Articles
A real time loop-mediated isothermal amplification (RealAmp) assay for rapid detection of Pleurostoma richardsiae in declining olive plants
Abdraouf SADALLAH- Serena Anna MINUTILLO
- Franco VALENTINI
- Maria Luisa RAIMONDO
- Francesco LOPS
- Antonia CARLUCCI
- Antonio IPPOLITO
- Anna Maria D’ONGHIA
Published 2022-07-19
Keywords
- IGS,
- molecular assay,
- olive decline,
- fungi
How to Cite
[1]
A. . SADALLAH, “A real time loop-mediated isothermal amplification (RealAmp) assay for rapid detection of Pleurostoma richardsiae in declining olive plants”, Phytopathol. Mediterr., vol. 61, no. 2, pp. 259–267, Jul. 2022.
Abstract
Pleurostoma richardsiae is associated with host trunk diseases, known to cause dieback, cankers and wilting of woody trees, and human infections. This fungus was isolated from wood tissues of declining olive trees and grapevines showing esca disease symptoms, in the Apulia region of Italy. Fungus detection has been based on morphological and molecular features, which are time-consuming to identify and require well-trained personnel. Improvement of Pl. richardsiae detection in olive was achieved through development of real time loop-mediated isothermal amplification targeting the intergenic spacer (IGS) region of the fungus. Specificity of the assay was confirmed using ten Pl. richardsiae strains and 36 other fungus strains of species usually isolated from declining olive trees. The achieved limit of detection was 7.5 × 10-2 ng μL-1 of Pl. richardsiae genomic DNA. A preliminary validation of RealAmp was also performed using material from infected olive plants artificially inoculated in a greenhouse.
Downloads
Download data is not yet available.
Metrics
Metrics Loading ...
References
Literature cited
Abdulmawjood A., Grabowski N., Fohler S., Kittler S., Nagengast H., Klein G., 2014. Development of loop-mediated isothermal amplification (LAMP) assay for rapid and sensitive identification of ostrich meat. PLoS One 9: e100717. DOI: 10.1371/journal.pone.0100717
Besuschio S. A., Llano Murcia M., Benatar A. F., Monnerat S., Cruz I., Picado A., ... Mori Y., 2017. Analytical sensitivity and specificity of a loop-mediated isothermal amplification (LAMP) kit prototype for detection of Trypanosoma cruzi DNA in human blood samples. PLoS neglected tropical diseases, 11(7), e0005779.
Canale M.C., Nunes Nesi C., Falkenbach B.R., Hunhoff da Silva C.A., Brugnara E.C., 2019. Pleurostomophora richardsiae associated with olive tree and grapevine decline in Southern Brazil. Phytopathologia Mediterranea 58: 201-205. doi: 10.13128/ Phytopathol_Mediterr-23357
Carlucci A., Cibelli F., Lops F., Phillips A.J., Ciccarone C., Raimundo M.L., 2015. Pleurostomophora richardsiae associated with trunk diseases of grapevines in southern Italy. Phytopathologia Mediterranea: 109-123. DOI: 10.14601/Phytopathol_Mediterr-15257
Carlucci A., Raimondo M.L., Cibelli F., Phillips A.J., Lops F., 2013. Pleurostomophora richardsiae, Neofusicoccum parvum and Phaeoacremonium aleophilum associated with a decline of olives in southern Italy. Phytopathologia Mediterranea 52: 517-527.
Duan Y., Ge C., Zhang X., Wang J., Zhou M., 2014. A rapid detection method for the plant pathogen Sclerotinia sclerotiorum based on loop-mediated isothermal amplification (LAMP). Australasian Plant Pathology 43: 61-66. DOI: 10.1007/s13313-013-0239-6
EU, 2017. COMMISSION IMPLEMENTING DECISION (EU) 2017/2352 of 14 December 2017. Official Journal of the European Union. https://eur-lex.europa.eu/legal-content/EN/TXT/HTML/?uri=CELEX:32017D2352&from=IT
Fukuta S., Takahashi R., Kuroyanagi S., Miyake N., Nagai H., ... Kageyama K., 2013. Detection of Pythium aphanidermatum in tomato using loop-mediated isothermal amplification (LAMP) with species-specific primers. European Journal of Plant Pathology 136: 689-701. DOI: 10.1007/s10658-013-0198-3
Gétaz M., Bühlmann A., Schneeberger P.H., Van Malderghem C., Duffy B., ... Cottyn B., 2017. A diagnostic tool for improved detection of Xanthomonas fragariae using a rapid and highly specific LAMP assay designed with comparative genomics. Plant Pathology 66: 1094-1102. DOI: 10.1111/ppa.12665
Gramaje D., Úrbez-Torres J.R., Sosnowskim R., 2018. Managing grapevine trunk diseases with respect to etiology and epidemiology: current strategies and future prospects. Plant Disease 102: 12-39. DOI: 10.1094/PDIS-04-17-0512-FE
Halleen F., Mostert L. and Crous P. W., 2007. Pathogenicity testing of lesser-known vascular fungi of grapevines. Australasian Plant Pathology, 2007, 36, 277–285.
Le T.H., Nguyen N.T.B., Truong N.H., De N.V., 2012. Development of Mitochondrial Loop-Mediated Isothermal Amplification for Detection of the Small Liver Fluke Opisthorchis viverrini (Opisthorchiidae; Trematoda; Platyhelminthes). Journal of Clinical Microbiology 50: 1178–1184. DOI: 10.1128/JCM.06277-11
Lee H. J., Jeong R. D., 2020. Reverse Transcription Loop-mediated Isothermal Amplification Assay for Detecting Peach Latent Mosaic Viroid in Peach Pollen. HORTICULTURAL SCIENCE & TECHNOLOGY, 38: 830-839.
Moral J., Agustí-Brisach C., Pérez-Rodríguez M., Xaviér C., Raya M.C., … Trapero A., 2017. Identification of fungal species associated with branch dieback of olive and resistance of table cultivars to Neofusicoccum mediterraneum and Botryosphaeria dothidea. Plant Disease 101: 306-316. DOI: 10.1094/PDIS-06-16-0806-RE
Mori, Y., Nagamine, K., Tomita, N., Notomi, T., 2001. Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation. Biochemical Biophysical Research Communications 289, 150–154.
Notomi T., Okayama H., Masubuchi H., Yonekawa T., Watanabe K., …., Hase T., 2000. Loop-mediated isothermal amplification of DNA. Nucleic Acids Research 28: e63-e63. DOI: 10.1093/nar/28.12.e63
Owczarzy R., Tataurov A.V., Wu Y., Manthey J.A., McQuisten K.A., … Peek A.S., 2008. IDT SciTools: a suite for analysis and design of nucleic acid oligomers. Nucleic Acids Research 36 (2): W163–W169. DOI: 10.1093/nar/gkn198
Ozben S., Demirci F., Değirmenci K., Uzunok S., 2017. Fisrt report of Pleurostoma richardsiae associated with grapevine decline disease of grapevine in Turkey. Journal of Plant Pathology 99: 804.
Parida M., Sannarangaiah S., Dash P. K., Rao P. V. L., Morita, K., 2008. Loop mediated isothermal amplification (LAMP): a new generation of innovative gene amplification technique; perspectives in clinical diagnosis of infectious diseases. Reviews in Medical Virology 18, 407-421. DOI: 10.1002/rmv.593
Pintos Varela C., Redondo Fernandez V., Aguin Casal O., Ferreiroa Martinez V., … Mansilla Vazquez J. P., 2016. First report of Pleurostoma richardsiae causing grapevine trunk disease in Spain. Plant Disease 100: 2168-2168. DOI: 10.1094/PDIS-04-16-0444-PDN
Pitrak D.L., Koneman E.W., Estupinan R.C., Jackson J., 1988. Phialophora richardsiae infection in humans. Clinical Infectious Diseases 10: 1195-1203. DOI: 10.1093/clinids/10.6.1195
Ravindran A., Levy J., Pierson E., Gross D.C., 2012. Development of a loop-mediated isothermal amplification procedure as a sensitive and rapid method for detection of ‘Candidatus Liberibacter solanacearum’ in potatoes and psyllids. Phytopathology 102: 899-907. DOI: 10.1094/PHYTO-03-12-0055-R
Saponari M., Boscia D., Nigro F., Martelli G.P., 2013. Identification of DNA sequences related to Xylella fastidiosa in oleander, almond and olive trees exhibiting leaf scorch symptoms in Apulia (southerrn Italy). Journal of Plant Pathology 95: 668. DOI: 10.4454/JPP.V95I3.035
Schol-Schwarz M.B., 1970. Revision of the genus Phialophora (Moniliales). Persoonia 6: 59-94.
Spies C. F. J., Moyo P., Halleen F., Mostert L., 2018. Phaeoacremonium species diversity on woody hosts in the Western Cape Province of South Africa. Persoonia: Molecular Phylogeny and Evolution of Fungi, 40: 26-62.
Tanner, N.A., Evans, T.C., 2014. Current Protocols in Molecular Biology. John Wiley & Sons, Inc., Somerset, USA : 15.14.1–15.14.14.
Thiessen L.D., Keune J.A., Neill T.M., Turechek W.W., Grove G.G., Mahaffee W.F., 2016. Development of a grower conducted inoculum detection assay for management of grape powdery mildew. Plant Pathology 65: 238-249. DOI: 10.1111/ppa.12421
Tomita, N., Mori, Y., Kanda, H., & Notomi, T. (2008). Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products. Nature Protocols, 3, 877-882. DOI: 10.1038/nprot.2008.57
Vijaykrishna D., Holmes E.C., Joseph U., Fourment M., Su Y.C., ... Stockwell T. B., 2015. The contrasting phylodynamics of human influenza B viruses. Elife 4: e05055. DOI: 10.7554/eLife.05055.023
Vijaykrishna D., Mostert L., Jeewon R., Gams W., Hyde K.D., Crous P.W., 2004. Pleurostomophora, an anamorph of Pleurostoma (Calosphaeriales), a new anamorph genus morphologically similar to Phialophora. Studies in Mycology 50: 387-395.
Yaseen T., Drago S., Valentini F., Elbeaino T., Stampone G., …D'Onghia A. M., 2015. On-site detection of Xylella fastidiosa in host plants and in” spy insects” using the real-time loop-mediated isothermal amplification method. Phytopathologia Mediterranea 54: 488-496. DOI: 10.14601/Phytopathol_Mediterr-1525
Abdulmawjood A., Grabowski N., Fohler S., Kittler S., Nagengast H., Klein G., 2014. Development of loop-mediated isothermal amplification (LAMP) assay for rapid and sensitive identification of ostrich meat. PLoS One 9: e100717. DOI: 10.1371/journal.pone.0100717
Besuschio S. A., Llano Murcia M., Benatar A. F., Monnerat S., Cruz I., Picado A., ... Mori Y., 2017. Analytical sensitivity and specificity of a loop-mediated isothermal amplification (LAMP) kit prototype for detection of Trypanosoma cruzi DNA in human blood samples. PLoS neglected tropical diseases, 11(7), e0005779.
Canale M.C., Nunes Nesi C., Falkenbach B.R., Hunhoff da Silva C.A., Brugnara E.C., 2019. Pleurostomophora richardsiae associated with olive tree and grapevine decline in Southern Brazil. Phytopathologia Mediterranea 58: 201-205. doi: 10.13128/ Phytopathol_Mediterr-23357
Carlucci A., Cibelli F., Lops F., Phillips A.J., Ciccarone C., Raimundo M.L., 2015. Pleurostomophora richardsiae associated with trunk diseases of grapevines in southern Italy. Phytopathologia Mediterranea: 109-123. DOI: 10.14601/Phytopathol_Mediterr-15257
Carlucci A., Raimondo M.L., Cibelli F., Phillips A.J., Lops F., 2013. Pleurostomophora richardsiae, Neofusicoccum parvum and Phaeoacremonium aleophilum associated with a decline of olives in southern Italy. Phytopathologia Mediterranea 52: 517-527.
Duan Y., Ge C., Zhang X., Wang J., Zhou M., 2014. A rapid detection method for the plant pathogen Sclerotinia sclerotiorum based on loop-mediated isothermal amplification (LAMP). Australasian Plant Pathology 43: 61-66. DOI: 10.1007/s13313-013-0239-6
EU, 2017. COMMISSION IMPLEMENTING DECISION (EU) 2017/2352 of 14 December 2017. Official Journal of the European Union. https://eur-lex.europa.eu/legal-content/EN/TXT/HTML/?uri=CELEX:32017D2352&from=IT
Fukuta S., Takahashi R., Kuroyanagi S., Miyake N., Nagai H., ... Kageyama K., 2013. Detection of Pythium aphanidermatum in tomato using loop-mediated isothermal amplification (LAMP) with species-specific primers. European Journal of Plant Pathology 136: 689-701. DOI: 10.1007/s10658-013-0198-3
Gétaz M., Bühlmann A., Schneeberger P.H., Van Malderghem C., Duffy B., ... Cottyn B., 2017. A diagnostic tool for improved detection of Xanthomonas fragariae using a rapid and highly specific LAMP assay designed with comparative genomics. Plant Pathology 66: 1094-1102. DOI: 10.1111/ppa.12665
Gramaje D., Úrbez-Torres J.R., Sosnowskim R., 2018. Managing grapevine trunk diseases with respect to etiology and epidemiology: current strategies and future prospects. Plant Disease 102: 12-39. DOI: 10.1094/PDIS-04-17-0512-FE
Halleen F., Mostert L. and Crous P. W., 2007. Pathogenicity testing of lesser-known vascular fungi of grapevines. Australasian Plant Pathology, 2007, 36, 277–285.
Le T.H., Nguyen N.T.B., Truong N.H., De N.V., 2012. Development of Mitochondrial Loop-Mediated Isothermal Amplification for Detection of the Small Liver Fluke Opisthorchis viverrini (Opisthorchiidae; Trematoda; Platyhelminthes). Journal of Clinical Microbiology 50: 1178–1184. DOI: 10.1128/JCM.06277-11
Lee H. J., Jeong R. D., 2020. Reverse Transcription Loop-mediated Isothermal Amplification Assay for Detecting Peach Latent Mosaic Viroid in Peach Pollen. HORTICULTURAL SCIENCE & TECHNOLOGY, 38: 830-839.
Moral J., Agustí-Brisach C., Pérez-Rodríguez M., Xaviér C., Raya M.C., … Trapero A., 2017. Identification of fungal species associated with branch dieback of olive and resistance of table cultivars to Neofusicoccum mediterraneum and Botryosphaeria dothidea. Plant Disease 101: 306-316. DOI: 10.1094/PDIS-06-16-0806-RE
Mori, Y., Nagamine, K., Tomita, N., Notomi, T., 2001. Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation. Biochemical Biophysical Research Communications 289, 150–154.
Notomi T., Okayama H., Masubuchi H., Yonekawa T., Watanabe K., …., Hase T., 2000. Loop-mediated isothermal amplification of DNA. Nucleic Acids Research 28: e63-e63. DOI: 10.1093/nar/28.12.e63
Owczarzy R., Tataurov A.V., Wu Y., Manthey J.A., McQuisten K.A., … Peek A.S., 2008. IDT SciTools: a suite for analysis and design of nucleic acid oligomers. Nucleic Acids Research 36 (2): W163–W169. DOI: 10.1093/nar/gkn198
Ozben S., Demirci F., Değirmenci K., Uzunok S., 2017. Fisrt report of Pleurostoma richardsiae associated with grapevine decline disease of grapevine in Turkey. Journal of Plant Pathology 99: 804.
Parida M., Sannarangaiah S., Dash P. K., Rao P. V. L., Morita, K., 2008. Loop mediated isothermal amplification (LAMP): a new generation of innovative gene amplification technique; perspectives in clinical diagnosis of infectious diseases. Reviews in Medical Virology 18, 407-421. DOI: 10.1002/rmv.593
Pintos Varela C., Redondo Fernandez V., Aguin Casal O., Ferreiroa Martinez V., … Mansilla Vazquez J. P., 2016. First report of Pleurostoma richardsiae causing grapevine trunk disease in Spain. Plant Disease 100: 2168-2168. DOI: 10.1094/PDIS-04-16-0444-PDN
Pitrak D.L., Koneman E.W., Estupinan R.C., Jackson J., 1988. Phialophora richardsiae infection in humans. Clinical Infectious Diseases 10: 1195-1203. DOI: 10.1093/clinids/10.6.1195
Ravindran A., Levy J., Pierson E., Gross D.C., 2012. Development of a loop-mediated isothermal amplification procedure as a sensitive and rapid method for detection of ‘Candidatus Liberibacter solanacearum’ in potatoes and psyllids. Phytopathology 102: 899-907. DOI: 10.1094/PHYTO-03-12-0055-R
Saponari M., Boscia D., Nigro F., Martelli G.P., 2013. Identification of DNA sequences related to Xylella fastidiosa in oleander, almond and olive trees exhibiting leaf scorch symptoms in Apulia (southerrn Italy). Journal of Plant Pathology 95: 668. DOI: 10.4454/JPP.V95I3.035
Schol-Schwarz M.B., 1970. Revision of the genus Phialophora (Moniliales). Persoonia 6: 59-94.
Spies C. F. J., Moyo P., Halleen F., Mostert L., 2018. Phaeoacremonium species diversity on woody hosts in the Western Cape Province of South Africa. Persoonia: Molecular Phylogeny and Evolution of Fungi, 40: 26-62.
Tanner, N.A., Evans, T.C., 2014. Current Protocols in Molecular Biology. John Wiley & Sons, Inc., Somerset, USA : 15.14.1–15.14.14.
Thiessen L.D., Keune J.A., Neill T.M., Turechek W.W., Grove G.G., Mahaffee W.F., 2016. Development of a grower conducted inoculum detection assay for management of grape powdery mildew. Plant Pathology 65: 238-249. DOI: 10.1111/ppa.12421
Tomita, N., Mori, Y., Kanda, H., & Notomi, T. (2008). Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products. Nature Protocols, 3, 877-882. DOI: 10.1038/nprot.2008.57
Vijaykrishna D., Holmes E.C., Joseph U., Fourment M., Su Y.C., ... Stockwell T. B., 2015. The contrasting phylodynamics of human influenza B viruses. Elife 4: e05055. DOI: 10.7554/eLife.05055.023
Vijaykrishna D., Mostert L., Jeewon R., Gams W., Hyde K.D., Crous P.W., 2004. Pleurostomophora, an anamorph of Pleurostoma (Calosphaeriales), a new anamorph genus morphologically similar to Phialophora. Studies in Mycology 50: 387-395.
Yaseen T., Drago S., Valentini F., Elbeaino T., Stampone G., …D'Onghia A. M., 2015. On-site detection of Xylella fastidiosa in host plants and in” spy insects” using the real-time loop-mediated isothermal amplification method. Phytopathologia Mediterranea 54: 488-496. DOI: 10.14601/Phytopathol_Mediterr-1525