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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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Vainio EJ, Hantula J. Genetic differentiation between European and North American populations ofPhlebiopsis gigantea. Mycologia 2019. [DOI: 10.1080/00275514.2000.12061179] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Eeva J. Vainio
- Finnish Forest Research Institute, P.O. Box 18, FIN-01301, Vantaa, Finland
| | - Jarkko Hantula
- Finnish Forest Research Institute, P.O. Box 18, FIN-01301, Vantaa, Finland
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Aanen DK, Kuyper TW, Boekhout T, Hoekstra RF. Phylogenetic relationships in the genus Hebeloma based on ITS1 and 2 sequences, with special emphasis on the Hebeloma crustuliniforme complex. Mycologia 2019. [DOI: 10.1080/00275514.2000.12061154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Duur K. Aanen
- Laboratory of Genetics, Wageningen Agricultural University, Dreyenlaan 2, 6703 HA Wageningen, The Netherlands
| | - Thomas W. Kuyper
- Department of Environmental Sciences, Section Soil Science and Plant Nutrition, P.O. Box 8005, 6700 EC Wageningen, The Netherlands
| | - Teun Boekhout
- Centraalbureau voor Schimmelcultures, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Rolf F. Hoekstra
- Laboratory of Genetics, Wageningen Agricultural University, Dreyenlaan 2, 6703 HA Wageningen, The Netherlands
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Affiliation(s)
- John F. Murphy
- Department of Botany, The Field Museum, Roosevelt Road at Lake Shore Drive, Chicago, Illinois 60605-2496
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Kuhls K, Lieckfeldt E, Samuels GJ, Meyer W, Kubicek CP, Börner T. Revision ofTrichodermasect.Longibrachiatumincluding related teleomorphs based on analysis of ribosomal DNA internal transcribed spacer sequences. Mycologia 2018. [DOI: 10.1080/00275514.1997.12026803] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Katrin Kuhls
- Humboldt-Universität zu Berlin, Institut für Biologie (Genetik), Chausseestr. 117, D-10115 Berlin, Germany
| | - Elke Lieckfeldt
- Humboldt-Universität zu Berlin, Institut für Biologie (Genetik), Chausseestr. 117, D-10115 Berlin, Germany
| | - Gary J. Samuels
- USDA-ARS, Systematic Botany and Mycology Laboratory, Rm.304, B-011A, BARC-West, Beltsville, Maryland 20705-2350
| | - Wieland Meyer
- Duke University Medical Center, Dept. of Microbiology, P.O. Box 3803, Durham, North Carolina 27710
| | - Christian P. Kubicek
- Technische Universität Wien, Institut für Biochemische Technologie und Mikrobiologie, Abteilung für Mikrobielle Biochemie, Getreidemarkt 9, A-1060 Wien, Austria
| | - Thomas Börner
- Humboldt-Universität zu Berlin, Institut für Biologie (Genetik), Chausseestr. 117, D-10115 Berlin, Germany
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Werner A, Łakomy P. Intraspecific variation inHeterobasidion annosumfor mortality rate onPinus sylvestrisandPicea abiesseedlings grown in pure culture. Mycologia 2017. [DOI: 10.1080/15572536.2003.11833179] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Antoni Werner
- Department of Phytopathology, Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Piotr Łakomy
- Department of Forest Pathology, August Cieszkowski University of Agriculture, Wojska Polskiego 71c, 60-625, Poznań, Poland
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Mucha J, Guzicka M, Lakomy P, Zadworny M. Iron and reactive oxygen responses in Pinus sylvestris root cortical cells infected with different species of Heterobasidion annosum sensu lato. PLANTA 2012; 236:975-988. [PMID: 22526502 DOI: 10.1007/s00425-012-1646-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 03/28/2012] [Indexed: 05/31/2023]
Abstract
Defence mechanisms in trees are not well understood. We assessed whether distribution of iron ions and their co-localisation with reactive oxygen species in Pinus sylvestris root cells reflect differential preferences of the pathogens Heterobasidion annosum sensu stricto, H. parviporum and H. abietinum to the host. Strains of H. annosum s.s. characterised by a greater preference for P. sylvestris induced accumulation of superoxide (O(2)(-)) in host cells 6 h after inoculation, whereas two peaks in accumulation of O(2)(-) (after 4 and 48 h) were observed after infection with strains of the pathogens H. parviporum and H. abietinum, which have a lower preference for P. sylvestris. Moreover, strains of H. annosum s.s. caused increased production of hydrogen peroxide (H(2)O(2)) in P. sylvestris cells, in contrast with strains of the other two species (H. parviporum and H. abietinum). Following inoculation with H. annosum s.s. strains, H(2)O(2) was correlated negatively with O(2)(-) and correlated positively with ferrous iron (Fe(2+)). Co-localisation of Fe(3+) with H(2)O(2) may suggest that they are involved in inducing hypersensitive responses and eventually cell death in roots inoculated with H. annosum s.s. strains, in contrast with H. parviporum, in which other mechanisms operate when the host is parasitised.
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Affiliation(s)
- Joanna Mucha
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland.
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Vainio EJ, Hantula J. Variation of RAMS markers within the intersterility groups of
Heterobasidion annosum
in Europe. ACTA ACUST UNITED AC 2008. [DOI: 10.1046/j.1439-0329.1999.00148.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- E. J. Vainio
- Finnish Forest Research Institute, Jokiniemenkuja 1, PO Box 18, FIN‐01301, Vantaa, Finland. E‐mail:
| | - J. Hantula
- Finnish Forest Research Institute, Jokiniemenkuja 1, PO Box 18, FIN‐01301, Vantaa, Finland. E‐mail:
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Asiegbu FO, Adomas A, Stenlid J. Conifer root and butt rot caused by Heterobasidion annosum (Fr.) Bref. s.l. MOLECULAR PLANT PATHOLOGY 2005; 6:395-409. [PMID: 20565666 DOI: 10.1111/j.1364-3703.2005.00295.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
UNLABELLED SUMMARY The root and butt rot caused by Heterobasidon annosum is one of the most destructive diseases of conifers in the northern temperate regions of the world, particularly in Europe. Economic losses attributable to Heterobasidion infection in Europe are estimated at 800 million euros annually. The fungus has been classified into three separate European intersterile species P (H. annosum), S (H. parviporum) and F (H. abietinum) based on their main host preferences: pine, spruce and fir, respectively. In North America, two intersterile groups are present, P and S/F, but these have not been given scientific names. The ecology of the disease spread has been intensively studied but the genetics, biochemistry and molecular aspects of pathogen virulence have been relatively little examined. Recent advances in transcript profiling, molecular characterization of pathogenicity factors and establishment of DNA-transformation systems have paved the way for future advances in our understanding of this pathosystem. TAXONOMY Heterobasidion annosum (Fr.) Bref., H. parviporum Niemelä & Korhonen and H. abietinum Niemelä & Korhonen; kingdom Fungi; class Basidiomycotina; order Aphyllophorales; family Bondarzewiaceae; genus Heterobasidion. IDENTIFICATION presence of the fungus fruit bodies, basidiocarps whitish in the margins, upper surface is tan to dark brown, usually irregular shaped, 3.5 (-7) cm thick and up to 40 cm in diameter; pores 5-19, 7-22 and 13-26 mm(2) for the P, F and S groups, respectively. Small brownish non-sporulating postules develop on the outside of infected roots. Asexual spores (conidiospores) are 3.8-6.6 x 2.8-5.0 microm in size. Mating tests are necessary for identification of intersterility groups. HOST RANGE The fungus attacks many coniferous tree species. In Europe, particularly trees of the genera Pinus and Juniperus (P), Picea (S), Abies (F) and in North America Pinus (P) and Picea, Tsuga and Abies (S/F). To a lesser extent it causes root rot on some decidous trees (Betula and Quercus). Disease symptoms: symptoms (e.g. exhudation of resin, crown deterioration) due to Heterobasidion root rot in living trees are not particularly characteristic and in most cases cannot be distinguished from those caused by other root pathogens. Heterobasidion annosum s.l. is a white rot fungus. Initial growth in wood causes a stain that varies in colour depending on host tree species. Incipient decay is normally pale yellow and it develops into a light brown decay to become a white pocket rot with black flecks in its advanced stage. CONTROL silvicultural methods (e.g. stump removal), chemicals (urea, borates) and biological control agent (Phlebiopsis gigantea, marketed as PG Suspension(R) in the UK, PG IBL(R) in Poland and Rotstop(R) in Fennoscandia) are commonly used approaches for minimizing the disease spread.
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Affiliation(s)
- Fred O Asiegbu
- Department of Forest Mycology & Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 07 Uppsala, Sweden
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Direct analysis of wood-inhabiting fungi using denaturing gradient gel electrophoresis of amplified ribosomal DNA. ACTA ACUST UNITED AC 2000. [DOI: 10.1017/s0953756200002471] [Citation(s) in RCA: 449] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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The relatedness of the Italian F intersterility group of Heterobasidion annosum with the S group, as revealed by RAPD assay. ACTA ACUST UNITED AC 1997. [DOI: 10.1017/s0953756297003730] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Berthier YT, Bruckart WL, Chaboudez P, Luster DG. Polymorphic restriction patterns of ribosomal internal transcribed spacers in the biocontrol fungus Puccinia carduorum correlate with weed host origin. Appl Environ Microbiol 1996; 62:3037-41. [PMID: 8702298 PMCID: PMC168092 DOI: 10.1128/aem.62.8.3037-3041.1996] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The internal transcribed spacer (ITS) regions of ribosomal DNA were amplified by PCR and used to develop genetic markers for isolates of Puccinia carduorum being evaluated for biological control of Carduus thoermeri (musk thistle). Unique patterns were produced upon restriction of ITS DNA amplified from four separate Puccinia spp. Restriction patterns of ITS DNA of isolates of P. carduorum from Carduus acanthoides and C. thoermeri were distinct from those of P. carduorum from Carduus tenuiflorus and Carduus pycnocephalus. By this technique, isolates of P. carduorum from four different weed hosts can be differentiated from other Puccinia spp. and separated into two host groups.
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Affiliation(s)
- Y T Berthier
- Foreign Disease-Weed Science Research, USDA Agricultural Research Service, Fort Detrick, Frederick, Maryland 21702-5023, USA
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White EE, Foord BM, Kinloch Jr. BB. Genetics ofCronartium ribicola. II. Variation in the ribosomal gene cluster. ACTA ACUST UNITED AC 1996. [DOI: 10.1139/b96-057] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The ribosomal gene repeat in Cronartium ribicola J.C. Fisch is highly variable among spore samples from British Columbia, Canada. Both restriction site variation and length variation occur. Length heterogeneity results from differences in the number of subrepeats in the intergenic spacer (IGS). The number of IGS size classes in haploid cultures is limited but is very large and highly variable in aeciospores from single cankers. The proportions of different size classes vary among cankers on different trees, and among subsamples taken around the periphery of large old cankers. The results are consistent with the fungus having a haploid infective mycelium that produces functional pycnia that result in localized dikaryotic areas following fusion between flexuous hyphae and pycnia. Restriction site variation appears lower than has been reported in range-wide samples of endemic fungal species, consistent with the hypothesis that introduction of C. ribicola to western North America was limited and does not represent the full genetic range of the species. No particular restriction site variants or IGS size classes characterize samples from particular geographic areas. No evidence for geographic races of the fungus was obtained. Keywords: rusts, rust races, ribosomal DNA, intergenic spacer, population structure, RFLP.
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Kusaba M, Tsuge T. Phylogeny of Alternaria fungi known to produce host-specific toxins on the basis of variation in internal transcribed spacers of ribosomal DNA. Curr Genet 1995; 28:491-8. [PMID: 8575025 DOI: 10.1007/bf00310821] [Citation(s) in RCA: 160] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The internal transcribed spacer regions (ITS1 and ITS2) of ribosomal DNA from Alternaria species, including seven fungi known to produce host-specific toxins, were analyzed by polymerase chain reaction-amplification and direct sequencing. Phylogenetic analysis of the sequence data by the Neighbor-joining method showed that the seven toxin-producing fungi belong to a monophyletic group together with A. alternata. In contract, A. dianthi, A. panax, A. dauci, A. bataticola, A. porri, A. sesami and A. solani, species that can be morphologically distinguished from A. alternata, could be clearly separated from A. alternata by phylogenetic of the ITS variation. These results suggest that Alternaria pathogens which produce host-specific toxins are pathogenic variants within a single variable species, A. alternata.
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Affiliation(s)
- M Kusaba
- School of Agricultural Sciences, Nagoya University, Japan
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Cheng J, Kasuga T, Mitchelson KR, Lightly ER, Watson ND, Martin WJ, Atkinson D. Polymerase chain reaction heteroduplex polymorphism analysis by entangled solution capillary electrophoresis. J Chromatogr A 1994; 677:169-77. [PMID: 7951979 DOI: 10.1016/0021-9673(94)80556-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Heteroduplex DNA polymorphism analysis (HPA) makes use of conformational polymorphisms to alter electrophoretic mobility of fragments and can be used to detect non-restrictable loci. We have developed a novel application of entangled solution capillary electrophoresis (ESCE) to separate heteroduplex and homoduplex DNA molecules. The addition of ethidium bromide and glycerol to the free solution sieving buffer resulted in the improved peak resolution and good reproducibility. Reannealed polymerase chain reaction products could be used directly for mutation screening and with fully automated ESCE the entire HPA may be completed in less than 30 min including sample handling. This technology could provide a rapid and highly efficient way for screening rare mutations among large numbers of individuals.
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Affiliation(s)
- J Cheng
- Department of Molecular and Cell Biology, University of Aberdeen, UK
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