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Hong-min Z, Jian Y, Ying L, Yuan Y, Cui-ping W, Yu-cheng D, Jia-jia C. Rapid detection of Heterobasidion annosum using a loop-mediated isothermal amplification assay. Front Cell Infect Microbiol 2023; 13:1134921. [PMID: 37187469 PMCID: PMC10175688 DOI: 10.3389/fcimb.2023.1134921] [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: 12/31/2022] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Heterobasidion annosum is one of the most aggressive pathogens of Pinus forests in Europe, causing considerable economic losses. To detect H. annosum for disease diagnosis and control, we developed a loop-mediated isothermal amplification (LAMP) reaction with a primer set designed from the glyceraldehyde 3-phosphate dehydrogenase (GAPDH) DNA sequences of H. annosum. In our study, this LAMP assay was found to be capable of efficiently amplifying the target gene within 60 min at 63°C. In specificity tests, H. annosum was positively detected, and other species were negative. The detection limit of this assay was found to be 100 pg·μL-1, and the assay was also successfully tested for use with basidiospore suspensions and wood samples. This study provides a rapid method for diagnosing root and butt rot caused by H. annosum, which will be of use in port surveillance of logs imported from Europe.
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Affiliation(s)
- Zhou Hong-min
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang, China
| | - Yu Jian
- College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang, China
| | - Liu Ying
- College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang, China
| | - Yuan Yuan
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Wu Cui-ping
- Animal, Plant and Food Inspection Center, Nanjing Customs, Nanjing, China
| | - Dai Yu-cheng
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- *Correspondence: Dai Yu-cheng, ; Chen Jia-jia,
| | - Chen Jia-jia
- College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang, China
- *Correspondence: Dai Yu-cheng, ; Chen Jia-jia,
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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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Hughes KW, McGhee LL, Methven AS, Johnson JE, Petersen RH. Patterns of geographic speciation in the genus Flammulina based on sequences of the ribosomal ITS1-5.8S-ITS2 area. Mycologia 2019. [DOI: 10.1080/00275514.1999.12061107] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Karen W. Hughes
- Department of Botany, University of Tennessee, Knoxville, Tennessee 37996–1100
| | - Laura Lee McGhee
- Theshold Scholar, Division of Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Andrew S. Methven
- Botany Department, Eastern Illinois University, Charleston, Illinois 61920-3099
| | - James E. Johnson
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Ronald H. Petersen
- Department of Botany, University of Tennessee, Knoxville, Tennessee 37996–1100
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Hughes KW, Toyohara TL, Petersen RH. DNA sequence and RFLP analysis of Pleurotopsis longinqua from three disjunct populations. Mycologia 2018. [DOI: 10.1080/00275514.1998.12026948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Karen W. Hughes
- Department of Botany, University of Tennessee, Knoxville, Tennessee 37996-1100
| | | | - Ronald H. Petersen
- Department of Botany, University of Tennessee, Knoxville, Tennessee 37996-1100
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Affiliation(s)
- Ronald H. Petersen
- Department of Botany, University of Tennessee, Knoxville Tennessee 37996
| | - Karen W. Hughes
- Department of Botany, University of Tennessee, Knoxville Tennessee 37996
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den Bakker HC, Gravendeel B, Kuyper TW. An ITS phylogeny of Leccinum and an analysis of the evolution of minisatellite-like sequences within ITS1. Mycologia 2017. [DOI: 10.1080/15572536.2005.11833001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Henk C. den Bakker
- Nationaal Herbarium Nederland, Universiteit Leiden branch, Phanerogams and Cryptogams of the Netherlands and Europe section, P.O. Box 9514, 2300 RA Leiden, The Netherlands
| | - Barbara Gravendeel
- Nationaal Herbarium Nederland, Universiteit Leiden branch, Molecular Systematics taskforce, P.O. Box 9514, 2300 RA Leiden, The Netherlands
| | - Thomas W. Kuyper
- Wageningen Agricultural University, Department of Environmental Sciences, Subdepartment of Soil Quality, P.O. Box 8005, 6700 EC Wageningen, The Netherlands
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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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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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DALMAN K, OLSON Å, STENLID J. Evolutionary history of the conifer root rot fungus Heterobasidion annosum sensu lato. Mol Ecol 2010; 19:4979-93. [DOI: 10.1111/j.1365-294x.2010.04873.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Johannesson H, Stenlid J. Molecular markers reveal genetic isolation and phylogeography of the S and F intersterility groups of the wood-decay fungus Heterobasidion annosum. Mol Phylogenet Evol 2003; 29:94-101. [PMID: 12967610 DOI: 10.1016/s1055-7903(03)00087-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The root-rot fungus Heterobasidion annosum (Fr.) Bref. species complex consists of three intersterility groups (S, F, and P), separated by their host affinity. The phylogenetic relationship of the species complex was studied, with the focus on the S and F groups, by comparing DNA sequences of four nuclear gene fragments: calmodulin, glyceraldehyde 3-phosphate dehydrogenase, heat stress protein 80-1, and elongation factor 1-alpha, and one anonymous locus, from 29 fungal isolates originating from Europe, Asia, and North America. The phylogeny of each separate gene locus as well as the combined dataset consisted of three main clades: European F group isolates, Euroasian S group isolates, and North American S group isolates, suggesting them to be separated into phylogenetic species. The results also support the hypothesis of an early separation between the S and F groups, indicating that their distribution have followed their host tree species for a considerable time period.
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Affiliation(s)
- Hanna Johannesson
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720-3102, USA
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Infragenic phylogeny of Collybia s. str. based on sequences of ribosomal ITS and LSU regions. ACTA ACUST UNITED AC 2001. [DOI: 10.1017/s0953756200003415] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Kasuga T, Woods C, Woodward S, Mitchelson K. Heterobasidion annosum 5.8s ribosomal DNA and internal transcribed spacer sequence: rapid identification of European intersterility groups by ribosomal DNA restriction polymorphism. Curr Genet 1993; 24:433-6. [PMID: 7905365 DOI: 10.1007/bf00351853] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Using conserved fungal ribosomal gene sequences the internal transcribed spacer (ITS) regions one and two (ITS1, ITS2) and the 5.8s ribosomal RNA gene (rRNA) of Heterobasidion annosum were amplified by the polymerase chain reaction (PCR). The nucleotide sequence was determined in three European intersterility groups (ISG-S, -F and -P). Three sequence variants of the ITS were found in ISG-S isolates. The sequence of the ITS of ISG-F differed by two residues from the major ISG-S sequence variant. The ISG-P sequence differed from ISG-S and ISG-F at 15-16 and 16 residues, respectively. Amplified intergenic spacer elements were informative for ISG fingerprinting following digestion with various 4-cutter restriction endonucleases. All differences in the restriction fragments between the ISGs were because of sequence differences in the ITS regions. The fingerprint patterns of isolates from the same intersterility group but from different European localities were identical. These results show that ribosomal DNA fingerprinting is a rapid technique to identify ISGs in Heterobasidion annosum.
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Affiliation(s)
- T Kasuga
- Department of Molecular and Cell Biology, University of Aberdeen, Scotland, UK
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