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Kogovšek P, Hodgetts J, Hall J, Prezelj N, Nikolić P, Mehle N, Lenarčič R, Rotter A, Dickinson M, Boonham N, Dermastia M, Ravnikar M. LAMP assay and rapid sample preparation method for on-site detection of flavescence dorée phytoplasma in grapevine. Plant Pathol 2015; 64:286-296. [PMID: 26146413 PMCID: PMC4480326 DOI: 10.1111/ppa.12266] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/21/2014] [Indexed: 05/23/2023]
Abstract
In Europe the most devastating phytoplasma associated with grapevine yellows (GY) diseases is a quarantine pest, flavescence dorée (FDp), from the 16SrV taxonomic group. The on-site detection of FDp with an affordable device would contribute to faster and more efficient decisions on the control measures for FDp. Therefore, a real-time isothermal LAMP assay for detection of FDp was validated according to the EPPO standards and MIQE guidelines. The LAMP assay was shown to be specific and extremely sensitive, because it detected FDp in all leaf samples that were determined to be FDp infected using quantitative real-time PCR. The whole procedure of sample preparation and testing was designed and optimized for on-site detection and can be completed in one hour. The homogenization procedure of the grapevine samples (leaf vein, flower or berry) was optimized to allow direct testing of crude homogenates with the LAMP assay, without the need for DNA extraction, and was shown to be extremely sensitive.
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Affiliation(s)
- P Kogovšek
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
- Department of Biology, Biotechnical Faculty, University of LjubljanaVečna pot 111, 1000, Ljubljana, SIovenia
| | - J Hodgetts
- The Food and Environment Research AgencySand Hutton, York, YO41 1LZ, UK
| | - J Hall
- The Food and Environment Research AgencySand Hutton, York, YO41 1LZ, UK
| | - N Prezelj
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
| | - P Nikolić
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
| | - N Mehle
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
| | - R Lenarčič
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
| | - A Rotter
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
| | - M Dickinson
- School of Biosciences, University of NottinghamSutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - N Boonham
- The Food and Environment Research AgencySand Hutton, York, YO41 1LZ, UK
| | - M Dermastia
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
| | - M Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
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Kogovšek P, Kladnik A, Mlakar J, Znidarič MT, Dermastia M, Ravnikar M, Pompe-Novak M. Distribution of Potato virus Y in potato plant organs, tissues, and cells. Phytopathology 2011; 101:1292-300. [PMID: 21692643 DOI: 10.1094/phyto-01-11-0020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The distribution of Potato virus Y (PVY) in the systemically infected potato (Solanum tuberosum) plants of the highly susceptible cultivar Igor was investigated. Virus presence and accumulation was analyzed in different plant organs and tissues using real-time polymerase chain reaction and transmission electron microscopy (TEM) negative staining methods. To get a complete insight into the location of viral RNA within the tissue, in situ hybridization was developed and optimized for the detection of PVY RNA at the cellular level. PVY was shown to accumulate in all studied leaf and stem tissues, in shoot tips, roots, and tubers; however, the level of virus accumulation was specific for each organ or tissue. The highest amounts of viral RNA and viral particles were found in symptomatic leaves and stem. By observing cell ultrastructure with TEM, viral cytoplasmic inclusion bodies were localized in close vicinity to the epidermis and in trichomes. Our results show that viral RNA, viral particles, and cytoplasmic inclusion bodies colocalize within the same type of cells or in close vicinity.
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Affiliation(s)
- P Kogovšek
- National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia.
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Kogovšek P, Gow L, Pompe-Novak M, Gruden K, Foster G, Boonham N, Ravnikar M. Single-step RT real-time PCR for sensitive detection and discrimination of Potato virus Y isolates. J Virol Methods 2008; 149:1-11. [DOI: 10.1016/j.jviromet.2008.01.025] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 01/16/2008] [Accepted: 01/21/2008] [Indexed: 10/22/2022]
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