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van Heerden A, Pham NQ, Wingfield BD, Wingfield MJ, Muro Abad JI, Durán A, Wilken PM. LAMP Assay to Detect Elsinoë necatrix, an Important Eucalyptus Shoot and Leaf Pathogen. PLANT DISEASE 2024; 108:2731-2739. [PMID: 38616388 DOI: 10.1094/pdis-01-24-0086-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Eucalyptus scab and shoot malformation caused by Elsinoë necatrix is an emerging disease and a serious threat to the global commercial forestry industry. The disease was first discovered in North Sumatra, Indonesia, and now requires a simple and effective method for early pathogen detection. In this study, a rapid and sensitive loop-mediated isothermal amplification (LAMP) assay was developed for E. necatrix. A unique region in a secondary metabolite gene cluster was used as a target for the assay. To test robustness of the assay, LAMP was verified in 15 strains of E. necatrix. A specificity test against 23 closely related Elsinoë species and three fungal species commonly isolated on Eucalyptus showed that the LAMP assay exclusively identified E. necatrix isolates. The assay had a high level of sensitivity, able to detect 0.01 ng (approximately 400 target copies) of pure E. necatrix DNA. Furthermore, using a simple DNA extraction method, it was possible to use this assay to detect E. necatrix in infected Eucalyptus leaves.
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Affiliation(s)
- Alishia van Heerden
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Nam Q Pham
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Jupiter I Muro Abad
- RGE Technology Center, Asia Pacific Resources International Holdings Ltd. (APRIL), Pangkalan Kerinci, Riau, Indonesia
| | - Alvaro Durán
- RGE Technology Center, Asia Pacific Resources International Holdings Ltd. (APRIL), Pangkalan Kerinci, Riau, Indonesia
| | - P Markus Wilken
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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2
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de Moraes Pontes JG, da Silva Pinheiro MS, Fill TP. Unveiling Chemical Interactions Between Plants and Fungi Using Metabolomics Approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:1-20. [PMID: 37843803 DOI: 10.1007/978-3-031-41741-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Metabolomics has been extensively used in clinical studies in the search for new biomarkers of human diseases. However, this approach has also been highlighted in agriculture and biological sciences, once metabolomics studies have been assisting researchers to deduce new chemical mechanisms involved in biological interactions that occur between microorganisms and plants. In this sense, the knowledge of the biological role of each metabolite (virulence factors, signaling compounds, antimicrobial metabolites, among others) and the affected biochemical pathways during the interaction contribute to a better understand of different ecological relationships established in nature. The current chapter addresses five different applications of the metabolomics approach in fungal-plant interactions research: (1) Discovery of biomarkers in pathogen-host interactions, (2) plant diseases diagnosis, (3) chemotaxonomy, (4) plant defense, and (5) plant resistance; using mass spectrometry and/or nuclear magnetic resonance spectroscopy, which are the techniques most used in metabolomics.
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Affiliation(s)
- João Guilherme de Moraes Pontes
- Universidade Estadual de Campinas (UNICAMP), Instituto de Química, Laboratório de Biologia Química Microbiana (LaBioQuiMi), Campinas, SP, Brazil
| | - Mayra Suelen da Silva Pinheiro
- Universidade Estadual de Campinas (UNICAMP), Instituto de Química, Laboratório de Biologia Química Microbiana (LaBioQuiMi), Campinas, SP, Brazil
| | - Taícia Pacheco Fill
- Universidade Estadual de Campinas (UNICAMP), Instituto de Química, Laboratório de Biologia Química Microbiana (LaBioQuiMi), Campinas, SP, Brazil.
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Brunetti A, Heungens K, Hubert J, Ioos R, Bianchi GL, De Amicis F, Chandelier A, Van Der Linde S, Perez-Sierra A, Gualandri V, Silletti MR, Trisciuzzi VN, Rimondi S, Baschieri T, Romano E, Lumia V, Luigi M, Faggioli F, Pilotti M. Interlaboratory Performance of a Real-Time PCR Method for Detection of Ceratocystisplatani, the Agent of Canker Stain of Platanus spp. J Fungi (Basel) 2022; 8:jof8080778. [PMID: 35893146 PMCID: PMC9330143 DOI: 10.3390/jof8080778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Ceratocystis platani (CP), an ascomycetous fungus, is the agent of canker stain, a lethal vascular disease of Platanus species. Ceratocystis platani has been listed as a quarantine pest (EPPO A2 list) due to extensive damage caused in Southern Europe and the Mediterranean region. As traditional diagnostic assays are ineffective, a Real-Time PCR detection method based on EvaGreen, SYBR Green, and Taqman assays was previously developed, validated in-house, and included in the official EPPO standard PM7/14 (2). Here, we describe the results of a test performance study performed by nine European laboratories for the purpose of an interlaboratory validation. Verification of the DNA extracted from biological samples guaranteed the high quality of preparations, and the stability and the homogeneity of the aliquots intended for the laboratories. All of the laboratories reproduced nearly identical standard curves with efficiencies close to 100%. Testing of blind-coded DNA extracted from wood samples revealed that all performance parameters—diagnostic sensitivity, diagnostic specificity, accuracy and reproducibility—were best fit in most cases both at the laboratory and at the assay level. The previously established limit of detection, 3 fg per PCR reaction, was also validated with similar excellent results. The high interlaboratory performance of this Real-Time PCR method confirms its value as a primary tool to safeguard C. platani-free countries by way of an accurate monitoring, and to investigate the resistance level of potentially canker stain-resistant Platanus genotypes.
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Affiliation(s)
- Angela Brunetti
- Council for Agricultural Research and Economics, Research Centre for Plant Protection and Certification (CREA-DC), 00156 Rome, Italy; (A.B.); (V.L.); (M.L.); (F.F.)
| | - Kurt Heungens
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9940 Merelbeke, Belgium;
| | - Jacqueline Hubert
- Plant Health Laboratory for the French Agency for Food, Environmental and Occupational Health & Safety (ANSES) Mycology Unit, 54220 Malzéville, France; (J.H.); (R.I.)
| | - Renaud Ioos
- Plant Health Laboratory for the French Agency for Food, Environmental and Occupational Health & Safety (ANSES) Mycology Unit, 54220 Malzéville, France; (J.H.); (R.I.)
| | - Gian Luca Bianchi
- Agenzia Regionale Per lo Sviluppo Rurale—ERSA Servizio Fitosanitario e Chimico, Ricerca, Sperimentazione ed Assistenza Tecnica, Struttura Stabile Laboratorio di Fitopatologia e Biotecnologie, Pozzuolo del Friuli, 33050 Udine, Italy; (G.L.B.); (F.D.A.)
| | - Francesca De Amicis
- Agenzia Regionale Per lo Sviluppo Rurale—ERSA Servizio Fitosanitario e Chimico, Ricerca, Sperimentazione ed Assistenza Tecnica, Struttura Stabile Laboratorio di Fitopatologia e Biotecnologie, Pozzuolo del Friuli, 33050 Udine, Italy; (G.L.B.); (F.D.A.)
| | - Anne Chandelier
- Walloon Agricultural Research Centre—CRA-W Life Sciences Department, 5030 Gembloux, Belgium;
| | - Sietse Van Der Linde
- Forest Research Tree Health Diagnostic & Advisory Service, Alice Holt Lodge, Farnham, Surrey GU10 4LH, UK; (S.V.D.L.); (A.P.-S.)
| | - Ana Perez-Sierra
- Forest Research Tree Health Diagnostic & Advisory Service, Alice Holt Lodge, Farnham, Surrey GU10 4LH, UK; (S.V.D.L.); (A.P.-S.)
| | - Valeria Gualandri
- FEM-IASMA, Centro Trasferimento Tecnologico Dipartimento Sperimentazione e Servizi Tecnologici, Unità Protezione Piante e Biodiversità Agroforestale, S. Michele all’Adige, 38098 Trento, Italy;
| | - Maria Rosaria Silletti
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura, Basile Caramia, Locorotondo, 70010 Bari, Italy; (M.R.S.); (V.N.T.)
| | - Vito Nicola Trisciuzzi
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura, Basile Caramia, Locorotondo, 70010 Bari, Italy; (M.R.S.); (V.N.T.)
| | - Silvia Rimondi
- Servizio Fitosanitario Regione Emilia-Romagna, 40129 Bologna, Italy; (S.R.); (T.B.)
| | - Tiziana Baschieri
- Servizio Fitosanitario Regione Emilia-Romagna, 40129 Bologna, Italy; (S.R.); (T.B.)
| | - Elio Romano
- Council for Agricultural Research and Economics, Research Centre for Engineering and Agro-Food Processing (CREA-IT) Treviglio, 24047 Bergamo, Italy;
| | - Valentina Lumia
- Council for Agricultural Research and Economics, Research Centre for Plant Protection and Certification (CREA-DC), 00156 Rome, Italy; (A.B.); (V.L.); (M.L.); (F.F.)
| | - Marta Luigi
- Council for Agricultural Research and Economics, Research Centre for Plant Protection and Certification (CREA-DC), 00156 Rome, Italy; (A.B.); (V.L.); (M.L.); (F.F.)
| | - Francesco Faggioli
- Council for Agricultural Research and Economics, Research Centre for Plant Protection and Certification (CREA-DC), 00156 Rome, Italy; (A.B.); (V.L.); (M.L.); (F.F.)
| | - Massimo Pilotti
- Council for Agricultural Research and Economics, Research Centre for Plant Protection and Certification (CREA-DC), 00156 Rome, Italy; (A.B.); (V.L.); (M.L.); (F.F.)
- Correspondence: ; Tel.: +39-06-82070357
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Shin K, Kwon SH, Lee SC, Moon YE. Sensitive and Rapid Detection of Citrus Scab Using an RPA-CRISPR/Cas12a System Combined with a Lateral Flow Assay. PLANTS 2021; 10:plants10102132. [PMID: 34685941 PMCID: PMC8539466 DOI: 10.3390/plants10102132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/02/2021] [Accepted: 10/02/2021] [Indexed: 12/14/2022]
Abstract
Citrus is the most extensively produced fruit tree crop in the world and is grown in over 130 countries. Fungal diseases in citrus can cause significant losses in yield and quality. An accurate diagnosis is critical for determining the best management practices and preventing future losses. In this study, a Recombinase polymerase amplification (RPA)-clustered regularly interspaced short palindromic repeats (CRISPR)/associated (Cas) system was established with the integration of a lateral flow assay (LFA) readout system for diagnosis of citrus scab. This detection can be completed within 1 h, is highly sensitive and prevents cross-reactions with other common fungal citrus diseases. Furthermore, the detection system is compatible with crude DNA extracted from infected plant tissue. This RPA-CRISPR/Cas12a-LFA system provides a sensitive, rapid, and cost-effective method with promising and significant practical value for point-of-care diagnosis of citrus scab. To our knowledge, this is the first report to establish an RPA- and CRISPR-based method with LFA for fungal diseases in plants.
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Ciampi-Guillardi M, Ramiro J, Moraes MHDD, Barbieri MCG, Massola NS. Multiplex qPCR Assay for Direct Detection and Quantification of Colletotrichum truncatum, Corynespora cassiicola, and Sclerotinia sclerotiorum in Soybean Seeds. PLANT DISEASE 2020; 104:3002-3009. [PMID: 32822262 DOI: 10.1094/pdis-02-20-0231-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Precise diagnosis of plant diseases is one of the most effective tools to minimize yield losses. Colletotrichum truncatum, Corynespora cassiicola, and Sclerotinia sclerotiorum are common soilborne pathogens that affect soybeans all over the world. We developed a multiplex quantitative real-time polymerase chain reaction (qPCR) assay to simultaneously detect and quantify the three pathogens in soybean seeds and to survey their occurrence in the main soybean production areas in Brazil. Species-specific primers and probes for C. truncatum and C. cassiicola were designed based on GAPDH and TEF1 genes, respectively, to be combined with qPCR detection of S. sclerotiorum previously reported. The multiplex qPCR assay was successful in the simultaneous detection of C. truncatum, C. cassiicola, and S. sclerotiorum, along with a host internal control. The four pathogens were detected and quantified in artificially and naturally infested soybean seeds, even in the lowest incidence level tested of 0.0625% or 1 infected seed out of 1,599 healthy ones. From 81 seed samples tested, C. truncatum was the most frequently detected pathogen and with higher incidence levels (0.25 to 0.125%), followed by S. sclerotiorum and C. cassiicola, both with lower incidence levels (0.125 to 0.0625%). Together, the results evidenced the high sensitivity of the multiplex qPCR assay, indicating its usefulness for a quick and reliable diagnosis of soybean diseases in seeds.
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Affiliation(s)
- Maísa Ciampi-Guillardi
- Department of Plant Pathology and Nematology, ESALQ, University of São Paulo, Piracicaba/SP, Brazil
| | - Juliana Ramiro
- Department of Plant Pathology and Nematology, ESALQ, University of São Paulo, Piracicaba/SP, Brazil
| | | | | | - Nelson S Massola
- Department of Plant Pathology and Nematology, ESALQ, University of São Paulo, Piracicaba/SP, Brazil
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New multiplex conventional PCR and quadruplex real-time PCR assays for one-tube detection of Phyllosticta citricarpa, Elsinoë fawcettii, Elsinoë australis, and Pseudocercospora angolensis in Citrus: development and validation. Appl Microbiol Biotechnol 2020; 104:9363-9385. [PMID: 32926221 DOI: 10.1007/s00253-020-10880-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/17/2020] [Accepted: 09/02/2020] [Indexed: 10/23/2022]
Abstract
Phyllosticta citricarpa, Elsinoë fawcettii, Elsinoë australis, and Pseudocercospora angolensis are major pathogens of citrus crops worldwide and can cause non-characteristic symptoms that may lead to confusion regarding the causative agent. These fungi are subject to international phytosanitary regulations, and testing on fruits or leaves requires accurate and easy-to-use tools. New multiplex conventional PCR and real-time PCR assays were developed here to achieve highly accurate simultaneous detection of all four fungal pathogens in fruit tissues. We designed new oligonucleotide combinations for P. citricarpa, E. fawcettii, and E. australis and combined them with already available primers and hydrolysis probes to be used in either PCR assay. The limit of detection for multiplex conventional PCR was as low as 100 pg μL-1 for P. citricarpa, E. fawcettii, and E. australis and 10 pg μL-1 of target DNA per reaction tube for P. angolensis. The quadruplex real-time PCR assay successfully yielded repeatable positive results with as low as 242, 243, 241, and 242 plasmidic copies of target DNA of P. citricarpa, E. fawcettii, E. australis, and P. angolensis, respectively. Moreover, analysis of 60 naturally infected citrus samples yielded 100% concordant results by both assays. Our validation experiment revealed that the multiplex real-time PCR assay showed high specificity except a cross-reaction with P. paracitricarpa DNA. Sensitivity, repeatability, reproducibility, and robustness were verified, and the assay could be used following different DNA extraction procedures, supporting fitness for routine analysis. These new multiplex tools should be of great interest as cost-effective solutions for regulatory authorities and diagnostic laboratories, enabling testing for four important pathogens in single-tube reactions. KEY POINTS: • Development of new conventional PCR and qPCR assays for four citrus pathogens. • Very low limits of detection were found for multiplex conventional PCR. • qPCR had high specificity, sensitivity, repeatability, reproducibility, and robustness.
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