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Iqbal Z, Masood M, Shafiq M, Briddon RW. Temporal changes in the levels of virus and betasatellite DNA in B. tabaci feeding on CLCuD affected cotton during the growing season. Front Microbiol 2024; 15:1410568. [PMID: 38841073 PMCID: PMC11150673 DOI: 10.3389/fmicb.2024.1410568] [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: 04/01/2024] [Accepted: 05/06/2024] [Indexed: 06/07/2024] Open
Abstract
Cotton, a key source of income for Pakistan, has suffered significantly by cotton leaf curl disease (CLCuD) since 1990. This disease is caused by a complex of phylogenetically-related begomovirus (genus Begomovirus, family Geminiviridae) species and a specific betasatellite (genus Betasatellite, family Tolecusatellitidae), cotton leaf curl Multan betasatellite. Additionally, another DNA satellite called alphasatellite (family Alphasatellitidae), is also frequently associated. All these virus components are vectored by a single species of whitefly (Bemisia tabaci). While many factors affect cotton productivity, including cotton variety, sowing time, and environmental cues such as temperature, humidity, and rainfall, CLCuD is a major biotic constraint. Although the understanding of begomoviruses transmission by whiteflies has advanced significantly over the past three decades, however, the in-field seasonal dynamics of the viruses in the insect vector remained an enigma. This study aimed to assess the levels of virus and betasatellite in whiteflies collected from cotton plants throughout the cotton growing season from 2014 to 2016. Notably, begomovirus levels showed no consistent pattern, with minimal variations, ranging from 0.0017 to 0.0074 ng.μg-1 of the genomic DNA in 2014, 0.0356 to 0.113 ng.μg-1 of the genomic DNA in 2015, and 0.0517 to 0.0791 ng.μg-1 of the genomic DNA in 2016. However, betasatellite levels exhibited a distinct pattern. During 2014 and 2015, it steadily increased throughout the sampling period (May to September). While 2016 showed a similar trend from the start of sampling (July) to September but a decline in October (end of sampling). Such a study has not been conducted previously, and could potentially provide valuable insights about the epidemiology of the virus complex causing CLCuD and possible means of controlling losses due to it.
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Affiliation(s)
- Zafar Iqbal
- Central Laboratories, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Mariyam Masood
- Department of Zoology, Government College Women University, Faisalabad, Pakistan
| | - Muhammad Shafiq
- Department of Biotechnology, University of Management and Technology, Sialkot Campus, Sialkot, Pakistan
| | - Rob W. Briddon
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
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2
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Veerakone S, W Waite D, Delmiglio C, Kanchiraopally D, Kelly M, Khan S, Liefting L, T Lilly S, Perez-Egusquiza Z, Tang J, Yan J, Tomiczek L, Thompson JR. Detection, Characterization, and Distribution of the First Case of Pepino Mosaic Virus in Aotearoa New Zealand. PLANT DISEASE 2024; 108:291-295. [PMID: 37755419 DOI: 10.1094/pdis-02-23-0381-sc] [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: 09/28/2023]
Abstract
Tomato (Solanum lycopersicum L., family Solanaceae) represents one of the most economically valuable horticultural crops worldwide. Tomato production is affected by numerous emerging plant viruses. We identified, for the first time in New Zealand (NZ), Pepino mosaic virus (PepMV) in greenhouse grown tomato crops using a combination of methods from electron microscopy and herbaceous indexing to RT-qPCR and high-throughput sequencing. Phylogenetic and genomic analysis of a near-complete PepMV genome determined that the detected strain belonged to the mild form of the CH2 lineage of the virus. Subsequently, a delimiting survey of PepMV was conducted, and PepMV was detected at four additional locations. PCR-derived sequences obtained from samples collected from different greenhouses and from herbaceous indicator plants were identical to the original sequence. Since PepMV has never been reported in NZ before, seed pathways are speculated to be the most likely source of entry into the country.
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Affiliation(s)
- Stella Veerakone
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
| | - David W Waite
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
| | - Catia Delmiglio
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
| | - Deepika Kanchiraopally
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
| | - Michelle Kelly
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
| | - Subuhi Khan
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
| | - Lia Liefting
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
| | - Sonia T Lilly
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
| | - Zoila Perez-Egusquiza
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
| | - Joe Tang
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
| | - Juncong Yan
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
| | - Laura Tomiczek
- Biosecurity Surveillance and Incursion Investigation, MPI, Auckland 1140, New Zealand
| | - Jeremy R Thompson
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
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3
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Atallah OO, Yassin SM, Verchot J. New Insights into Hop Latent Viroid Detection, Infectivity, Host Range, and Transmission. Viruses 2023; 16:30. [PMID: 38257731 PMCID: PMC10819085 DOI: 10.3390/v16010030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Hop latent viroid (HLVd), a subviral pathogen from the family Pospiviroidae, is a major threat to the global cannabis industry and is the causative agent for "dudding disease". Infected plants can often be asymptomatic for a period of growth and then develop symptoms such as malformed and yellowing leaves, as well as stunted growth. During flowering, HLVd-infected plants show reduced levels of valuable metabolites. This study was undertaken to expand our basic knowledge of HLVd infectivity, transmission, and host range. HLVd-specific primers were used for RT-PCR detection in plant samples and were able to detect HLVd in as little as 5 picograms of total RNA. A survey of hemp samples obtained from a diseased production system proved sole infection of HLVd (72%) with no coexistence of hop stunt viroid. HLVd was infectious through successive passage assays using a crude sap or total RNA extract derived from infected hemp. HLVd was also highly transmissible through hemp seeds at rates of 58 to 80%. Host range assays revealed new hosts for HLVd: tomato, cucumber, chrysanthemum, Nicotiana benthamiana, and Arabidopsis thaliana (Col-0). Sequence analysis of 77 isolates revealed only 3 parsimony-informative sites, while 10 sites were detected among all HLVd isolates available in the GenBank. The phylogenetic relationship among HLVd isolates allowed for inferring two major clades based on the genetic distance. Our findings facilitate further studies on host-viroid interaction and viroid management.
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Affiliation(s)
| | | | - Jeanmarie Verchot
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX 77843, USA; (O.O.A.); (S.M.Y.)
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Fernandez I Marti A, Parungao M, Hollin J, Selimotic B, Farrar G, Seyler T, Anand A, Ahmad R. A Novel, Precise and High-Throughput Technology for Viroid Detection in Cannabis (MFDetect TM). Viruses 2023; 15:1487. [PMID: 37515174 PMCID: PMC10385567 DOI: 10.3390/v15071487] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Hop latent viroid (HLVd) is a severe disease of cannabis, causing substantial economic losses in plant yield and crop value for growers worldwide. The best way to control the disease is early detection to limit the spread of the viroid in grow facilities. This study describes MFDetectTM as a rapid, highly sensitive, and high-throughput tool for detecting HLVd in the early stages of plant development. Furthermore, in the largest research study conducted so far for HLVd detection in cannabis, we compared MFDetectTM with quantitative RT-PCR in a time course experiment using different plant tissues, leaves, petioles, and roots at different plant developmental stages to demonstrate both technologies are comparable. Our study found leaf tissue is a suitable plant material for HLVd detection, with the viroid titer increasing in the infected leaf tissue with the age of plants. The study showed that other tissue types, including petiole and roots, were equally sensitive to detection via MFDetectTM. The assay developed in this research allows the screening of thousands of plants in a week. The assay can be scaled easily to provide growers with a quick turnaround and a cost-effective diagnostic tool for screening many plants and tissue types at different stages of development.
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Affiliation(s)
- Angel Fernandez I Marti
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
- MyFloraDNA, Inc., 1451 River Park Dr., Sacramento, CA 95815, USA
| | - Marcus Parungao
- MyFloraDNA, Inc., 1451 River Park Dr., Sacramento, CA 95815, USA
| | - Jonathan Hollin
- MyFloraDNA, Inc., 1451 River Park Dr., Sacramento, CA 95815, USA
| | - Berin Selimotic
- MyFloraDNA, Inc., 1451 River Park Dr., Sacramento, CA 95815, USA
| | - Graham Farrar
- Glass House Farms, 645 W Laguna Road, Camarillo, CA 93012, USA
| | - Tristan Seyler
- Glass House Farms, 645 W Laguna Road, Camarillo, CA 93012, USA
| | - Ajith Anand
- MyFloraDNA, Inc., 1451 River Park Dr., Sacramento, CA 95815, USA
| | - Riaz Ahmad
- MyFloraDNA, Inc., 1451 River Park Dr., Sacramento, CA 95815, USA
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5
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Venbrux M, Crauwels S, Rediers H. Current and emerging trends in techniques for plant pathogen detection. FRONTIERS IN PLANT SCIENCE 2023; 14:1120968. [PMID: 37223788 PMCID: PMC10200959 DOI: 10.3389/fpls.2023.1120968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 03/21/2023] [Indexed: 05/25/2023]
Abstract
Plant pathogenic microorganisms cause substantial yield losses in several economically important crops, resulting in economic and social adversity. The spread of such plant pathogens and the emergence of new diseases is facilitated by human practices such as monoculture farming and global trade. Therefore, the early detection and identification of pathogens is of utmost importance to reduce the associated agricultural losses. In this review, techniques that are currently available to detect plant pathogens are discussed, including culture-based, PCR-based, sequencing-based, and immunology-based techniques. Their working principles are explained, followed by an overview of the main advantages and disadvantages, and examples of their use in plant pathogen detection. In addition to the more conventional and commonly used techniques, we also point to some recent evolutions in the field of plant pathogen detection. The potential use of point-of-care devices, including biosensors, have gained in popularity. These devices can provide fast analysis, are easy to use, and most importantly can be used for on-site diagnosis, allowing the farmers to take rapid disease management decisions.
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Affiliation(s)
- Marc Venbrux
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
| | - Sam Crauwels
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
| | - Hans Rediers
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
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6
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Tsushima D, Fuji SI. Infectivity of highly pathogenic isolates of potato spindle tuber viroid in dahlia. Arch Virol 2023; 168:131. [PMID: 37022484 DOI: 10.1007/s00705-023-05761-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/16/2023] [Indexed: 04/07/2023]
Abstract
Dahlias that are naturally infected with potato spindle tuber viroid (PSTVd) do not exhibit symptoms. Therefore, if PSTVd isolates that are highly pathogenic in tomato plants infect dahlias, there is a significant risk of PSTVd infecting other plants via dahlias. In this study, we found that almost all highly pathogenic isolates were able to infect dahlia plants, but the symptoms varied depending on the cultivar. When mixed inocula composed of dahlia isolates and highly pathogenic isolates were tested, the dahlia isolates dominantly infected dahlia plants; however, the highly pathogenic isolates also coinfected plants. Our results also suggest that seed or pollen transmission from infected dahlia plants does not occur.
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Affiliation(s)
- Daiki Tsushima
- Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano, Shimoshinjo, Akita, 010-0195, Japan
| | - Shin-Ichi Fuji
- Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano, Shimoshinjo, Akita, 010-0195, Japan.
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7
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Luigi M, Manglli A, Dragone I, Antonelli MG, Contarini M, Speranza S, Bertin S, Tiberini A, Gentili A, Varvaro L, Tomassoli L, Faggioli F. Effects of Biochar on the Growth and Development of Tomato Seedlings and on the Response of Tomato Plants to the Infection of Systemic Viral Agents. Front Microbiol 2022; 13:862075. [PMID: 35615512 PMCID: PMC9125222 DOI: 10.3389/fmicb.2022.862075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Biochar is a rich carbon product obtained by pyrolysis of biomass under a limited supply of oxygen. It is composed mainly of aromatic molecules, but its agronomic value is hard to evaluate and difficult to predict due to its great variable characteristics depending on the type of starting biomass and the conditions of pyrolysis. Anyway, it could be used as soil amendment because it increases the soil fertility of acidic soils, increases the agricultural productivity, and seems to provide protection against some foliar and soilborne diseases. In this study, the effects of biochar, obtained from olive pruning, have been evaluated on tomato seedlings growth and on their response to systemic agents' infection alone or added with beneficial microorganisms (Bacillus spp. and Trichoderma spp.). First, experimental data showed that biochar seems to promote the development of the tomato seedlings, especially at concentrations ranging from 1 to 20% (w/w with peat) without showing any antimicrobial effects on the beneficial soil bacteria at the tomato rhizosphere level and even improving their growth. Thus, those concentrations were used in growing tomato plants experimentally infected with tomato spotted wilt virus (TSWV) and potato spindle tuber viroid (PSTVd). The biochar effect was estimated by evaluating three parameters, namely, symptom expression, number of infected plants, and pathogen quantification, using RT-qPCR technique and −ΔΔCt analysis. Biochar at 10–15% and when added with Trichoderma spp. showed that it reduces the replication of PSTVd and the expression of symptoms even if it was not able to block the start of infection. The results obtained on TSWV-infected plants suggested that biochar could contribute to reducing both infection rate and virus replication. For systemic viral agents, such as PSTVd and TSWV, there are no curative control methods, and therefore, the use of prevention means, as can be assumed the use biochar, for example, in the nursery specialized in horticultural crops, can be of great help. These results can be an encouraging starting point to introduce complex biochar formulates among the sustainable managing strategies of plant systemic diseases.
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Affiliation(s)
- Marta Luigi
- Council for Agricultural Research and Economics-Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
| | - Ariana Manglli
- Council for Agricultural Research and Economics-Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
| | - Immacolata Dragone
- Council for Agricultural Research and Economics-Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
| | | | - Mario Contarini
- Department of Agriculture and Forest Sciences, University of Tuscia, Viterbo, Italy
| | - Stefano Speranza
- Department of Agriculture and Forest Sciences, University of Tuscia, Viterbo, Italy
| | - Sabrina Bertin
- Council for Agricultural Research and Economics-Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
| | - Antonio Tiberini
- Council for Agricultural Research and Economics-Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
| | - Andrea Gentili
- Council for Agricultural Research and Economics-Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
| | - Leonardo Varvaro
- Department of Agriculture and Forest Sciences, University of Tuscia, Viterbo, Italy
| | - Laura Tomassoli
- Council for Agricultural Research and Economics-Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
| | - Francesco Faggioli
- Council for Agricultural Research and Economics-Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
- *Correspondence: Francesco Faggioli
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8
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Bester R, Maree HJ. A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of plum viroid I (PlVd-I). J Virol Methods 2022; 306:114543. [DOI: 10.1016/j.jviromet.2022.114543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/03/2022] [Accepted: 05/12/2022] [Indexed: 10/18/2022]
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9
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Katsarou K, Adkar-Purushothama CR, Tassios E, Samiotaki M, Andronis C, Lisón P, Nikolaou C, Perreault JP, Kalantidis K. Revisiting the Non-Coding Nature of Pospiviroids. Cells 2022; 11:265. [PMID: 35053381 PMCID: PMC8773695 DOI: 10.3390/cells11020265] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/05/2022] [Accepted: 01/07/2022] [Indexed: 12/14/2022] Open
Abstract
Viroids are small, circular, highly structured pathogens that infect a broad range of plants, causing economic losses. Since their discovery in the 1970s, they have been considered as non-coding pathogens. In the last few years, the discovery of other RNA entities, similar in terms of size and structure, that were shown to be translated (e.g., cirRNAs, precursors of miRNA, RNA satellites) as well as studies showing that some viroids are located in ribosomes, have reignited the idea that viroids may be translated. In this study, we used advanced bioinformatic analysis, in vitro experiments and LC-MS/MS to search for small viroid peptides of the PSTVd. Our results suggest that in our experimental conditions, even though the circular form of PSTVd is found in ribosomes, no produced peptides were identified. This indicates that the presence of PSTVd in ribosomes is most probably not related to peptide production but rather to another unknown function that requires further study.
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Affiliation(s)
- Konstantina Katsarou
- Department of Biology, University of Crete, Vassilika Vouton, 71409 Heraklion, Greece; (E.T.); (C.N.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, 71110 Heraklion, Greece;
| | - Charith Raj Adkar-Purushothama
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; (C.R.A.-P.); (J.-P.P.)
| | - Emilios Tassios
- Department of Biology, University of Crete, Vassilika Vouton, 71409 Heraklion, Greece; (E.T.); (C.N.)
- Biomedical Sciences Research Center “Alexander Fleming”, Institute for Bioinnovation, 16672 Vari, Greece;
| | - Martina Samiotaki
- Biomedical Sciences Research Center “Alexander Fleming”, Institute for Bioinnovation, 16672 Vari, Greece;
| | - Christos Andronis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, 71110 Heraklion, Greece;
| | - Purificación Lisón
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València (UPV), Ciudad Politécnica de la Innovación (CPI) 8 E, Ingeniero Fausto Elio s/n, 46011 Valencia, Spain;
| | - Christoforos Nikolaou
- Department of Biology, University of Crete, Vassilika Vouton, 71409 Heraklion, Greece; (E.T.); (C.N.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, 71110 Heraklion, Greece;
- Biomedical Sciences Research Center “Alexander Fleming”, Institute for Bioinnovation, 16672 Vari, Greece;
| | - Jean-Pierre Perreault
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; (C.R.A.-P.); (J.-P.P.)
| | - Kriton Kalantidis
- Department of Biology, University of Crete, Vassilika Vouton, 71409 Heraklion, Greece; (E.T.); (C.N.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, 71110 Heraklion, Greece;
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Tsushima D, Fuji SI. Comparison of two highly sensitive methods to detect potato spindle tuber viroid in Dahlia using quantitative-reverse transcription-polymerase chain reaction assays. J Virol Methods 2021; 300:114401. [PMID: 34883102 DOI: 10.1016/j.jviromet.2021.114401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 08/30/2021] [Accepted: 12/02/2021] [Indexed: 10/19/2022]
Abstract
Potato spindle tuber viroid (PSTVd) belongs to the Pospiviroidae family and is the type species for the genus Pospiviroid. In 2011, PSTVd was first detected in dahlias in Japan. Since that time, unregistered PSTVd isolates have been identified in seven field-grown dahlia cultivars. None of the infected dahlias showed disease symptoms during the early stages of infection, however, growth suppression occasionally occurred during later stages. Therefore, in dahlia, diagnosing PSTVd by the external appearance of plants is difficult, and the threat of new PSTVd isolates spreading to other susceptible hosts still remains. In this study, we developed an efficient inspection method using several dahlia plant tissues and organs including dried bulbs. This developed method will be useful for inspecting seedlings to prevent the invasion of PSTVd at the border.
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Affiliation(s)
- Daiki Tsushima
- Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| | - Shin-Ichi Fuji
- Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan.
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11
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Tseng YW, Wu CF, Lee CH, Chang CJ, Chen YK, Jan FJ. Universal Primers for Rapid Detection of Six Pospiviroids in Solanaceae Plants Using One-Step Reverse-Transcription PCR and Reverse-Transcription Loop-Mediated Isothermal Amplification. PLANT DISEASE 2021; 105:2867-2872. [PMID: 33851864 DOI: 10.1094/pdis-12-20-2730-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A number of viruses and viroids infect solanaceous plants causing severe yield losses. Several seed-borne viroids are listed as quarantine pathogens in many countries. Among them, columnea latent viroid, pepper chat fruit viroid, potato spindle tuber viroid, tomato apical stunt viroid, tomato chlorotic dwarf viroid, and tomato planta macho viroid are of major concerns. The objective of this study was to design and test universal primers that could be used to detect six viroids in solanaceous plants using one-step reverse transcription PCR (RT-PCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP). Results revealed that a pair of degenerate primers could be used in a one-step RT-PCR to amplify six pospiviroids from Solanaceae seeds and plants. Moreover, five primers were designed and used in RT-LAMP to amplify six pospiviroids. The minimal concentration of viroid RNA required for a successful detection varied, ranging from 1 fg to 10 ng, depending on the species of viroid and detection method. In general, RT-LAMP was more sensitive than RT-PCR, but both assays were rapid and highly sensitive tools to detect six pospiviroids. Detection methods in use for these viroids require at least two different sets of primers. The assays developed in this research could facilitate the ability to screen a large number of solanaceous plants and seeds intended for import and export.
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Affiliation(s)
- Yi-Wen Tseng
- Department of Plant Pathology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Chien-Fu Wu
- Department of Plant Pathology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Chia-Hwa Lee
- Department of Plant Pathology, National Chung Hsing University, Taichung 40227, Taiwan
- PhD Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung 40227, Taiwan
| | - Chung-Jan Chang
- Department of Plant Pathology, National Chung Hsing University, Taichung 40227, Taiwan
- Department of Plant Pathology, University of Georgia, Griffin, GA 30223, U.S.A
| | - Yuh-Kun Chen
- Department of Plant Pathology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Fuh-Jyh Jan
- Department of Plant Pathology, National Chung Hsing University, Taichung 40227, Taiwan
- PhD Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung 40227, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
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12
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Venkataraman S, Badar U, Shoeb E, Hashim G, AbouHaidar M, Hefferon K. An Inside Look into Biological Miniatures: Molecular Mechanisms of Viroids. Int J Mol Sci 2021; 22:2795. [PMID: 33801996 PMCID: PMC8001946 DOI: 10.3390/ijms22062795] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 11/17/2022] Open
Abstract
Viroids are tiny single-stranded circular RNA pathogens that infect plants. Viroids do not encode any proteins, yet cause an assortment of symptoms. The following review describes viroid classification, molecular biology and spread. The review also discusses viroid pathogenesis, host interactions and detection. The review concludes with a description of future prospects in viroid research.
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Affiliation(s)
| | | | | | | | | | - Kathleen Hefferon
- Cell and System Biology, University of Toronto, Toronto, ON M5S 3B2, Canada; (S.V.); (U.B.); (E.S.); (G.H.); (M.A.)
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13
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Improvement in the sensitivity of viroid detection by adapting the reverse transcription step in one-step RT-qPCR assays. J Virol Methods 2021; 292:114123. [PMID: 33711376 DOI: 10.1016/j.jviromet.2021.114123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/11/2020] [Accepted: 03/07/2021] [Indexed: 11/22/2022]
Abstract
Over the course of developing and applying a new real-time PCR assay for the detection of the newly described apple chlorotic fruit spot viroid (ACFSVd), slight modifications of the reverse transcription (RT) step were found to improve significantly the detection limit of the assay. To prove this hypothesis, three different one-step RT-qPCR kits for the detection of three plant viroids and three plant viruses were compared. The results showed both extension of the RT reaction time from 10 or 15 min-30 min or the increase in reaction temperature from 49 to 52 °C for the cDNA synthesis step results in a 10 times higher sensitivity for potato spindle tuber viroid and apple scar skin viroid one-step RT-qPCR assay and 45 higher sensitivity for ACFSVd one-step RT-qPCR assay. No variation in the detection limit was observed when the modifications were tested on tomato brown rugose fruit virus, plum pox virus and tomato ringspot virus assays. This finding is highly valuable for the investigation of viroids in general and could contribute to enhance sensitivity in their detection and to benefit regulatory outcomes for national plant protection organisations.
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14
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Leichtfried T, Reisenzein H, Steinkellner S, Gottsberger RA. Transmission studies of the newly described apple chlorotic fruit spot viroid using a combined RT-qPCR and droplet digital PCR approach. Arch Virol 2020; 165:2665-2671. [PMID: 32638117 PMCID: PMC7547948 DOI: 10.1007/s00705-020-04704-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/15/2020] [Indexed: 01/17/2023]
Abstract
The transmission of the apscaviroid tentatively named apple chlorotic fruit spot viroid (ACFSVd) was investigated using a one-step reverse-transcription (RT) droplet digital PCR assay for absolute quantification of the viroid, followed by quantification of relative standard curves by RT-qPCR. Our results indicate that ACFSVd is effectively transmitted by grafting, budding and seeds. No transmission has yet been observed to the viroid-inoculated pome fruit species Pyrus sp. and Cydonia sp. ACFSVd was detected in viruliferous aphids (Myzus persicae, Dysaphis plantaginea) and in codling moths (Cydia pomonella). The viroid was also detected systemically in the infected hemiparasitic plant Viscum album subsp. album (mistletoe).
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Affiliation(s)
- Thomas Leichtfried
- Institute for Sustainable Plant Protection, Austrian Agency for Health and Food Safety, 1220, Vienna, Austria
| | - Helga Reisenzein
- Institute for Sustainable Plant Protection, Austrian Agency for Health and Food Safety, 1220, Vienna, Austria
| | - Siegrid Steinkellner
- Institute of Plant Protection, University of Natural Resources and Life Sciences, 3430, Tulln an der Donau, Austria.
| | - Richard A Gottsberger
- Institute for Sustainable Plant Protection, Austrian Agency for Health and Food Safety, 1220, Vienna, Austria
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15
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Ivanov AV, Shmyglya IV, Zherdev AV, Dzantiev BB, Safenkova IV. The Challenge for Rapid Detection of High-Structured Circular RNA: Assay of Potato Spindle Tuber Viroid Based on Recombinase Polymerase Amplification and Lateral Flow Tests. PLANTS 2020; 9:plants9101369. [PMID: 33076508 PMCID: PMC7650583 DOI: 10.3390/plants9101369] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 01/14/2023]
Abstract
An assay was developed to detect the potato spindle tuber viroid (PSTVd), a dangerous plant pathogen that causes crop damage resulting in economic losses in the potato agriculture sector. The assay was based on the reverse transcription and recombinase polymerase amplification (RT-RPA) of PSTVd RNA coupled with amplicon detection via lateral flow assay (LFA). Primers labeled with fluorescein and biotin were designed for RT-RPA for effective recognition of the loop regions in the high-structured circular RNA of PSTVd. The labeled DNA amplicon was detected using lateral flow test strips consisting of a conjugate of gold nanoparticles with antibodies specific to fluorescein and streptavidin in the test zone. The RT-RPA-LFA detected 106 copies of in vitro transcribed PSTVd RNA in reaction or up to 1:107 diluted extracts of infected plant leaves. The assay took 30 min, including the RT-RPA stage and the LFA stage. The testing of healthy and infected potato samples showed full concordance between the developed RT-RPA-LFA and quantitative reverse transcription polymerase chain reaction (RT-qPCR) and the commercial kit. The obtained results proved the feasibility of using the developed assay to detect PSTVd from a natural source.
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Affiliation(s)
- Aleksandr V. Ivanov
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.I.); (A.V.Z.); (I.V.S.)
| | - Irina V. Shmyglya
- A. G. Lorch Russian Potato Research Center, Kraskovo 140051, Russia;
| | - Anatoly V. Zherdev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.I.); (A.V.Z.); (I.V.S.)
| | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.I.); (A.V.Z.); (I.V.S.)
- Correspondence: ; Tel.: +7-495-954-3142
| | - Irina V. Safenkova
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.I.); (A.V.Z.); (I.V.S.)
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16
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Botermans M, Roenhorst JW, Hooftman M, Verhoeven JTJ, Metz E, van Veen EJ, Geraats BPJ, Kemper M, Beugelsdijk DCM, Koenraadt H, Jodlowska A, Westenberg M. Development and validation of a real-time RT-PCR test for screening pepper and tomato seed lots for the presence of pospiviroids. PLoS One 2020; 15:e0232502. [PMID: 32970706 PMCID: PMC7514017 DOI: 10.1371/journal.pone.0232502] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 08/05/2020] [Indexed: 11/18/2022] Open
Abstract
Potato spindle tuber viroid and other pospiviroids can cause serious diseases in potato and tomato crops. Consequently, pospiviroids are regulated in several countries. Since seed transmission is considered as a pathway for the introduction and spread of pospiviroids, some countries demand for the testing of seed lots of solanaceous crops for the presence of pospiviroids. A real-time RT-PCR test, named PospiSense, was developed for testing pepper (Capsicum annuum) and tomato (Solanum lycopersicum) seeds for seven pospiviroid species known to occur naturally in these crops. The test consists of two multiplex reactions running in parallel, PospiSense 1 and PospiSense 2, that target Citrus exocortis viroid (CEVd), Columnea latent viroid (CLVd), pepper chat fruit viroid (PCFVd), potato spindle tuber viroid (PSTVd), tomato apical stunt viroid (TASVd), tomato chlorotic dwarf viroid (TCDVd) and tomato planta macho viroid (TPMVd, including the former Mexican papita viroid). Dahlia latent viroid (DLVd) is used as an internal isolation control. Validation of the test showed that for both pepper and tomato seeds the current requirements of a routine screening test are fulfilled, i.e. the ability to detect one infested seed in a sample of c.1000 seeds for each of these seven pospiviroids. Additionally, the PospiSense test performed well in an inter-laboratory comparison, which included two routine seed-testing laboratories, and as such provides a relatively easy alternative to the currently used tests.
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Affiliation(s)
- Marleen Botermans
- National Plant Protection Organization, Wageningen, The Netherlands
- * E-mail:
| | | | | | | | - Eveline Metz
- National Plant Protection Organization, Wageningen, The Netherlands
| | | | | | - Mark Kemper
- BASF Vegetable Seeds, Nunhem, The Netherlands
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17
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Ekrami E, Pouresmaieli M, Barati F, Asghari S, Ziarani FR, Shariati P, Mamoudifard M. Potential Diagnostic Systems for Coronavirus Detection: a Critical Review. Biol Proced Online 2020; 22:21. [PMID: 32884452 PMCID: PMC7462115 DOI: 10.1186/s12575-020-00134-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/23/2020] [Indexed: 02/06/2023] Open
Abstract
Abstract Currently there are no effective anti-viral drugs for SARS-CoV-2, so the primary line of defense is to detect infected cases as soon as possible. The high rate of contagion for this virus and the highly nonspecific symptoms of the disease (Coronovirus disease 2019, (Covid-19)) that it causes, such as respiratory symptoms, cough, dyspnea, fever, and viral pneumonia, require the urgent establishment of precise and fast diagnostic tests to verify suspected cases, screen patients, and conduct virus surveillance. Nowadays, several virus detection methods are available for viral diseases, which act on specific properties of each virus or virus family, therefore, further investigations and trials are needed to find a highly efficient and accurate detection method to detect and prevent the outcomes of the disease. Hence, there is an urgent need for more and precise studies in this field. In this review, we discussed the properties of a new generation of coronaviruses (SARS-CoV-2) following routine virus detection methods and proposed new strategies and the use of potential samples for SARS-CoV-2 detection. Graphical Abstract ![]()
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Affiliation(s)
- Elena Ekrami
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Mahdi Pouresmaieli
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Fatemeh Barati
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Sahar Asghari
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Farzad Ramezani Ziarani
- Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Parvin Shariati
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Matin Mamoudifard
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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18
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Ramesh SV, Shivakumar M, Ramteke R, Bhatia VS, Chouhan BS, Goyal S, Singh A, Praveen S, Gill BS, Chand S. Quantification of a legume begomovirus to evaluate soybean genotypes for resistance to yellow mosaic disease. J Virol Methods 2019; 268:24-31. [PMID: 30890330 DOI: 10.1016/j.jviromet.2019.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 02/28/2019] [Accepted: 03/05/2019] [Indexed: 11/19/2022]
Abstract
Mungbean yellow mosaic India virus (MYMIV) infecting soybean and other legumes causes yellow mosaic disease (YMD). Evaluation of soybean genotypes for YMD resistance involves field screening at disease hot spots or in a protected environment using infectious clones or viruliferous whiteflies as sources of virus inocula. Development of efficient virus inoculation and quantification protocols to screen soybean genetic stocks against YMD is imperative for breeding resistant varieties. Binary plasmids harbouring complete, tandem dimeric genomic components DNA A and DNA B of MYMIV-soybean isolate were engineered. The infectivity of the clones was demonstrated in soybean genotypes JS335 and UPSM534 that display contrasting YMD resistance. As a follow-up, soybean germplasm lines, breeding lines, and representative cultivars that were initially screened at an YMD hot-spot were then subjected to Agrobacterium-based infection with MYMIV. Quantitative real time polymerase chain reaction (qRT-PCR) based copy number analysis of MYMIV genomic components allowed soybean genotypes to be classified into three discrete categories; resistant, moderately resistant and susceptible to the viral infection. Thus, a soybean germplasm disease screening system based on agro-infection and qRT-PCR based quantification of MYMIV was developed to facilitate breeding YMD resistant soybean. The implications of this study for obtaining YMD resistant soybean cultivars are discussed.
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Affiliation(s)
- Shunmugiah V Ramesh
- ICAR-Indian Institute of Soybean Research, Khandwa Road, Indore, Madhya Pradesh, India.
| | - Maranna Shivakumar
- ICAR-Indian Institute of Soybean Research, Khandwa Road, Indore, Madhya Pradesh, India
| | - Rajkumar Ramteke
- ICAR-Indian Institute of Soybean Research, Khandwa Road, Indore, Madhya Pradesh, India
| | - Virender S Bhatia
- ICAR-Indian Institute of Soybean Research, Khandwa Road, Indore, Madhya Pradesh, India
| | - Bhagat S Chouhan
- School of Life Sciences, Devi Ahilya Vishwavidhyalaya, Indore, Madhya Pradesh, India
| | - Shwetha Goyal
- ICAR-Indian Institute of Soybean Research, Khandwa Road, Indore, Madhya Pradesh, India
| | - Ajeet Singh
- ICAR-Indian Agricultural Research Institute, (ICAR-IARI), New Delhi, India
| | - Shelly Praveen
- ICAR-Indian Agricultural Research Institute, (ICAR-IARI), New Delhi, India
| | | | - Suresh Chand
- School of Life Sciences, Devi Ahilya Vishwavidhyalaya, Indore, Madhya Pradesh, India
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19
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Adkar-Purushothama CR, Perreault JP. Suppression of RNA-Dependent RNA Polymerase6 Favors the Accumulation of Potato Spindle Tuber Viroid in Nicotiana Benthamiana. Viruses 2019; 11:E345. [PMID: 31013994 PMCID: PMC6520914 DOI: 10.3390/v11040345] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/12/2019] [Accepted: 04/12/2019] [Indexed: 01/23/2023] Open
Abstract
To date, two plant genes encoding RNA-dependent RNA polymerases (RdRs) that play major roles in the defense against RNA viruses have been identified: (i) RdR1, which is responsible for the viral small RNAs (vsRNAs) found in virus-infected plants, and, (ii) RdR6, which acts as a surrogate in the absence of RdR1. In this study, the role of RdR6 in the defense against viroid infection was examined by knock-down of RdR6 followed by potato spindle tuber viroid (PSTVd) infection. The suppression of RdR6 expression increased the plant's growth, as was illustrated by the plant's increased height. PSTVd infection of RdR6 compromised plants resulted in an approximately three-fold increase in the accumulation of viroid RNA as compared to that seen in control plants. Additionally, RNA gel blot assay revealed an increase in the number of viroids derived small RNAs in RdR6 suppressed plants as compared to control plants. These data provide a direct correlation between RdR6 and viroid accumulation and indicate the role of RDR6 in the plant's susceptibility to viroid infection.
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Affiliation(s)
- Charith Raj Adkar-Purushothama
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC J1E 4K8, Canada.
| | - Jean-Pierre Perreault
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC J1E 4K8, Canada.
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20
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Adkar‐Purushothama CR, Sano T, Perreault J. Viroid-derived small RNA induces early flowering in tomato plants by RNA silencing. MOLECULAR PLANT PATHOLOGY 2018; 19:2446-2458. [PMID: 30011126 PMCID: PMC6637976 DOI: 10.1111/mpp.12721] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 05/15/2018] [Accepted: 05/29/2018] [Indexed: 06/01/2023]
Abstract
Viroid infection often leads to early flowering in the host plant. This report describes the targeting of the FRIGIDA-like protein 3 (FRL3) mRNA in tomato plants by a small RNA derived from the conserved left terminal region of the potato spindle tuber viroid (PSTVd). This targeting leads to the silencing of the FRL3 mRNA. Viroid infection assays using a severe variant of PSTVd induced early flowering in tomato plants by the down-regulation of greater amounts of the target than did a mild PSTVd variant. The targeting of the FRL3 mRNA by RNA silencing was validated by both an artificial microRNA experiment transiently expressing viroid-derived small RNAs in tomato plants, and by 5' RNA ligase-mediated rapid amplification of cDNA ends (RACE). These data unambiguously demonstrated the role of small RNAs in the early flowering seen in viroid-infected plants.
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Affiliation(s)
- Charith Raj Adkar‐Purushothama
- RNA Group/Groupe ARN, Département de BiochimieFaculté de Médecine des Sciences de la SantéPavillon de Recherche Appliquée au CancerUniversité de Sherbrooke3201 rue JeanMignaultSherbrookeQCJ1E 4K8Canada
- MYM Nutraceuticals Inc1500 ‐ 409 Granville StreetVancouverBCV6C 1T2Canada
| | - Teruo Sano
- Faculty of Agriculture and Life ScienceHirosaki UniversityHirosaki036‐8561Japan
| | - Jean‐Pierre Perreault
- RNA Group/Groupe ARN, Département de BiochimieFaculté de Médecine des Sciences de la SantéPavillon de Recherche Appliquée au CancerUniversité de Sherbrooke3201 rue JeanMignaultSherbrookeQCJ1E 4K8Canada
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21
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Adkar-Purushothama CR, Perreault JP. Alterations of the viroid regions that interact with the host defense genes attenuate viroid infection in host plant. RNA Biol 2018; 15:955-966. [PMID: 29683389 DOI: 10.1080/15476286.2018.1462653] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
Understanding in intimate details how the viroid interaction with host's defense genes is a cornerstone for developing viroid resistant plants. In this present study, small RNAs (sRNA) derived from Potato spindle tuber viroid (PSTVd) were studied in silico in order to detect any interactions with the serine threonine kinase receptor, a transmembrane protein that plays a role in disease resistance in plants. Using molecular biology techniques, it was determined that PSTVd infection negatively affects at least three serine threonine kinase receptors as well as with three other genes that are known to be involved in the overall development of the tomato plants. The transient expression of these putative PSTVd-sRNAs, using the microRNA sequence as a backbone, in tomato plants induced phenotypes similar to viroid infection. Mutants created by altering the sequence of PSTVd in these regions failed to infect the tomato plant. The data presented here illustrates the importance of these regions in viroid survival, and suggests a possible avenue of exploration for the development of viroid resistant plants.
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Affiliation(s)
- Charith Raj Adkar-Purushothama
- a RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine des sciences de la santé, Pavillon de Recherche Appliquée au Cancer , Université de Sherbrooke , 3201 rue Jean-Mignault, Sherbrooke , Québec , Canada
| | - Jean-Pierre Perreault
- a RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine des sciences de la santé, Pavillon de Recherche Appliquée au Cancer , Université de Sherbrooke , 3201 rue Jean-Mignault, Sherbrooke , Québec , Canada
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22
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Zhang Z, Cui X, Jiang J, Xiao H, Wang H, Wu Q, Habili N, Li S. Improved detection of grapevine latent viroid by RT-qPCR, its bioassay analysis, and its rare occurrence worldwide. J Virol Methods 2018; 254:13-17. [PMID: 29407207 DOI: 10.1016/j.jviromet.2018.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/20/2018] [Accepted: 01/21/2018] [Indexed: 10/18/2022]
Abstract
Three of the five well-known viroids infecting grapevine belong to the genus Apscaviroid. Grapevine latent viroid (GLVd) is a novel grapevine viroid. Although GLVd has the typical sequence motifs of the genus Apscaviroid, it is still an unassigned viroid. In this study, a sensitive, convenient, and rapid one-step RT-qPCR method using hydrolysis probes for the detection of GLVd was developed. Survey and bioassays were also performed for this viroid. Using this method in the survey of GLVd, a low infection rate of 2/226 in a grapevine germplasm resource nursery and a demonstration vineyard in China was determined. Bioassays using agroinfiltration showed that GLVd can infect 'Kyoho' grapevine but not any of the tested herbaceous plants. Furthermore, sequence variability of GLVd was analyzed in six GLVd-infected grapevines. Sequencing revealed a predominant variant with only a few nucleotide changes compared with the reference variant of GLVd. Therefore, the developed RT-qPCR method should be helpful for determining GLVd in other vineyards of the world. The low infection rate, host range, and sequence variability of GLVd have important implications to further improve our knowledge on this novel grapevine viroid.
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Affiliation(s)
- Zhixiang Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiyun Cui
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jihong Jiang
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Hong Xiao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongqing Wang
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Qi Wu
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide 5000, Australia
| | - Nuredin Habili
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide 5000, Australia
| | - Shifang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
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23
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Fox A, Mumford RA. Plant viruses and viroids in the United Kingdom: An analysis of first detections and novel discoveries from 1980 to 2014. Virus Res 2017; 241:10-18. [PMID: 28690070 DOI: 10.1016/j.virusres.2017.06.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 06/30/2017] [Accepted: 06/30/2017] [Indexed: 11/25/2022]
Abstract
This review covers 35 years (1980-2014) representing a period of changing land use and agricultural practices in the United Kingdom (UK), which have also witnessed a marked change in the availability and application of new diagnostic technologies. During this period there have been 53 first records of viruses and viroids, of which 36 were first UK findings and a further 17 previously undescribed viruses. Given the challenges in detection and diagnosis of plant viruses, the field of plant virology has been an early adopter of new diagnostic technologies and these data highlight the transition from a reliance on biological, morphological, and serological based identification to the increased application of nucleic acid based detection methods and latterly the emergence of Next-Generation Sequencing. This review presents a comprehensive record of these findings and an analysis of how the potential drivers of change such as commodity based research, trade, as well as the application of diagnostic technology, could have influenced the frequency and type of findings.
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Affiliation(s)
- A Fox
- Fera Science Ltd., Sand Hutton, York, YO41 1LZ, UK.
| | - R A Mumford
- Fera Science Ltd., Sand Hutton, York, YO41 1LZ, UK
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24
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Babu BK, Mesapogu S, Sharma A, Somasani SR, Arora DK. Quantitative real-time PCR assay for rapid detection of plant and human pathogenic Macrophomina phaseolina from field and environmental samples. Mycologia 2017; 103:466-73. [DOI: 10.3852/10-181] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | | | - Dilip K. Arora
- National Bureau of Agriculturally Important Microorganisms (NBAIM), Post Box 06, Maunath Bhanjan, Uttar Pradesh-275 101, India
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25
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Fast detection of Southern tomato virus by one-step transcription loop-mediated isothermal amplification (RT-LAMP). J Virol Methods 2016; 241:11-14. [PMID: 27965036 DOI: 10.1016/j.jviromet.2016.12.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 12/02/2016] [Accepted: 12/07/2016] [Indexed: 11/21/2022]
Abstract
Southern tomato virus (STV) is a double stranded RNA (dsRNA) virus belonging to genus Amalgavirus (family Amalgamaviridae) which has been detected in tomato plants showing stunting, fruit discoloration and size reduction. A one-step reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the detection of STV in total RNA or sap extracts (obtained just by grinding in buffer) from STV-infected tomato plants by using a set of three primers pairs which were designed to the sequence of the STV putative coat protein. Amplification products were visualized by gel electrophoresis or direct staining of DNA. The sensitivity of RT-LAMP was identical to that of the conventional RT-PCR and less affected by the presence of polymerase inhibitors. STV was detected by RT-LAMP in different tomato tissues, i.e. leaves, roots, fruits and seeds. Also the virus was successfully detected by RT-LAMP from sap extracts obtained from field tomato plants whereas conventional RT-PCR did not. Results of this work show that RT-LAMP is a specific, rapid and cheap procedure to detect STV and it could be implemented on field surveys and sanitation programs.
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26
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Babu B, Jeyaprakash A, Jones D, Schubert TS, Baker C, Washburn BK, Miller SH, Poduch K, Knox GW, Ochoa-Corona FM, Paret ML. Development of a rapid, sensitive TaqMan real-time RT-PCR assay for the detection of Rose rosette virus using multiple gene targets. J Virol Methods 2016; 235:41-50. [PMID: 27210549 DOI: 10.1016/j.jviromet.2016.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 05/02/2016] [Accepted: 05/15/2016] [Indexed: 12/30/2022]
Abstract
Rose rosette virus (RRV), belonging to the genus Emaravirus, is a highly destructive pathogen that causes rose rosette disease. The disease is a major concern for the rose industry in the U.S. due to the lack of highly sensitive methods for early detection of RRV. This is critical, as early identification of the infected plants and eradication is necessary in minimizing the risks associated with the spread of the disease. A highly reliable, specific and sensitive detection assay is thus required to test and confirm the presence of RRV in suspected plant samples. In this study a TaqMan real-time reverse transcription-polymerase chain reaction (RT-PCR) assay was developed for the detection of RRV from infected roses, utilizing multiple gene targets. Four pairs of primers and probes; two of them (RRV_2-1 and RRV_2-2) based on the consensus sequences of the glycoprotein gene (RNA2) and the other two (RRV_3-2 and RRV_3-5) based on the nucleocapsid gene (RNA3) were designed. The specificity of the primers and probes was evaluated against other representative viruses infecting roses, belonging to the genera Alfamovirus, Cucumovirus, Ilarvirus, Nepovirus, Tobamovirus, and Tospovirus and one Emaravirus (Wheat mosaic virus). Dilution assays using the in vitro transcripts (spiked with total RNA from healthy plants, and non-spiked) showed that all the primers and probes are highly sensitive in consistently detecting RRV with a detection limit of 1 fg. Testing of the infected plants over a period of time (three times in monthly intervals) indicated high reproducibility, with the primer/probe RRV_3-5 showing 100% positive detection, while RRV_2-1, RRV_2-2 and RRV_3-2 showed 90% positive detection. The developed real-time RT-PCR assay is reliable, highly sensitive, and can be easily used in diagnostic laboratories for testing and confirmation of RRV.
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Affiliation(s)
- Binoy Babu
- North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Quincy, FL 32351, United States.
| | - Ayyamperumal Jeyaprakash
- Division of Plant Industry, Florida Department of Agriculture and Consumer Services, Gainesville, FL 32608, United States
| | - Debra Jones
- Division of Plant Industry, Florida Department of Agriculture and Consumer Services, Gainesville, FL 32608, United States
| | - Timothy S Schubert
- Division of Plant Industry, Florida Department of Agriculture and Consumer Services, Gainesville, FL 32608, United States
| | - Carlye Baker
- Division of Plant Industry, Florida Department of Agriculture and Consumer Services, Gainesville, FL 32608, United States
| | - Brian K Washburn
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, United States
| | - Steven H Miller
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, United States
| | - Kristina Poduch
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, United States
| | - Gary W Knox
- North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Quincy, FL 32351, United States
| | - Francisco M Ochoa-Corona
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, United States
| | - Mathews L Paret
- North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Quincy, FL 32351, United States.
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Development of a duplex one-step RT-qPCR assay for the simultaneous detection of Apple scar skin viroid and plant RNA internal control. J Virol Methods 2015; 221:100-5. [DOI: 10.1016/j.jviromet.2015.04.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 04/28/2015] [Accepted: 04/29/2015] [Indexed: 11/19/2022]
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Adkar-Purushothama CR, Brosseau C, Giguère T, Sano T, Moffett P, Perreault JP. Small RNA Derived from the Virulence Modulating Region of the Potato spindle tuber viroid Silences callose synthase Genes of Tomato Plants. THE PLANT CELL 2015; 27:2178-94. [PMID: 26290537 PMCID: PMC4568511 DOI: 10.1105/tpc.15.00523] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/23/2015] [Accepted: 07/31/2015] [Indexed: 05/20/2023]
Abstract
The tomato (Solanum lycopersicum) callose synthase genes CalS11-like and CalS12-like encode proteins that are essential for the formation of callose, a major component of pollen mother cell walls; these enzymes also function in callose formation during pathogen infection. This article describes the targeting of these callose synthase mRNAs by a small RNA derived from the virulence modulating region of two Potato spindle tuber viroid variants. More specifically, viroid infection of tomato plants resulted in the suppression of the target mRNAs up to 1.5-fold, depending on the viroid variant used and the gene targeted. The targeting of these mRNAs by RNA silencing was validated by artificial microRNA experiments in a transient expression system and by RNA ligase-mediated rapid amplification of cDNA ends. Viroid mutants incapable of targeting callose synthase mRNAs failed to induce typical infection phenotypes, whereas a chimeric viroid obtained by swapping the virulence modulating regions of a mild and a severe variant of Potato spindle tuber viroid greatly affected the accumulation of viroids and the severity of disease symptoms. These data provide evidence of the silencing of multiple genes by a single small RNA derived from a viroid.
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Affiliation(s)
- Charith Raj Adkar-Purushothama
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, Quebec J1E 4K8, Canada
| | - Chantal Brosseau
- Centre SÈVE, Département de Biologie, Université de Sherbrooke, Quebec J1K 2R1, Canada
| | - Tamara Giguère
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, Quebec J1E 4K8, Canada
| | - Teruo Sano
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
| | - Peter Moffett
- Centre SÈVE, Département de Biologie, Université de Sherbrooke, Quebec J1K 2R1, Canada
| | - Jean-Pierre Perreault
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, Quebec J1E 4K8, Canada
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Noris E, Miozzi L. Real-time PCR protocols for the quantification of the begomovirus tomato yellow leaf curl Sardinia virus in tomato plants and in its insect vector. Methods Mol Biol 2015; 1236:61-72. [PMID: 25287496 DOI: 10.1007/978-1-4939-1743-3_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Tomato yellow leaf curl Sardinia virus (TYLCSV) (Geminiviridae) is an important pathogen, transmitted by the whitefly Bemisia tabaci, that severely affects the tomato production in the Mediterranean basin. Here, we describe real-time PCR protocols suitable for relative and absolute quantification of TYLCSV in tomato plants and in whitefly extracts. Using primers and probe specifically designed for TYLCSV, the protocols for relative quantification allow to compare the amount of TYLCSV present in different plant or whitefly samples, normalized to the amount of DNA present in each sample using endogenous tomato or Bemisia genes as internal references. The absolute quantification protocol allows to calculate the number of genomic units of TYLCSV over the genomic units of the plant host (tomato), with a sensitivity of as few as ten viral genome copies per sample. The described protocols are potentially suitable for several applications, such as plant breeding for resistance, analysis of virus replication, and virus-vector interaction studies.
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Affiliation(s)
- Emanuela Noris
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Strada delle Cacce 73, 10135, Torino, Italy,
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30
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Bakker D, Bruinsma M, Dekter R, Toonen M, Verhoeven JTJ, Koenraadt H. Detection of PSTVd and TCDVd in seeds of tomato using real-time RT-PCR. ACTA ACUST UNITED AC 2015. [DOI: 10.1111/epp.12195] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- D. Bakker
- Naktuinbouw; PO Box 40 2370 AA Roelofarendsveen the Netherlands
| | - M. Bruinsma
- Naktuinbouw; PO Box 40 2370 AA Roelofarendsveen the Netherlands
| | - R.W. Dekter
- Naktuinbouw; PO Box 40 2370 AA Roelofarendsveen the Netherlands
| | - M.A.J. Toonen
- Naktuinbouw; PO Box 40 2370 AA Roelofarendsveen the Netherlands
| | - J. Th. J. Verhoeven
- National Plant Protection Organization; PO Box 9102 6700 HC Wageningen the Netherlands
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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 PATHOLOGY 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] [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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Malandraki I, Varveri C, Olmos A, Vassilakos N. One-step multiplex quantitative RT-PCR for the simultaneous detection of viroids and phytoplasmas of pome fruit trees. J Virol Methods 2015; 213:12-7. [DOI: 10.1016/j.jviromet.2014.11.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/21/2014] [Accepted: 11/25/2014] [Indexed: 12/21/2022]
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Li R, Baysal-Gurel F, Abdo Z, Miller SA, Ling KS. Evaluation of disinfectants to prevent mechanical transmission of viruses and a viroid in greenhouse tomato production. Virol J 2015; 12:5. [PMID: 25623384 PMCID: PMC4312592 DOI: 10.1186/s12985-014-0237-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/30/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In recent years, a number of serious disease outbreaks caused by viruses and viroids on greenhouse tomatoes in North America have resulted in significant economic losses to growers. The objectives of this study were to evaluate the effectiveness of commercial disinfectants against mechanical transmission of these pathogens, and to select disinfectants with broad spectrum reactivity to control general virus and viroid diseases in greenhouse tomato production. METHODS A total of 16 disinfectants were evaluated against Pepino mosaic virus (PepMV), Potato spindle tuber viroid (PSTVd), Tomato mosaic virus (ToMV), and Tobacco mosaic virus (TMV). The efficacy of each disinfectant to deactivate the pathogen's infectivity was evaluated in replicate experiments from at least three independent experiments. Any infectivity that remained in the treated solutions was assessed through bioassays on susceptible tomato plants through mechanical inoculation using inocula that had been exposed with the individual disinfectant for three short time periods (0-10 sec, 30 sec and 60 sec). A positive infection on the inoculated plant was determined through symptom observation and confirmed with enzyme-linked immunosorbent assay (PepMV, ToMV, and TMV) and real-time reverse transcription-PCR (PSTVd). Experimental data were analyzed using Logistic regression and the Bayesian methodology. RESULTS Statistical analyses using logistic regression and the Bayesian methodology indicated that two disinfectants (2% Virkon S and 10% Clorox regular bleach) were the most effective to prevent transmission of PepMV, PSTVd, ToMV, and TMV from mechanical inoculation. Lysol all-purpose cleaner (50%) and nonfat dry milk (20%) were also effective against ToMV and TMV, but with only partial effects for PepMV and PSTVd. CONCLUSION With the broad spectrum efficacy against three common viruses and a viroid, several disinfectants, including 2% Virkon S, 10% Clorox regular bleach and 20% nonfat dry milk, are recommend to greenhouse facilities for consideration to prevent general virus and viroid infection on tomato plants.
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Affiliation(s)
- Rugang Li
- USDA-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC, 29414, USA.
| | - Fulya Baysal-Gurel
- Department of Plant Pathology, The Ohio State University, OARDC, 1680 Madison Avenue, Wooster, OH, 44691, USA.
| | - Zaid Abdo
- USDA-ARS, South Atlantic Area, 950 College Station Road, Athens, GA, 30605, USA.
| | - Sally A Miller
- Department of Plant Pathology, The Ohio State University, OARDC, 1680 Madison Avenue, Wooster, OH, 44691, USA.
| | - Kai-Shu Ling
- USDA-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC, 29414, USA.
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Van Bogaert N, De Jonghe K, Van Damme EJM, Maes M, Smagghe G. Quantitation and localization of pospiviroids in aphids. J Virol Methods 2014; 211:51-4. [PMID: 25455904 DOI: 10.1016/j.jviromet.2014.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 10/06/2014] [Accepted: 10/10/2014] [Indexed: 11/28/2022]
Abstract
In this paper, the potential role of aphids in viroid transmission was explored. Apterous aphids were fed on pospiviroid-infected plants and viroid targets in the aphids were consequently quantified through RT-qPCR and localized within the aphid body using fluorescence in situ hybridization (FISH). Based on the analytical sensitivity test, the limit of detection (LOD) was estimated at 1.69×10(6) viroid copies per individual aphid body. To localize the viroids in the aphids, a pospiviroid-generic Cy5-labelled probe was used and the fluorescent signal was determined by confocal microscopy. Viroids were clearly observed in the aphid's stylet and stomach, but not in the embryos. Viroids were detected in 29% of the aphids after a 24h feeding period, which suggests only a partial and low concentration viroid uptake by the aphid population including viroid concentrations under the LOD. However, these results show that viroids can be ingested by aphids while feeding on infected plants, thus potentially increasing the transmission risk. The combination of FISH and RT-qPCR provides reliable and fast localization and quantitation of viroid targets in individual aphids and thus constitutes a valuable tool in future epidemiological research.
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Affiliation(s)
- N Van Bogaert
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Plant Sciences Unit - Crop Protection, Institute for Agricultural and Fisheries Research (ILVO), Burgemeester Van Gansberghelaan 96, 9820 Merelbeke, Belgium
| | - K De Jonghe
- Plant Sciences Unit - Crop Protection, Institute for Agricultural and Fisheries Research (ILVO), Burgemeester Van Gansberghelaan 96, 9820 Merelbeke, Belgium
| | - E J M Van Damme
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - M Maes
- Plant Sciences Unit - Crop Protection, Institute for Agricultural and Fisheries Research (ILVO), Burgemeester Van Gansberghelaan 96, 9820 Merelbeke, Belgium
| | - G Smagghe
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
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Boonham N, Kreuze J, Winter S, van der Vlugt R, Bergervoet J, Tomlinson J, Mumford R. Methods in virus diagnostics: From ELISA to next generation sequencing. Virus Res 2014; 186:20-31. [DOI: 10.1016/j.virusres.2013.12.007] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 12/08/2013] [Accepted: 12/09/2013] [Indexed: 01/02/2023]
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Dobnik D, Morisset D, Lenarčič R, Ravnikar M. Simultaneous detection of RNA and DNA targets based on multiplex isothermal amplification. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:2989-96. [PMID: 24625323 DOI: 10.1021/jf5002149] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The detection of pathogenic microorganisms present in food, feed, plant, and other samples is important for providing safe food as well as for preventing the spread of microbes. The genome of pathogens is made of DNA or RNA, therefore a multiplex diagnostics tool would ideally be able to amplify and detect both RNA and DNA targets in parallel. With this goal we have developed an isothermal nucleic acid sequence based amplification [NASBA] implemented microarray analysis (NAIMA) procedure, suitable for the simultaneous multiplex amplification of RNA and DNA targets, coupled with the detection on ArrayTubes. The method is demonstrated to be very sensitive and specific for the detection of two economically important quarantine plant pathogens of potato, the potato spindle tuber viroid (RNA target) and Ralstonia solanacearum (DNA target). Because of its isothermal amplification and simple detection equipment, the method is also applicable for on-site analyses. NAIMA can be used in any domain where there is the need to detect RNA and DNA targets simultaneously.
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Affiliation(s)
- David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology , Večna pot 11, Ljubljana 1000, Slovenia
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van Brunschot SL, Bergervoet JHW, Pagendam DE, de Weerdt M, Geering ADW, Drenth A, van der Vlugt RAA. Development of a multiplexed bead-based suspension array for the detection and discrimination of pospiviroid plant pathogens. PLoS One 2014; 9:e84743. [PMID: 24404188 PMCID: PMC3880322 DOI: 10.1371/journal.pone.0084743] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/19/2013] [Indexed: 12/25/2022] Open
Abstract
Efficient and reliable diagnostic tools for the routine indexing and certification of clean propagating material are essential for the management of pospiviroid diseases in horticultural crops. This study describes the development of a true multiplexed diagnostic method for the detection and identification of all nine currently recognized pospiviroid species in one assay using Luminex bead-based suspension array technology. In addition, a new data-driven, statistical method is presented for establishing thresholds for positivity for individual assays within multiplexed arrays. When applied to the multiplexed array data generated in this study, the new method was shown to have better control of false positives and false negative results than two other commonly used approaches for setting thresholds. The 11-plex Luminex MagPlex-TAG pospiviroid array described here has a unique hierarchical assay design, incorporating a near-universal assay in addition to nine species-specific assays, and a co-amplified plant internal control assay for quality assurance purposes. All assays of the multiplexed array were shown to be 100% specific, sensitive and reproducible. The multiplexed array described herein is robust, easy to use, displays unambiguous results and has strong potential for use in routine pospiviroid indexing to improve disease management strategies.
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Affiliation(s)
- Sharon L. van Brunschot
- Plant Biosecurity Cooperative Research Centre, Bruce, Australian Capital Territory, Australia
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Jan H. W. Bergervoet
- Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Daniel E. Pagendam
- Commonwealth Scientific and Industrial Research Organisation Mathematics, Informatics and Statistics, Dutton Park, Queensland, Australia
| | - Marjanne de Weerdt
- Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Andrew D. W. Geering
- Plant Biosecurity Cooperative Research Centre, Bruce, Australian Capital Territory, Australia
- Centre for Plant Science, The University of Queensland, St Lucia, Queensland, Australia
| | - André Drenth
- Centre for Plant Science, The University of Queensland, St Lucia, Queensland, Australia
| | - René A. A. van der Vlugt
- Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands
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Survival and transmission of potato virus Y, pepino mosaic virus, and potato spindle tuber viroid in water. Appl Environ Microbiol 2013; 80:1455-62. [PMID: 24334672 DOI: 10.1128/aem.03349-13] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Hydroponic systems and intensive irrigation are used widely in horticulture and thus have the potential for rapid spread of water-transmissible plant pathogens. Numerous plant viruses have been reported to occur in aqueous environments, although information on their survival and transmission is minimal, due mainly to the lack of effective detection methods and to the complexity of the required transmission experiments. We have assessed the role of water as a source of plant infection using three mechanically transmissible plant pathogens that constitute a serious threat to tomato and potato production: pepino mosaic virus (PepMV), potato virus Y (PVY), and potato spindle tuber viroid (PSTVd). PepMV remains infectious in water at 20 ± 4°C for up to 3 weeks, PVY (NTN strain) for up to 1 week, and PSTVd for up to 7 weeks. Experiments using a hydroponic system show that PepMV (Ch2 genotype) and PVY (NTN strain) can be released from plant roots into the nutrient solution and can infect healthy plants through their roots, ultimately spreading to the green parts, where they can be detected after a few months. In addition, tubers developed on plants grown in substrate watered with PSTVd-infested water were confirmed to be the source of viroid infection. Our data indicate that although well-known pathways of virus spread are more rapid than water-mediated infection, like insect or mechanical transmission through leaves, water is a route that provides a significant bridge for rapid virus/viroid spread. Consequently, water should be taken into account in future epidemiology and risk assessment studies.
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Koo C, Malapi-Wight M, Kim HS, Cifci OS, Vaughn-Diaz VL, Ma B, Kim S, Abdel-Raziq H, Ong K, Jo YK, Gross DC, Shim WB, Han A. Development of a real-time microchip PCR system for portable plant disease diagnosis. PLoS One 2013; 8:e82704. [PMID: 24349341 PMCID: PMC3861469 DOI: 10.1371/journal.pone.0082704] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 10/26/2013] [Indexed: 11/19/2022] Open
Abstract
Rapid and accurate detection of plant pathogens in the field is crucial to prevent the proliferation of infected crops. Polymerase chain reaction (PCR) process is the most reliable and accepted method for plant pathogen diagnosis, however current conventional PCR machines are not portable and require additional post-processing steps to detect the amplified DNA (amplicon) of pathogens. Real-time PCR can directly quantify the amplicon during the DNA amplification without the need for post processing, thus more suitable for field operations, however still takes time and require large instruments that are costly and not portable. Microchip PCR systems have emerged in the past decade to miniaturize conventional PCR systems and to reduce operation time and cost. Real-time microchip PCR systems have also emerged, but unfortunately all reported portable real-time microchip PCR systems require various auxiliary instruments. Here we present a stand-alone real-time microchip PCR system composed of a PCR reaction chamber microchip with integrated thin-film heater, a compact fluorescence detector to detect amplified DNA, a microcontroller to control the entire thermocycling operation with data acquisition capability, and a battery. The entire system is 25 × 16 × 8 cm(3) in size and 843 g in weight. The disposable microchip requires only 8-µl sample volume and a single PCR run consumes 110 mAh of power. A DNA extraction protocol, notably without the use of liquid nitrogen, chemicals, and other large lab equipment, was developed for field operations. The developed real-time microchip PCR system and the DNA extraction protocol were used to successfully detect six different fungal and bacterial plant pathogens with 100% success rate to a detection limit of 5 ng/8 µl sample.
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Affiliation(s)
- Chiwan Koo
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Martha Malapi-Wight
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
| | - Hyun Soo Kim
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Osman S. Cifci
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Vanessa L. Vaughn-Diaz
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
| | - Bo Ma
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Sungman Kim
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Haron Abdel-Raziq
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Kevin Ong
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
| | - Young-Ki Jo
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
| | - Dennis C. Gross
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
| | - Won-Bo Shim
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
| | - Arum Han
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas, United States of America
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, United States of America
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40
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Randhawa GJ, Singh M, Morisset D, Sood P, Zel J. Loop-mediated isothermal amplification: rapid visual and real-time methods for detection of genetically modified crops. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:11338-46. [PMID: 24188249 DOI: 10.1021/jf4030085] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
A rapid, reliable, and sensitive loop-mediated isothermal amplification (LAMP) system was developed for screening of genetically modified organisms (GMOs). The optimized LAMP assays using designed primers target commonly employed promoters, i.e., Cauliflower Mosaic Virus 35S (P-35S) and Figwort Mosaic Virus promoter (P-FMV), and marker genes, i.e., aminoglycoside 3'-adenyltransferase (aadA), neomycin phosphotransferase II (nptII), and β-glucuronidase (uidA). The specificity and performance of the end-point and real-time LAMP assays were confirmed using eight genetically modified (GM) cotton events on four detection systems, employing two chemistries. LAMP assays on the isothermal real-time system were found to be most sensitive, detecting up to four target copies, within 35 min. The LAMP assays herein presented using alternate detection systems can be effectively utilized for rapid and cost-effective screening of the GM status of a sample, irrespective of the crop species or GM trait. These assays coupled with a fast and simple DNA extraction method may further facilitate on-site GMO screening.
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Affiliation(s)
- Gurinder Jit Randhawa
- Division of Genomic Resources (National Research Centre on DNA Fingerprinting), National Bureau of Plant Genetic Resources , New Delhi 110 012, India
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41
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Zhang Y, Yin J, Jiang D, Xin Y, Ding F, Deng Z, Wang G, Ma X, Li F, Li G, Li M, Li S, Zhu S. A universal oligonucleotide microarray with a minimal number of probes for the detection and identification of viroids at the genus level. PLoS One 2013; 8:e64474. [PMID: 23734201 PMCID: PMC3667192 DOI: 10.1371/journal.pone.0064474] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 04/15/2013] [Indexed: 11/19/2022] Open
Abstract
A major challenge in the agricultural industry is the development of techniques that can screen plant samples for viroid infection. Microarrays are promising in this regard, as their high throughput nature can potentially allow for the detection of a range of viroids in a single test. In this paper we present a microarray that can detect a wide spectrum of all 8 reported viroid genera including 37 known plant viroid species. The array was constructed using an automated probe design protocol which generated a minimal number of probes to detect viroids at the genus level. The designed microarray showed a high specificity and sensitivity when tested with a set of standard virus samples. Finally, the microarray was applied to screen infected field samples, with Hop stunt viroid infection identified as the major disease causing pathogen for an infected citrus sample.
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Affiliation(s)
- Yongjiang Zhang
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Jun Yin
- School of Medicine and Medical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Dongmei Jiang
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanyan Xin
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Fang Ding
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ziniu Deng
- Horticulture and Landscape College, Hunan Agricultural University, Changsha, China
| | - Guoping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xianfeng Ma
- Horticulture and Landscape College, Hunan Agricultural University, Changsha, China
| | - Fang Li
- Horticulture and Landscape College, Hunan Agricultural University, Changsha, China
| | - Guifen Li
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Mingfu Li
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Shifang Li
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shuifang Zhu
- Chinese Academy of Inspection and Quarantine, Beijing, China
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42
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Verhoeven JTJ, Meekes ETM, Roenhorst JW, Flores R, Serra P. Dahlia latent viroid: a recombinant new species of the family Pospiviroidae posing intriguing questions about its origin and classification. J Gen Virol 2012; 94:711-719. [PMID: 23255620 DOI: 10.1099/vir.0.048751-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A viroid-like RNA has been detected in two asymptomatic dahlia accessions by return and double PAGE. It appeared smaller than Chrysanthemum stunt viroid and Potato spindle tuber viroid, the two members of the genus Pospiviroid, family Pospiviroidae, reported in this ornamental previously. RT-PCR with primers designed for amplifying all pospiviroids produced no amplicons, but RT-PCR with random primers revealed a 342 nt RNA. The sequence of this RNA was confirmed with specific primers, which additionally revealed its presence in many dahlia cultivars. The RNA was named Dahlia latent viroid (DLVd) because it replicates autonomously, but symptomlessly, in dahlia and shares maximum sequence identity with other viroids of less than 56 %. Furthermore, DLVd displays characteristic features of the family Pospiviroidae: a predicted rod-like secondary structure of minimum free energy with a central conserved region (CCR), and the ability to form the metastable structures hairpins I and II. Its CCR is identical to that of Hop stunt viroid (HSVd, genus Hostuviroid). However, DLVd: (i) has the terminal conserved region present in members of the genus Pospiviroid, but absent in HSVd, and (ii) lacks the terminal conserved hairpin present in HSVd. Phylogenetic reconstructions indicate that HSVd and Pepper chat fruit viroid (genus Pospiviroid) are the closest relatives of DLVd, but DLVd differs from these viroids in its host range, restricted to dahlia so far. Therefore, while DLVd fulfils the criteria to be a novel species of the family Pospiviroidae, its recombinant origin makes assignment to the genera Pospiviroid or Hostuviroid problematic.
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Affiliation(s)
- Jacobus Th J Verhoeven
- National Plant Protection Organization, National Reference Centre, P.O. Box 9102, 6700 HC Wageningen, The Netherlands
| | - Ellis T M Meekes
- Naktuinbouw, P.O. Box 40, 2370 AA Roelofarendsveen, The Netherlands
| | - Johanna W Roenhorst
- National Plant Protection Organization, National Reference Centre, P.O. Box 9102, 6700 HC Wageningen, The Netherlands
| | - Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Valencia 46022, Spain
| | - Pedro Serra
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Valencia 46022, Spain
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43
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Ruščić J, Gutiérrez-Aguirre I, Urbas L, Kramberger P, Mehle N, Škorić D, Barut M, Ravnikar M, Krajačić M. A novel application of methacrylate based short monolithic columns: concentrating Potato spindle tuber viroid from water samples. J Chromatogr A 2012; 1274:129-36. [PMID: 23298847 DOI: 10.1016/j.chroma.2012.12.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 12/01/2012] [Accepted: 12/07/2012] [Indexed: 11/25/2022]
Abstract
Potato spindle tuber viroid (PSTVd) is the causal agent of a number of agriculturally important diseases. It is a single-stranded, circular and unencapsidated RNA molecule with only 356-360 nucleotides and no coding capacity. Because of its peculiar structural features, it is very stable ex vivo and it is easily transmitted mechanically by contaminated hands, tools, machinery, etc. In this work, we describe the development and optimization of a method for concentrating PSTVd using Convective Interaction Media (CIM) monolithic columns. The ion-exchange chromatography on diethylamine (DEAE) monolithic analytical column (CIMac DEAE-0.1 mL) resulted in up to 30% PSTVd recovery whilst the hydrophobic interaction chromatography on C4 monolithic analytical column (CIMac C4-0.1 mL) improved it up to 60%. This was due to the fact that the binding of the viroid to the C4 matrix was less strong than to the highly charged anion-exchange matrix and could be easier and more completely eluted under the applied chromatographic conditions. Based on these preliminary results, a C4 HLD-1 (High Ligand Density) 1 mL monolithic tube column was selected for further experiments. One-litre-water samples were mixed with different viroid quantities and loaded onto the column. By using reverse transcription quantitative polymerase chain reaction (RT-qPCR), the viroid RNA was quantified in the elution fraction (≈5 mL) indicating that 70% of the viroid was recovered and concentrated by at least two orders of magnitude. This approach will be helpful in screening irrigation waters and/or hydroponic systems' nutrient solutions for the presence of even extremely low concentrations of PSTVd.
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Affiliation(s)
- Jelena Ruščić
- University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov trg 6, 10000 Zagreb, Croatia
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44
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Jiang D, Hou W, Sano T, Kang N, Qin L, Wu Z, Li S, Xie L. Rapid detection and identification of viroids in the genus Coleviroid using a universal probe. J Virol Methods 2012; 187:321-6. [PMID: 23142252 DOI: 10.1016/j.jviromet.2012.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 09/28/2012] [Accepted: 10/22/2012] [Indexed: 02/03/2023]
Abstract
A simple, low-cost hybridization assay using a universal DIG-labeled riboprobe for the rapid detection and identification of coleus viroids is presented. An octamer of 32-nucleotide sequence derived from the central conserved region (CCR) of viroids in the genus Coleviroid was used to develop a universal cRNA probe (8-central-conserved-region probe, 8CCR probe) for coleus viroids. Dot-blot hybridization assays demonstrated that the sensitivity of this probe was similar to specific probes for each CbVd, and Northern hybridization results revealed that at least four coleus viroids could be distinguished readily and simultaneously using the 8CCR probe. Batch detection assay showed that hybridization using the 8CCR probe can identify coleus viroids rapidly and effectively. This rapid and low-cost molecular hybridization technique is an effective way to survey the occurrence of coleus viroids, and has reference for the detection of other viroids and possibly viruses.
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Affiliation(s)
- Dongmei Jiang
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China
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45
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Botermans M, van de Vossenberg BTLH, Verhoeven JTJ, Roenhorst JW, Hooftman M, Dekter R, Meekes ETM. Development and validation of a real-time RT-PCR assay for generic detection of pospiviroids. J Virol Methods 2012; 187:43-50. [PMID: 22981990 DOI: 10.1016/j.jviromet.2012.09.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 08/30/2012] [Accepted: 09/03/2012] [Indexed: 11/27/2022]
Abstract
In many countries phytosanitary regulations apply to Potato spindle tuber viroid, because it can cause serious diseases in potato and tomato crops. Other pospiviroids, some of which are distributed widely in ornamental crops, can cause similar diseases. Consequently, there is a need for a reliable and cost-effective generic testing method. An assay was developed that detects all known species of the genus Pospiviroid, using real-time RT-PCR based on TaqMan technology. This GenPospi assay consists of two reactions running in parallel, the first targeting all pospiviroids, except Columnea latent viroid, the second specifically targeting the latter viroid (already published). To monitor the RNA extraction a nad5 internal control was included. Method validation on tomato leaves showed that the GenPospi assay detects all pospiviroids up to a relative infection rate of 0.13% (equals 770 times dilution). The assay was specific because no cross reactivity was observed with other viroids, viruses or nucleic acid from plant hosts. Repeatability and reproducibility were 100% and the assay appeared robust in an inter-laboratory comparison. The GenPospi assay has been shown to be a suitable tool for large-scale screening for all known pospiviroids. Although it has been validated for tomato leaves it can potentially be used for any crop.
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Affiliation(s)
- M Botermans
- National Plant Protection Organization, Wageningen, The Netherlands.
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46
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Optimization and improvement of oligonucleotide microarray-based detection of tomato viruses and pospiviroids. J Virol Methods 2012; 185:43-51. [PMID: 22710323 DOI: 10.1016/j.jviromet.2012.05.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 05/29/2012] [Accepted: 05/30/2012] [Indexed: 01/21/2023]
Abstract
Tomato (Solanum lycopersicum L.) is a vegetable crop which is affected by many viruses and several viroids, causing significant economic loss. Their detection and identification is of critical importance for plant protection and quarantine and certification programs. The potential was examined of an array based on the Combimatrix platform for the detection of 37 viruses belonging to 13 families, one of which is unassigned, together with six pospiviroid species, genus Pospiviroid, family Pospiviroidae. More than 470 oligonucleotide probes (40-mer) were selected for the microarray diagnostic technique developed in this investigation. Most of the virus probes were highly specific and were able to identify tomato viruses. Most pospiviroid probes, however, were non-specific in terms of species, but were specific at the genus level as they hybridized to members of the genus Pospiviroid. Only one probe of the Tomato apical stem viroid was species specific. The repeatability and specificity of the Combimatrix method showed that it can be considered for routine diagnostic use in suspected tomato germplasm since it detected 37 viruses and one pospiviroid at the species level and 5-6 pospiviroids at the genus level. The estimated cost for testing of a single tomato virus is similar to or less than the cost of using ELISA.
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47
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Papayiannis LC, Harkou IS, Markou YM, Demetriou CN, Katis NI. Rapid discrimination of Tomato chlorosis virus, Tomato infectious chlorosis virus and co-amplification of plant internal control using real-time RT-PCR. J Virol Methods 2011; 176:53-9. [DOI: 10.1016/j.jviromet.2011.05.036] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 05/18/2011] [Accepted: 05/25/2011] [Indexed: 02/09/2023]
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48
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Scientific Opinion on the assessment of the risk of solanaceous pospiviroids for the EU territory and the identification and evaluation of risk management options. EFSA J 2011. [DOI: 10.2903/j.efsa.2011.2330] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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49
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Parisi O, Lepoivre P, Jijakli MH. Development of a Quick Quantitative Real-Time PCR for the In Vivo Detection and Quantification of Peach latent mosaic viroid. PLANT DISEASE 2011; 95:137-142. [PMID: 30743421 DOI: 10.1094/pdis-07-10-0512] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Viroids are plant pathogens infecting a broad range of herbaceous and tree crops. Among them, the Peach latent mosaic viroid (PLMVd) infects mainly peach trees, causing a loss of production with no curative options. Detecting this viroid is thus important for certification procedures aiming to avoid the release of infected material into orchards. Presented here is a complete detection method based on reverse transcription (RT) followed by a quantitative real-time polymerase chain reaction (PCR). New primers were selected and optimal reaction conditions determined for routine application of the method. The technique is 105 times more sensitive than the endpoint RT-PCR used for PLMVd detection, and permits earlier detection of PLMVd in infected plants. The quick, low-cost extraction procedure used and the quality of the results obtained make this method suitable for routine testing.
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Affiliation(s)
- Olivier Parisi
- Université de Liège, Gembloux Agro-Bio Tech, Plant Pathology Unit, Passage des Déportés 2, 5030 Gembloux, Belgium
| | - Philippe Lepoivre
- Université de Liège, Gembloux Agro-Bio Tech, Plant Pathology Unit, Passage des Déportés 2, 5030 Gembloux, Belgium
| | - M Haissam Jijakli
- Université de Liège, Gembloux Agro-Bio Tech, Plant Pathology Unit, Passage des Déportés 2, 5030 Gembloux, Belgium
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50
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Luigi M, Luison D, Tomassoli L, Faggioli F. First report of
Potato spindle tuber
and
Citrus exocortis viroids
in
Cestrum
spp. in Italy. ACTA ACUST UNITED AC 2011. [DOI: 10.5197/j.2044-0588.2011.023.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- M. Luigi
- CRA ‐ Centro di Ricerca per la Patologia Vegetale. Via C.G. Bertero22 – 00156RomeItaly
- Dipartimento di Gestione dei Sistemi Agrari e ForestaliUniversità di Reggio Calabria
| | - D. Luison
- CRA ‐ Centro di Ricerca per la Patologia Vegetale. Via C.G. Bertero22 – 00156RomeItaly
| | - L. Tomassoli
- CRA ‐ Centro di Ricerca per la Patologia Vegetale. Via C.G. Bertero22 – 00156RomeItaly
| | - F. Faggioli
- CRA ‐ Centro di Ricerca per la Patologia Vegetale. Via C.G. Bertero22 – 00156RomeItaly
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