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Hadidi A, Sun L, Randles JW. Modes of Viroid Transmission. Cells 2022; 11:cells11040719. [PMID: 35203368 PMCID: PMC8870041 DOI: 10.3390/cells11040719] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/14/2022] [Accepted: 02/14/2022] [Indexed: 12/23/2022] Open
Abstract
Studies on the ways in which viroids are transmitted are important for understanding their epidemiology and for developing effective control measures for viroid diseases. Viroids may be spread via vegetative propagules, mechanical damage, seed, pollen, or biological vectors. Vegetative propagation is the most prevalent mode of spread at the global, national and local level while further dissemination can readily occur by mechanical transmission through crop handling with viroid-contaminated hands or pruning and harvesting tools. The current knowledge of seed and pollen transmission of viroids in different crops is described. Biological vectors shown to transmit viroids include certain insects, parasitic plants, and goats. Under laboratory conditions, viroids were also shown to replicate in and be transmitted by phytopathogenic ascomycete fungi; therefore, fungi possibly serve as biological vectors of viroids in nature. The term “mycoviroids or fungal viroids” has been introduced in order to denote these viroids. Experimentally, known sequence variants of viroids can be transmitted as recombinant infectious cDNA clones or transcripts. In this review, we endeavor to provide a comprehensive overview of the modes of viroid transmission under both natural and experimental situations. A special focus is the key findings which can be applied to the control of viroid diseases.
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Affiliation(s)
- Ahmed Hadidi
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA
- Correspondence:
| | - Liying Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Xianyang 712100, China;
| | - John W. Randles
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA 5005, Australia;
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2
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In Memoriam of Ricardo Flores: The Career, Achievements, and Legacy of an inspirational plant virologist. Virus Res 2022. [DOI: 10.1016/j.virusres.2022.198718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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3
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Donovan NJ, Chambers GA, Cao M. Detection of Viroids by RT-PCR. Methods Mol Biol 2022; 2316:143-151. [PMID: 34845692 DOI: 10.1007/978-1-0716-1464-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Reverse transcription-polymerase chain reaction (RT-PCR) is an effective method for detecting the presence of viroids in plant tissue. Viroid RNA is converted to cDNA and amplified to detectable levels, making it a fast and useful detection tool, even when the viroid is present at low levels. Methods of viroid detection using conventional RT-PCR are described in this chapter.
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Affiliation(s)
- Nerida J Donovan
- Elizabeth Macarthur Agricultural Institute, New South Wales Department of Primary Industries, Menangle, NSW, Australia.
| | - Grant A Chambers
- Elizabeth Macarthur Agricultural Institute, New South Wales Department of Primary Industries, Menangle, NSW, Australia
| | - Mengji Cao
- National Citrus Engineering Research Centre, Citrus Research Institute, Southwest University, Chongqing, China
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4
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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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5
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Verhoeven JTJ, Botermans M, Schoen R, Koenraadt H, Roenhorst JW. Possible Overestimation of Seed Transmission in the Spread of Pospiviroids in Commercial Pepper and Tomato Crops Based on Large-Scale Grow-Out Trials and Systematic Literature Review. PLANTS 2021; 10:plants10081707. [PMID: 34451751 PMCID: PMC8400851 DOI: 10.3390/plants10081707] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 11/22/2022]
Abstract
Several outbreaks of pospiviroids have been reported in pepper and tomato crops worldwide. Tracing back the origin of the infections has led to different sources. In some cases, the infections were considered to result from seed transmission. Other outbreaks were related to transmission from ornamental crops and weeds. Pospiviroids, in particular potato spindle tuber viroid, are regulated by many countries because they can be harmful to potatoes and tomatoes. Seed transmission has been considered an important pathway of introduction and spread. However, the importance of this pathway can be questioned. This paper presents data on seed transmission from large-scale grow-out trials of infested pepper and tomato seed lots produced under standard seed-industry conditions. In addition, it presents the results of a systematic review of published data on seed transmission and outbreaks in commercial pepper and tomato crops. Based on the results of the grow-out trials and review of the literature, it was concluded that the role of seed transmission in the spread of pospiviroids in practice is possibly overestimated.
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Affiliation(s)
- Jacobus T. J. Verhoeven
- National Plant Protection Organization of the Netherlands, P.O. Box 9102, 6700 HC Wageningen, The Netherlands; (J.T.J.V.); (M.B.); (R.S.)
| | - Marleen Botermans
- National Plant Protection Organization of the Netherlands, P.O. Box 9102, 6700 HC Wageningen, The Netherlands; (J.T.J.V.); (M.B.); (R.S.)
| | - Ruben Schoen
- National Plant Protection Organization of the Netherlands, P.O. Box 9102, 6700 HC Wageningen, The Netherlands; (J.T.J.V.); (M.B.); (R.S.)
| | - Harrie Koenraadt
- Naktuinbouw Research and Development, P.O. Box 40, 2370 AA Roelofarendsveen, The Netherlands;
| | - Johanna W. Roenhorst
- National Plant Protection Organization of the Netherlands, P.O. Box 9102, 6700 HC Wageningen, The Netherlands; (J.T.J.V.); (M.B.); (R.S.)
- Correspondence:
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6
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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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7
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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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8
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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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9
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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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Batuman O, Çiftçi ÖC, Osei MK, Miller SA, Rojas MR, Gilbertson RL. Rasta Disease of Tomato in Ghana is Caused by the Pospiviroids Potato spindle tuber viroid and Tomato apical stunt viroid. PLANT DISEASE 2019; 103:1525-1535. [PMID: 31012822 DOI: 10.1094/pdis-10-18-1751-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Rasta is a virus-like disease of unknown etiology affecting tomato (Solanum lycopersicum) plants in Ghana. Symptoms include stunting; epinasty, crumpling, and chlorosis of leaves; and necrosis of leaf veins, petioles, and stems. Leaf samples with rasta symptoms were collected from commercial tomato fields in Ghana in October 2012 and applied to FTA cards, and RNA extracts were prepared. Reverse-transcription polymerase chain reaction (RT-PCR) tests with primers for Columnea latent viroid, which causes rasta-like symptoms in tomato plants in Mali, were negative, whereas tests with degenerate viroid primer pairs were inconclusive. However, tomato seedlings (Early Pak 7) mechanically inoculated with RNA extracts of 10 of 13 samples developed rasta-like symptoms. In RT-PCR tests with RNA from leaves of the 10 symptomatic seedlings and primers for Potato spindle tuber viroid (PSTVd) or Tomato apical stunt viroid (TASVd), the expected size (approximately 360 bp) of DNA fragment was amplified from eight and two seedlings, respectively. Sequence analyses confirmed that these fragments were from PSTVd and TASVd isolates, and revealed a single PSTVd haplotype and two TASVd haplotypes. The PSTVd and TASVd isolates from Ghana had high nucleotide identities (>94%) with isolates from other geographic regions. In a host range study, PSTVd and TASVd isolates from Ghana induced rasta symptoms in the highly susceptible tomato cultivar Early Pak 7 and mild or no symptoms in Glamour, and symptomless infections in a number of other solanaceous species. PSTVd and TASVd isolates were seed associated and possibly seed transmitted.
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Affiliation(s)
- Ozgur Batuman
- 1 Department of Plant Pathology, Southwest Florida Research and Education Center, University of Florida-IFAS, Immokalee, FL 34142, U.S.A
| | - Ö Cem Çiftçi
- 2 Molecular Biology, Genetics and Bioengineering, Sabancı University, Istanbul, Turkey
| | - Michael K Osei
- 3 CSIR-Crops Research Institute, P.O. BOX 3785, Kumasi, Ghana
| | - Sally A Miller
- 4 Department of Plant Pathology, The Ohio State University, Wooster, OH 44691, U.S.A.; and
| | - Maria R Rojas
- 5 Department of Plant Pathology, University of California-Davis, Davis, CA 95616, U.S.A
| | - Robert L Gilbertson
- 5 Department of Plant Pathology, University of California-Davis, Davis, CA 95616, U.S.A
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Constable F, Chambers G, Penrose L, Daly A, Mackie J, Davis K, Rodoni B, Gibbs M. Viroid-infected Tomato and Capsicum Seed Shipments to Australia. Viruses 2019; 11:v11020098. [PMID: 30682856 PMCID: PMC6410188 DOI: 10.3390/v11020098] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/15/2019] [Accepted: 01/19/2019] [Indexed: 11/30/2022] Open
Abstract
Pospiviroid species are transmitted through capsicum and tomato seeds. Trade in these seeds represents a route for the viroids to invade new regions, but the magnitude of this hazard has not been adequately investigated. Since 2012, tomato seed lots sent to Australia have been tested for pospiviroids before they are released from border quarantine, and capsicum seed lots have been similarly tested in quarantine since 2013. Altogether, more than 2000 seed lots have been tested. Pospiviroids were detected in more than 10% of the seed lots in the first years of mandatory testing, but the proportion of lots that were infected declined in subsequent years to less than 5%. Six pospiviroid species were detected: Citrus exocortis viroid, Columnea latent viroid, Pepper chat fruit viroid, Potato spindle tuber viroid, Tomato chlorotic dwarf viroid and Tomato apical stunt viroid. They were detected in seed lots exported from 18 countries from every production region. In many seed lots, the detectable fraction (prevalence) of infected seeds was estimated to be very small, as low as 6 × 10−5 (~1 in 16,000; CI 5 × 10−6 to 2.5 × 10−4) for some lots. These findings raise questions about seed production practices, and the study indicates the geographic distributions of these pathogens are uncertain, and there is a continuing threat of invasion.
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Affiliation(s)
- Fiona Constable
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio, 5 Ring Road, Bundoora, VIC 3083, Australia.
| | - Grant Chambers
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute (EMAI), Woodbridge Road, Menangle, NSW 2568, Australia.
| | - Lindsay Penrose
- Australian Government Department of Agriculture and Water Resources, 7 London Circuit, Canberra City, ACT 2601, Australia.
| | - Andrew Daly
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute (EMAI), Woodbridge Road, Menangle, NSW 2568, Australia.
| | - Joanne Mackie
- Australian Government Department of Agriculture and Water Resources, 7 London Circuit, Canberra City, ACT 2601, Australia.
| | - Kevin Davis
- Australian Government Department of Agriculture and Water Resources, 7 London Circuit, Canberra City, ACT 2601, Australia.
| | - Brendan Rodoni
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio, 5 Ring Road, Bundoora, VIC 3083, Australia.
| | - Mark Gibbs
- Australian Government Department of Agriculture and Water Resources, 7 London Circuit, Canberra City, ACT 2601, Australia.
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12
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Vertical and Horizontal Transmission of Pospiviroids. Viruses 2018; 10:v10120706. [PMID: 30545048 PMCID: PMC6315636 DOI: 10.3390/v10120706] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/03/2018] [Accepted: 12/05/2018] [Indexed: 12/14/2022] Open
Abstract
Viroids are highly structured, single-stranded, non-protein-coding circular RNA pathogens. Some viroids are vertically transmitted through both viroid-infected ovule and pollen. For example, potato spindle tuber viroid, a species that belongs to Pospiviroidae family, is delivered to the embryo through the ovule or pollen during the development of reproductive tissues before embryogenesis. In addition, some of Pospiviroidae are also horizontally transmitted by pollen. Tomato planta macho viroid in pollen infects to the ovary from pollen tube during pollen tube elongation and eventually causes systemic infection, resulting in the establishment of horizontal transmission. Furthermore, fertilization is not required to accomplish the horizontal transmission. In this review, we will overview the recent research progress in vertical and horizontal transmission of viroids, mainly by focusing on histopathological studies, and also discuss the impact of seed transmission on viroid dissemination and seed health.
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13
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Aviña-Padilla K, Rivera-Bustamante R, Kovalskaya NY, Hammond RW. Pospiviroid Infection of Tomato Regulates the Expression of Genes Involved in Flower and Fruit Development. Viruses 2018; 10:v10100516. [PMID: 30241423 PMCID: PMC6213050 DOI: 10.3390/v10100516] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 09/11/2018] [Accepted: 09/14/2018] [Indexed: 12/22/2022] Open
Abstract
Viroids are unencapsidated, single-stranded, covalently-closed circular, highly structured, noncoding RNAs of 239–401 nucleotides that cause disease in several economically important crop plants. In tomato (Solanum lycopersicum cv. Rutgers), symptoms of pospiviroid infection include stunting, reduced vigor, flower abortion, and reduced size and number of fruits, resulting in significant crop losses. Dramatic alterations in plant development triggered by viroid infection are the result of differential gene expression; in our study, we focused on the effect of tomato planta macho viroid (TPMVd) and Mexican papita viroid (MPVd) infection on gene networks associated with the regulation of flower and fruit development. The expression of several of the genes were previously reported to be affected by viroid infection, but two genes not previously studied were included. Changes in gene expression of SlBIGPETAL1 (bHLH transcription factor) and SlOVA6 (proline-like tRNA synthetase) are involved in petal morphology and fertility, respectively. Expression of SlOVA6 was down-regulated in flowers of TPMVd- and MPVd-infected plants, while expression of SlBIGPETAL1 was up-regulated in flowers. Up-regulation of SlBIGPETAL1 and down-regulation of SlOVA6 were positively correlated with symptoms such as reduced petal size and flower abortion. Expression analysis of additional tomato genes and a prediction of a global network association of genes involved in flower and fruit development and impacted by viroid infection may further elucidate the pathways underlying viroid pathogenicity.
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Affiliation(s)
- Katia Aviña-Padilla
- Campus Juriquilla, Universidad Nacional Autónoma de Mexico, Querátaro Qro 76300, Mexico.
- Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, Guanajuato 36821, Mexico.
| | - Rafael Rivera-Bustamante
- Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, Guanajuato 36821, Mexico.
| | - Natalia Y Kovalskaya
- United States Department of Agriculture, Agricultural Research Service, Molecular Plant Pathology Laboratory, Beltsville, MD 20705, USA.
| | - Rosemarie W Hammond
- United States Department of Agriculture, Agricultural Research Service, Molecular Plant Pathology Laboratory, Beltsville, MD 20705, USA.
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14
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Tangkanchanapas P, Höfte M, De Jonghe K. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) designed for fast and sensitive on-site detection of Pepper chat fruit viroid (PCFVd). J Virol Methods 2018; 259:81-91. [PMID: 29894712 DOI: 10.1016/j.jviromet.2018.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 06/01/2018] [Accepted: 06/08/2018] [Indexed: 01/06/2023]
Abstract
Pepper chat fruit viroid (PCFVd) is one of the most important tomato and pepper diseases causing serious losses, affecting productivity, fruit quality and even international seed trade. Reverse transcription Loop-mediated isothermal amplification (RT-LAMP) is a fast and reliable RNA amplification assay, out competing conventional reverse transcription polymerase chain reaction (RT-PCR) in robustness, analytical sensitivity and specificity, and cost-effectiveness. In this work, a PCFVd specific RT-LAMP detection assay, based on a set of six primers was developed. Under the optimized conditions, PCFVd could be detected within 15 min, with a sensitivity of detecting PCFVd that was almost the same as a probe-based qRT-PCR and 10-100 times higher than the available RT-PCR methods. No cross-amplification with other viroids and tomato viruses was observed. The validated assay was also adapted for convenient on-site detection. Besides replacing the full RNA extraction with a simple lysis procedure, several visualization options, of which the use of SYTO9 was the most convenient, were presented to accommodate any in-field application of the method.
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Affiliation(s)
- Parichate Tangkanchanapas
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Plant Sciences Unit, Crop Protection, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Burgemeester Van Gansberghelaan 96, B-9820 Merelbeke, Belgium
| | - Monica Höfte
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Kris De Jonghe
- Plant Sciences Unit, Crop Protection, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Burgemeester Van Gansberghelaan 96, B-9820 Merelbeke, Belgium.
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15
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Giguère T, Perreault JP. Classification of the Pospiviroidae based on their structural hallmarks. PLoS One 2017; 12:e0182536. [PMID: 28783761 PMCID: PMC5544226 DOI: 10.1371/journal.pone.0182536] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/19/2017] [Indexed: 02/04/2023] Open
Abstract
The simplest known plant pathogens are the viroids. Because of their non-coding single-stranded circular RNA genome, they depend on both their sequence and their structure for both a successful infection and their replication. In the recent years, important progress in the elucidation of their structures was achieved using an adaptation of the selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE) protocol in order to probe viroid structures in solution. Previously, SHAPE has been adapted to elucidate the structures of all of the members of the family Avsunviroidae, as well as those of a few members of the family Pospiviroidae. In this study, with the goal of providing an entire compendium of the secondary structures of the various viroid species, a total of thirteen new Pospiviroidae members were probed in solution using the SHAPE protocol. More specifically, the secondary structures of eleven species for which the genus was previously known were initially elucidated. At this point, considering all of the SHAPE elucidated secondary structures, a classification system for viroids in their respective genera was proposed. On the basis of the structural classification reported here, the probings of both the Grapevine latent viroid and the Dahlia latent viroid provide sound arguments for the determination of their respective genera, which appear to be Apscaviroid and Hostuviroid, respectively. More importantly, this study provides the complete repertoire of the secondary structures, mapped in solution, of all of the accepted viroid species reported thus far. In addition, a classification scheme based on structural hallmarks, an important tool for many biological studies, is proposed.
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Affiliation(s)
- Tamara Giguère
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Pavillon de recherche appliquée sur le cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-Pierre Perreault
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Pavillon de recherche appliquée sur le cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
- * E-mail:
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16
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Characterization of tomato apical stunt viroid isolated from a 24-year old seed lot of Capsicum annuum. Arch Virol 2017; 162:1741-1744. [PMID: 28204897 DOI: 10.1007/s00705-017-3277-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/17/2017] [Indexed: 10/20/2022]
Abstract
Tomato apical stunt viroid (TASVd) has been identified in a 24-year old seed lot of Capsicum annuum produced in Taiwan. It is the first finding of TASVd in this plant species. The isolate could be discriminated from all reported isolates of TASVd based on its nucleotide sequence, which showed only 94.8% identity with the most related genotype of TASVd. This discrimination was substantiated by phylogenetic analysis. Inoculation of a RNA extract of contaminated seeds to healthy pepper plants showed that the infectivity of the viroid had remained over time. Nevertheless, no transmission to seedlings was observed.
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17
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Gago-Zachert S. Viroids, infectious long non-coding RNAs with autonomous replication. Virus Res 2015; 212:12-24. [PMID: 26319312 DOI: 10.1016/j.virusres.2015.08.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/20/2015] [Accepted: 08/22/2015] [Indexed: 10/23/2022]
Abstract
Transcriptome deep-sequencing studies performed during the last years confirmed that the vast majority of the RNAs transcribed in higher organisms correspond to several types of non-coding RNAs including long non-coding RNAs (lncRNAs). The study of lncRNAs and the identification of their functions, is still an emerging field in plants but the characterization of some of them indicate that they play an important role in crucial regulatory processes like flowering regulation, and responses to abiotic stress and plant hormones. A second group of lncRNAs present in plants is formed by viroids, exogenous infectious subviral plant pathogens well known since many years. Viroids are composed of circular RNA genomes without protein-coding capacity and subvert enzymatic activities of their hosts to complete its own biological cycle. Different aspects of viroid biology and viroid-host interactions have been elucidated in the last years and some of them are the main topic of this review together with the analysis of the state-of-the-art about the growing field of endogenous lncRNAs in plants.
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Affiliation(s)
- Selma Gago-Zachert
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany.
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18
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Verhoeven J, Roenhorst J, Hooftman M, Meekes E, Flores R, Serra P. A pospiviroid from symptomless portulaca plants closely related to iresine viroid 1. Virus Res 2015; 205:22-6. [DOI: 10.1016/j.virusres.2015.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 05/06/2015] [Accepted: 05/07/2015] [Indexed: 11/30/2022]
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19
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Matsushita Y, Tsuda S. Distribution of potato spindle tuber viroid in reproductive organs of petunia during its developmental stages. PHYTOPATHOLOGY 2014; 104:964-969. [PMID: 25116641 DOI: 10.1094/phyto-10-13-0294-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Embryo infection is important for efficient seed transmission of viroids. To identify the major pattern of seed transmission of viroids, we used in situ hybridization to histochemically analyze the distribution of Potato spindle tuber viroid (PSTVd) in each developmental stage of petunia (flowering to mature seed stages). In floral organs, PSTVd was present in the reproductive tissues of infected female × infected male and infected female × healthy male but not of healthy female × infected male before embryogenesis. After pollination, PSTVd was detected in the developed embryo and endosperm in all three crosses. These findings indicate that PSTVd is indirectly delivered to the embryo through ovule or pollen during the development of reproductive tissues before embryogenesis but not directly through maternal tissues as cell-to-cell movement during embryogenesis.
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20
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What has been happening with viroids? Virus Genes 2014; 49:175-84. [DOI: 10.1007/s11262-014-1110-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 08/18/2014] [Indexed: 12/18/2022]
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21
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Yoon JY, Cho IS, Choi GS, Choi SK. Construction of Infectious cDNA Clone of a Chrysanthemum stunt viroid Korean Isolate. THE PLANT PATHOLOGY JOURNAL 2014; 30:68-74. [PMID: 25288987 PMCID: PMC4174829 DOI: 10.5423/ppj.oa.08.2013.0076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/30/2013] [Accepted: 09/30/2013] [Indexed: 06/02/2023]
Abstract
Chrysanthemum stunt viroid (CSVd), a noncoding infectious RNA molecule, causes seriously economic losses of chrysanthemum for 3 or 4 years after its first infection. Monomeric cDNA clones of CSVd isolate SK1 (CSVd-SK1) were constructed in the plasmids pGEM-T easy vector and pUC19 vector. Linear positive-sense transcripts synthesized in vitro from the full-length monomeric cDNA clones of CSVd-SK1 could infect systemically tomato seedlings and chrysanthemum plants, suggesting that the linear CSVd RNA transcribed from the cDNA clones could be replicated as efficiently as circular CSVd in host species. However, direct inoculation of plasmid cDNA clones containing full-length monomeric cDNA of CSVd-SK1 failed to infect tomato and chrysanthemum and linear negative-sense transcripts from the plasmid DNAs were not infectious in the two plant species. The cDNA sequences of progeny viroid in systemically infected tomato and chrysanthemum showed a few substitutions at a specific nucleotide position, but there were no deletions and insertions in the sequences of the CSVd progeny from tomato and chrysanthemum plants.
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Affiliation(s)
- Ju-Yeon Yoon
- Department of Horticulture and Landscape, Seoul Women’s University, Seoul 139-774, Korea
| | - In-Sook Cho
- Department of Horticultural Environment, National Institute of Horticultural and Herbal Science, RDA 441-440, Korea
| | - Gug-Seoun Choi
- Department of Horticultural Environment, National Institute of Horticultural and Herbal Science, RDA 441-440, Korea
| | - Seung-Kook Choi
- Department of Horticultural Environment, National Institute of Horticultural and Herbal Science, RDA 441-440, Korea
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22
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Olivier T, Demonty E, Fauche F, Steyer S. Generic detection and identification of pospiviroids. Arch Virol 2014; 159:2097-102. [DOI: 10.1007/s00705-014-1978-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 01/03/2014] [Indexed: 11/30/2022]
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23
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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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24
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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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25
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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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26
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Navarro B, Gisel A, Rodio ME, Delgado S, Flores R, Di Serio F. Viroids: how to infect a host and cause disease without encoding proteins. Biochimie 2012; 94:1474-80. [PMID: 22738729 DOI: 10.1016/j.biochi.2012.02.020] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 02/16/2012] [Indexed: 10/28/2022]
Abstract
Despite being composed by a single-stranded, circular, non-protein-coding RNA of just 246-401 nucleotides (nt), viroids can incite in their host plants symptoms similar to those caused by DNA and RNA viruses, which have genomes at least 20-fold bigger and encode proteins. On the other hand, certain non-protein-coding plant satellite RNAs display structural similarities with viroids but for replication and transmission they need to parasitize specific helper viruses (modifying concomitantly the symptoms they induce). While phenotypic alterations accompanying infection by viruses may partly result from expressing the proteins they code for, how the non-protein-coding viroids (and satellite RNAs) cause disease remains a conundrum. Initial ideas on viroid pathogenesis focused on a direct interaction of the genomic RNA with host proteins resulting in their malfunction. With the advent of RNA silencing, it was alternatively proposed that symptoms could be produced by viroid-derived small RNAs (vd-sRNAs) -generated by the host defensive machinery- targeting specific host mRNA or DNA sequences for post-transcriptional or transcriptional gene silencing, respectively, a hypothesis that could also explain pathogenesis of non-protein-coding satellite RNAs. Evidence sustaining this view has been circumstantial, but recent data provide support for it in two cases: i) the yellow symptoms associated with a specific satellite RNA result from a 22-nt small RNA (derived from the 24-nt fragment of the satellite genome harboring the pathogenic determinant), which is complementary to a segment of the mRNA of the chlorophyll biosynthetic gene CHLI and targets it for cleavage by the RNA silencing machinery, and ii) two 21-nt vd-sRNAS containing the pathogenic determinant of the albino phenotype induced by a chloroplast-replicating viroid target for cleavage the mRNA coding for the chloroplastic heat-shock protein 90 via RNA silencing too. This evidence, which is compelling for the satellite RNA, does not exclude alternative mechanisms.
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Affiliation(s)
- Beatriz Navarro
- Istituto di Virologia Vegetale (CNR), Unità Organizzativa di Bari, Via Amendola 165/A, 70126 Bari, Italy
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27
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Reanwarakorn K, Klinkong S, Porsoongnurn J. First report of natural infection of
Pepper chat fruit viroid
in tomato plants in Thailand. ACTA ACUST UNITED AC 2011. [DOI: 10.5197/j.2044-0588.2011.024.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- K. Reanwarakorn
- Department of Plant PathologyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityKamphaeng SaenNakhon Pathom73140Thailand
| | - S. Klinkong
- Department of Plant PathologyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityKamphaeng SaenNakhon Pathom73140Thailand
| | - J. Porsoongnurn
- Department of Plant PathologyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityKamphaeng SaenNakhon Pathom73140Thailand
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28
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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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29
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Verhoeven JTJ, Roenhorst JW, Owens RA. Mexican papita viroid and tomato planta macho viroid belong to a single species in the genus Pospiviroid. Arch Virol 2011; 156:1433-7. [PMID: 21442229 DOI: 10.1007/s00705-011-0975-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Accepted: 03/08/2011] [Indexed: 11/29/2022]
Abstract
Tomato planta macho viroid (TPMVd) and Mexican papita viroid (MPVd) are two closely related (>90% sequence identity) members of the genus Pospiviroid. Their current status as members of separate species is based upon the reported ability of TPMVd to replicate in Gomphrena globosa and the inability of this viroid to evoke flower break in N. glutinosa. Characterization of a viroid recently isolated from diseased tomato plants grown in Mexico (identical to GenBank accession GQ131573) casts doubt on this earlier report and indicates that these viroids should be classified as members of a single species. Giving priority to the older name, we propose including both of these viroids in the current species Tomato planta macho viroid.
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Affiliation(s)
- J Th J Verhoeven
- Plant Protection Service, P.O. Box 9102, 6700 HC, Wageningen, The Netherlands.
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30
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Verhoeven J, Botermans M, Jansen C, Roenhorst J. First report of
Pepper chat fruit viroid
in capsicum pepper in Canada. ACTA ACUST UNITED AC 2011. [DOI: 10.5197/j.2044-0588.2011.023.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- J.Th.J. Verhoeven
- Plant Protection ServiceP.O. Box 91026700HCWageningenThe Netherlands
| | - M. Botermans
- Plant Protection ServiceP.O. Box 91026700HCWageningenThe Netherlands
| | - C.C.C. Jansen
- Plant Protection ServiceP.O. Box 91026700HCWageningenThe Netherlands
| | - J.W. Roenhorst
- Plant Protection ServiceP.O. Box 91026700HCWageningenThe Netherlands
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31
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Takeda R, Petrov AI, Leontis NB, Ding B. A three-dimensional RNA motif in Potato spindle tuber viroid mediates trafficking from palisade mesophyll to spongy mesophyll in Nicotiana benthamiana. THE PLANT CELL 2011; 23:258-72. [PMID: 21258006 PMCID: PMC3051236 DOI: 10.1105/tpc.110.081414] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 12/13/2010] [Accepted: 12/25/2010] [Indexed: 05/04/2023]
Abstract
Cell-to-cell trafficking of RNA is an emerging biological principle that integrates systemic gene regulation, viral infection, antiviral response, and cell-to-cell communication. A key mechanistic question is how an RNA is specifically selected for trafficking from one type of cell into another type. Here, we report the identification of an RNA motif in Potato spindle tuber viroid (PSTVd) required for trafficking from palisade mesophyll to spongy mesophyll in Nicotiana benthamiana leaves. This motif, called loop 6, has the sequence 5'-CGA-3'...5'-GAC-3' flanked on both sides by cis Watson-Crick G/C and G/U wobble base pairs. We present a three-dimensional (3D) structural model of loop 6 that specifies all non-Watson-Crick base pair interactions, derived by isostericity-based sequence comparisons with 3D RNA motifs from the RNA x-ray crystal structure database. The model is supported by available chemical modification patterns, natural sequence conservation/variations in PSTVd isolates and related species, and functional characterization of all possible mutants for each of the loop 6 base pairs. Our findings and approaches have broad implications for studying the 3D RNA structural motifs mediating trafficking of diverse RNA species across specific cellular boundaries and for studying the structure-function relationships of RNA motifs in other biological processes.
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Affiliation(s)
- Ryuta Takeda
- Molecular, Cellular, and Developmental Biology Program, Ohio State University, Columbus, Ohio 43210
| | - Anton I. Petrov
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio 43403
| | - Neocles B. Leontis
- Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, Ohio 43403
| | - Biao Ding
- Molecular, Cellular, and Developmental Biology Program, Ohio State University, Columbus, Ohio 43210
- Department of Plant Cellular and Molecular Biology and Plant Biotechnology Center, Ohio State University, Columbus, Ohio 43210
- The Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
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32
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Verhoeven JTJ, Roenhorst JW. High stability of original predominant pospiviroid genotypes upon mechanical inoculation from ornamentals to potato and tomato. Arch Virol 2009; 155:269-74. [PMID: 20012658 DOI: 10.1007/s00705-009-0572-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2009] [Accepted: 11/18/2009] [Indexed: 12/22/2022]
Abstract
Eleven pospiviroid isolates from ornamental plants and one from pepper were successfully transmitted to potato and tomato by mechanical inoculation. All isolates with characteristic predominant genotypes were inoculated to a series of potato and tomato plants and propagated for up to four passages. In total, 385 nucleotide sequences were determined, in which 17 new predominant genotypes were identified with minimal differences to the original predominant genotype. In addition, in the original ornamental hosts, only one of eleven predominant pospiviroid genotypes had changed during the experiments over a period of 2 years. These results confirm the high stability of predominant pospiviroid genotypes.
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Affiliation(s)
- J Th J Verhoeven
- Plant Protection Service, 6700, HC, Wageningen, The Netherlands.
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