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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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Gao K, Chen Q, Pan B, Sun Y, Xu Y, Chen D, Liu H, Luo C, Chen X, Li H, Huang C. Current Achievements and Future Prospects in Virus Elimination Technology for Functional Chrysanthemum. Viruses 2023; 15:1770. [PMID: 37632112 PMCID: PMC10459880 DOI: 10.3390/v15081770] [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] [Received: 07/24/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Chrysanthemum is an important functional plant that is used for food, medicine and tea. Functional chrysanthemums become infected with viruses all around the world, seriously lowering their quality and yield. Viral infection has become an important limiting factor in chrysanthemum production. Functional chrysanthemum is often propagated asexually by cutting during production, and viral infection of seedlings is becoming increasingly serious. Chrysanthemums can be infected by a variety of viruses causing different symptoms. With the development of biotechnology, virus detection and virus-free technologies for chrysanthemum seedlings are becoming increasingly effective. In this study, the common virus species, virus detection methods and virus-free technology of chrysanthemum infection are reviewed to provide a theoretical basis for virus prevention, treatment and elimination in functional chrysanthemum.
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Affiliation(s)
- Kang Gao
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (K.G.); (D.C.); (H.L.); (C.L.); (X.C.)
| | - Qingbing Chen
- College of Architecture, North China University of Water Resources and Electric Power, Zhengzhou 450046, China; (Q.C.); (B.P.); (Y.S.); (Y.X.)
| | - Bo Pan
- College of Architecture, North China University of Water Resources and Electric Power, Zhengzhou 450046, China; (Q.C.); (B.P.); (Y.S.); (Y.X.)
| | - Yahui Sun
- College of Architecture, North China University of Water Resources and Electric Power, Zhengzhou 450046, China; (Q.C.); (B.P.); (Y.S.); (Y.X.)
| | - Yuran Xu
- College of Architecture, North China University of Water Resources and Electric Power, Zhengzhou 450046, China; (Q.C.); (B.P.); (Y.S.); (Y.X.)
| | - Dongliang Chen
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (K.G.); (D.C.); (H.L.); (C.L.); (X.C.)
| | - Hua Liu
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (K.G.); (D.C.); (H.L.); (C.L.); (X.C.)
| | - Chang Luo
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (K.G.); (D.C.); (H.L.); (C.L.); (X.C.)
| | - Xi Chen
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (K.G.); (D.C.); (H.L.); (C.L.); (X.C.)
| | - Haiying Li
- College of Architecture, North China University of Water Resources and Electric Power, Zhengzhou 450046, China; (Q.C.); (B.P.); (Y.S.); (Y.X.)
| | - Conglin Huang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (K.G.); (D.C.); (H.L.); (C.L.); (X.C.)
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Ortolá B, Daròs JA. Viroids: Non-Coding Circular RNAs Able to Autonomously Replicate and Infect Higher Plants. BIOLOGY 2023; 12:biology12020172. [PMID: 36829451 PMCID: PMC9952643 DOI: 10.3390/biology12020172] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023]
Abstract
Viroids are a unique type of infectious agent, exclusively composed of a relatively small (246-430 nt), highly base-paired, circular, non-coding RNA. Despite the small size and non-coding nature, the more-than-thirty currently known viroid species infectious of higher plants are able to autonomously replicate and move systemically through the host, thereby inducing disease in some plants. After recalling viroid discovery back in the late 60s and early 70s of last century and discussing current hypotheses about their evolutionary origin, this article reviews our current knowledge about these peculiar infectious agents. We describe the highly base-paired viroid molecules that fold in rod-like or branched structures and viroid taxonomic classification in two families, Pospiviroidae and Avsunviroidae, likely gathering nuclear and chloroplastic viroids, respectively. We review current knowledge about viroid replication through RNA-to-RNA rolling-circle mechanisms in which host factors, notably RNA transporters, RNA polymerases, RNases, and RNA ligases, are involved. Systemic movement through the infected plant, plant-to-plant transmission and host range are also discussed. Finally, we focus on the mechanisms of viroid pathogenesis, in which RNA silencing has acquired remarkable importance, and also for the initiation of potential biotechnological applications of viroid molecules.
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Aviña-Padilla K, Zamora-Macorra EJ, Ochoa-Martínez DL, Alcántar-Aguirre FC, Hernández-Rosales M, Calderón-Zamora L, Hammond RW. Mexico: A Landscape of Viroid Origin and Epidemiological Relevance of Endemic Species. Cells 2022; 11:cells11213487. [PMID: 36359881 PMCID: PMC9653797 DOI: 10.3390/cells11213487] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
Abstract
Viroids are single-stranded, circular RNA molecules (234-406 nt) that infect a wide range of crop species and cause economic losses in agriculture worldwide. They are characterized by the existence of a population of sequence variants, attributed to the low fidelity of RNA polymerases involved in their transcription, resulting in high mutation rates. Therefore, these biological entities exist as quasispecies. This feature allows them to replicate within a wide range of host plants, both monocots and dicots. Viroid hosts include economically important crops such as tomato, citrus, and fruit trees such as peach and avocado. Given the high risk of introducing viroids to viroid disease-free countries, these pathogens have been quarantined globally. As discussed herein, Mexico represents a geographical landscape of viroids linked to their origin and comprises considerable biodiversity. The biological features of viroid species endemic to Mexico are highlighted in this communication. In addition, we report the phylogenetic relationships among viroid and viroid strains, their economic impact, geographical distribution, and epidemiological features, including a broad host range and possible long-distance, seed, or insect-mediated transmission. In summary, this review could be helpful for a better understanding of the biology of viroid diseases and future programs on control of movement and spread to avoid economic losses in agricultural industries.
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Affiliation(s)
- Katia Aviña-Padilla
- Centro de Investigacion y de Estudios Avanzados del I.P.N. Unidad Irapuato, Irapuato 36821, Mexico
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Correspondence: or (K.A.-P.); (R.W.H.); Tel.: +1-301-504-5203 (R.W.H.)
| | | | | | | | | | - Loranda Calderón-Zamora
- Facultad de Biologia, Universidad Autonoma de Sinaloa, Calzada de las Americas y calle Universitarios, s/n Ciudad Universitaria, Culiacan 80013, Mexico
| | - Rosemarie W. Hammond
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
- Correspondence: or (K.A.-P.); (R.W.H.); Tel.: +1-301-504-5203 (R.W.H.)
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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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Lee HJ, Han YS, Cho IS, Jeong RD. Development and application of reverse transcription droplet digital PCR assay for sensitive detection of apple scar skin viroid during in vitro propagation of apple plantlets. Mol Cell Probes 2021; 61:101789. [PMID: 34965481 DOI: 10.1016/j.mcp.2021.101789] [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: 11/18/2021] [Revised: 12/14/2021] [Accepted: 12/23/2021] [Indexed: 11/28/2022]
Abstract
Apple scar skin viroid (ASSVd), of the genus Apscaviroid, causes serious pome fruit diseases, such as apple scar skin, dapple apple, pear rusty skin, pear fruit crinkle, and pear dimple fruit. This study aimed at establishing a sensitive and accurate method for quantification of ASSVd in apple leaves and plantlets using a reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) assay. The specificity was analyzed using other apple viruses, and the negative amplification of the cross-reaction assay demonstrated the high specificity of RT-ddPCR. The detection limit of ASSVd by RT-ddPCR was 1.75 × 102 copies/μL (0.14 concentration), and the sensitivity was ten-fold higher than that of RT-qPCR. Similarly, positive detection in apple plantlet samples by RT-ddPCR was higher than that by RT-qPCR. The RT-ddPCR assay represents a promising alternative for accurate quantitative detection and diagnosis of ASSVd infection in ASSVd-free certification programs.
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Affiliation(s)
- Hyo-Jeong Lee
- Department of Applied Biology and Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61185, South Korea
| | - Yeon Soo Han
- Department of Applied Biology and Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61185, South Korea
| | - In-Sook Cho
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, RDA, Wanju, 55365, South Korea
| | - Rae-Dong Jeong
- Department of Applied Biology and Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61185, South Korea.
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Digital PCR: What Relevance to Plant Studies? BIOLOGY 2020; 9:biology9120433. [PMID: 33266157 PMCID: PMC7760125 DOI: 10.3390/biology9120433] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 01/01/2023]
Abstract
Simple Summary Digital PCR is a third-generation technology based on the subdivision of the analytical sample into numerous partitions that are amplified individually. This review presents the major applications of digital PCR (dPCR) technology developed so far in the field of plant science. In greater detail, dPCR assays have been developed to trace genetically modified plant components, pathogenic and non-pathogenic microorganisms, and plant species. Other applications have concerned the study of the aspects of structural and functional genetics. Abstract Digital PCR (dPCR) is a breakthrough technology that able to provide sensitive and absolute nucleic acid quantification. It is a third-generation technology in the field of nucleic acid amplification. A unique feature of the technique is that of dividing the sample into numerous separate compartments, in each of which an independent amplification reaction takes place. Several instrumental platforms have been developed for this purpose, and different statistical approaches are available for reading the digital output data. The dPCR assays developed so far in the plant science sector were identified in the literature, and the major applications, advantages, disadvantages, and applicative perspectives of the technique are presented and discussed in this review.
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