capacity in natural conditions has not been previously studied. We introduced a mycovirus to a heavily diseased forest site by inoculating Norway spruce stumps with heartrot decay using a mycelial suspension of Heterobasidion parviporum strain RT3.49C hosting the partitivirus strain HetRV4-pa1. The Heterobasidion population at the sample plot was screened for mycoviruses prior to and after the inoculation. Based on sequence analysis, the resident H. parviporum strains harbored six different strains of the virus species Heterobasidion RNA virus 6 (HetRV6) and one strain of HetRV4 prior to the inoculation. After three growth seasons, the inoculated H. parviporum host strain was not detected, but the introduced virus had infected two resident H. parviporum genets. The presence of a preexisting HetRV6 infection did not hinder spread of the introduced partitivirus but resulted in coinfections instead. The resident HetRV6 virus population seemed to be highly stable during the incubation period, while the single indigenous HetRV4 infection was not detected after the inoculation. In laboratory infection experiments, the introduced virus could be transmitted successfully into all of the resident H. parviporum genets. This study shows for the first time transmission of a Heterobasidion virus between somatically incompatible hosts in natural conditions.
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Affiliation(s)
- Eeva J Vainio
- Vantaa Research Unit, Finnish Forest Research Institute, PO Box 18, 01301, Vantaa, Finland.
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48
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Hansson D, Menkis A, Olson K, Stenlid J, Broberg A, Karlsson M. Biosynthesis of fomannoxin in the root rotting pathogen Heterobasidion occidentale. PHYTOCHEMISTRY 2012; 84:31-39. [PMID: 22981000 DOI: 10.1016/j.phytochem.2012.08.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 08/08/2012] [Accepted: 08/13/2012] [Indexed: 06/01/2023]
Abstract
Fomannoxin is a biologically active benzohydrofuran, which has been suggested to be involved in the pathogenicity of the root rotting fungus Heterobasidion annosum sensu lato. The biosynthesis of fomannoxin was investigated through an isotopic enrichment study utilizing [1-¹³C]glucose as metabolic tracer. ¹³C NMR spectroscopic analysis revealed the labeling pattern and showed that the isoprene building block originates from the mevalonic acid pathway, whereas the aromatic motif is formed via the shikimic acid route by elimination of pyruvate from chorismic acid. A natural product, 4-hydroxy-3-(3-methylbut-2-enyl)benzaldehyde, was isolated and characterized, and was suggested to be a key intermediate in the biosynthesis of fomannoxin and related secondary metabolites previously identified from the H. annosum fungal species complex.
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Affiliation(s)
- David Hansson
- Department of Chemistry, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-75007 Uppsala, Sweden
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49
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Gonthier P, Lione G, Giordano L, Garbelotto M. The American forest pathogen Heterobasidion irregulare colonizes unexpected habitats after its introduction in Italy. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2012; 22:2135-2143. [PMID: 23387115 DOI: 10.1890/12-0420.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Habitat preference of an invasive fungal tree pathogen is here compared with that of a sympatric and native closely related congener to test the hypothesis that the invasive ability of the exotic organism may be linked to its capacity to colonize substrates unavailable to the indigenous relative. We compared the distribution of infectious airspora of the North American Heterobasidion irregulare introduced into Italy with that of the native H. annosum, both regarded to be able to establish only in the presence of conifers. Geostatistical and statistical analyses were employed to test for association between both species and five Mediterranean vegetation types. Results show that H. annosum is positively associated with pines and negatively associated with deciduous oaks. The probability of finding its spores decreases to almost 0 at distances over 500 m from pines, and this species is virtually absent in pure oak forests. Spores of H. irregulare are present irrespective of vegetation type, and this species can be found not only where pines are present, but also in pure oak forests. This knowledge implies that spread of H. irregulare is not limited by the fragmented distribution of pine woodlands in central Italy and is essential to both predict and hinder its progress in Europe.
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Affiliation(s)
- Paolo Gonthier
- Department of Agricultural, Forest and Food Sciences, University of Turin, Via L. da Vinci 44, I-10095 Grugliasco, Italy
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50
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Lind M, van der Nest M, Olson Å, Brandström-Durling M, Stenlid J. A 2nd generation linkage map of Heterobasidion annosum s.l. based on in silico anchoring of AFLP markers. PLoS One 2012; 7:e48347. [PMID: 23139779 PMCID: PMC3489678 DOI: 10.1371/journal.pone.0048347] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 09/24/2012] [Indexed: 11/18/2022] Open
Abstract
In this study, we present a 2nd generation genetic linkage map of a cross between the North American species Heterobasidion irregulare and H. occidentale, based on the alignment of the previously published 1st generation map to the parental genomes. We anchored 216 of the original 308 AFLP markers to their respective restriction sites using an in silico-approach. The map resolution was improved by adding 146 sequence-tagged microsatellite markers and 39 sequenced gene markers. The new markers confirmed the positions of the anchored AFLP markers, fused the original 39 linkage groups together into 17, and fully expanded 12 of these to single groups covering entire chromosomes. Map coverage of the genome increased from 55.3% to 92.8%, with 96.3% of 430 markers collinearly aligned with the genome sequence. The anchored map also improved the H. irregulare assembly considerably. It identified several errors in scaffold arrangements and assisted in reducing the total number of major scaffolds from 18 to 15. This denser, more comprehensive map allowed sequence-based mapping of three intersterility loci and one mating type locus. This demonstrates the possibility to utilize an in silico procedure to convert anonymous markers into sequence-tagged ones, as well as the power of a sequence-anchored linkage map and its usefulness in the assembly of a whole genome sequence.
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Affiliation(s)
- Mårten Lind
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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