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Thompson JR, Langenhan JL, Fuchs M, Perry KL. Genotyping of Cucumber mosaic virus isolates in western New York State during epidemic years: Characterization of an emergent plant virus population. Virus Res 2015; 210:169-77. [PMID: 26254084 DOI: 10.1016/j.virusres.2015.07.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/30/2015] [Accepted: 07/31/2015] [Indexed: 11/24/2022]
Abstract
In the early 2000s an epidemic of cucumber mosaic virus (CMV) spread within the Midwestern and Eastern US affecting snap and dry bean (Phaseolus vulgaris L.) cultivation. Fifty one CMV isolates from this period were partially characterized from varied hosts by sequencing a section from each of the three genomic RNAs. Aside from one subgroup II strain from pepper, all isolates, including those from snap bean, fell within the IA subgroup. The nucleotide sequence diversity of virus populations sampled at multiple sites and at different years was significantly higher than that of a population from single site in a single year, although in general the number of polymorphisms was low (<11%). Complementary DNA (cDNA) clones of Bn57, a representative isolate from snap bean, were engineered for the production of infectious in vitro RNA transcripts initiated from a T7 promoter. Infections from these cDNAs resulted in symptoms consistent with those of the original field isolate, indicating that a satellite RNA is not involved in symptom expression in snap bean. These infectious clones were used to assess symptom determinants and the effects of virus infection on plant growth. Inoculations with pseudorecombinants derived from Bn57 and the non-bean infecting strain Fny confirmed RNA2 as a specific determinant for snap bean infection. Bn57, along with almost all isolates identified in this study contained the Y631 locus in the 2a protein, a determinant for systemic infection in bean. The presence of this locus extended to all non-bean hosts except two pepper infecting isolates. Infection by Bn57 in snap bean had a significant effect on pod number and mass with a 55 and 41 percent reduction in greenhouse assays, respectively. To our knowledge Bn57 is the first CMV strain isolated from P. vulgaris to be fully sequenced and cloned, providing a useful tool for analyses of CMV-host interactions.
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Affiliation(s)
- Jeremy R Thompson
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853-5904, USA.
| | - Jamie L Langenhan
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853-5904, USA
| | - Marc Fuchs
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456, USA
| | - Keith L Perry
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853-5904, USA
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Kawamura R, Shimura H, Mochizuki T, Ohki ST, Masuta C. Pollen transmission of asparagus virus 2 (AV-2) may facilitate mixed infection by two AV-2 isolates in asparagus plants. PHYTOPATHOLOGY 2014; 104:1001-6. [PMID: 25116643 DOI: 10.1094/phyto-12-13-0348-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Asparagus virus 2 (AV-2) is a member of the genus Ilarvirus and thought to induce the asparagus decline syndrome. AV-2 is known to be transmitted by seed, and the possibility of pollen transmission was proposed 25 years ago but not verified. In AV-2 sequence analyses, we have unexpectedly found mixed infection by two distinct AV-2 isolates in two asparagus plants. Because mixed infections by two related viruses are normally prevented by cross protection, we suspected that pollen transmission of AV-2 is involved in mixed infection. Immunohistochemical analyses and in situ hybridization using AV-2-infected tobacco plants revealed that AV-2 was localized in the meristem and associated with pollen grains. To experimentally produce a mixed infection via pollen transmission, two Nicotiana benthamiana plants that were infected with each of two AV-2 isolates were crossed. Derived cleaved-amplified polymorphic sequence analysis identified each AV-2 isolate in the progeny seedlings, suggesting that pollen transmission could indeed result in a mixed infection, at least in N. benthamiana.
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Phan MSV, Seo JK, Choi HS, Lee SH, Kim KH. Pseudorecombination between Two Distinct Strains of Cucumber mosaic virus Results in Enhancement of Symptom Severity. THE PLANT PATHOLOGY JOURNAL 2014; 30:316-22. [PMID: 25289019 PMCID: PMC4181118 DOI: 10.5423/ppj.nt.04.2014.0031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 05/08/2014] [Indexed: 05/21/2023]
Abstract
Recently, a Cucumber mosaic virus (CMV) strain, named as CMV-209, was isolated from Glycine soja. In this study, symptom expression of CMV-209 was analyzed in detail in Nicotiana benthamiana by comparing with that of CMV-Fny, which is a representative strain of CMV. Using infectious cDNA clones of CMV strains 209 and Fny, symptom expression of various pseudorecombinants between these two strains were examined in the early and late infection stages. In the early infection stage, the pseudorecombinants containing Fny-RNA2 induced stunting and leaf distortion on the newly emerged leaves whereas the pseudorecombinants containing 209-RNA2 caused no obvious symptoms. In the late infection stage, the pseudorecombinants containing 209-RNA1 and Fny-RNA2 induced severe leaf distortion and stunting, while CMV-209 induced mild symptom and CMV-Fny caused typical mosaic, general stunting, and leaf distortion symptoms, indicating that RNA 2 encodes a symptom determinant(s) of CMV, which is capable of enhancing symptoms. Furthermore, our results support the possibility that natural recombination between compatible viruses can result in emergence of novel viruses causing severe damages in crop fields.
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Affiliation(s)
- Mi Sa Vo Phan
- Department of Agricultural Biotechnology and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
| | - Jang-Kyun Seo
- Crop Protection Division, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea
| | - Hong-Soo Choi
- Crop Protection Division, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea
| | - Su-Heon Lee
- Department of Applied Biology, Kyungpook National University, Daegu 702-701, Korea
| | - Kook-Hyung Kim
- Department of Agricultural Biotechnology and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
- Corresponding author. Phone) +82-2-880-4677, FAX) +82-2-873-2317 E-mail)
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Dai J, Peng H, Chen W, Cheng J, Wu Y. Development of multiplex real-time PCR for simultaneous detection of three Potyviruses in tobacco plants. J Appl Microbiol 2013; 114:502-8. [PMID: 23164070 DOI: 10.1111/jam.12071] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 09/21/2012] [Accepted: 10/26/2012] [Indexed: 11/29/2022]
Abstract
AIMS To develop a multiplex real-time PCR assay using TaqMan probes for the simultaneous detection and quantification of Tobacco etch virus (TEV), Potato virus Y (PVY) and Tobacco vein banding mosaic virus (TVBMV). METHODS AND RESULTS Specific primer and probe combinations for TEV and TVBMV were developed from the coat protein region of the viral genome. To detect PVY, a primer and probe combination PVY-Univ F, PVY-Univ R and PVY-Univ P for amplifying the coat protein region of the virus genome was employed. The detection limit of multiplex real-time PCR for these viruses was 10 copies μl(-1) of the standard plasmid. The multiplex reaction was successful in the detection of these three pathogens, with no non-specific amplification and cross-reaction. CONCLUSIONS This multiplex real-time PCR provides a rapid, effective, specific and sensitive method for the simultaneous detection and quantification of the three pathogens on infected tobacco plants. SIGNIFICANCE AND IMPACT OF THE STUDY This multiplex real-time PCR will be useful not only for diagnostic, ecological, epidemiological and pathogenesis studies, but also for investigating host/virus or virus/virus interactions, in particular during mix infection.
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Affiliation(s)
- J Dai
- State Key Laboratory of Crop Stress Biology in Arid Areas and Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, China
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Dai J, Cheng J, Huang T, Zheng X, Wu Y. A multiplex reverse transcription PCR assay for simultaneous detection of five tobacco viruses in tobacco plants. J Virol Methods 2012; 183:57-62. [PMID: 22484613 DOI: 10.1016/j.jviromet.2012.03.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 03/13/2012] [Accepted: 03/21/2012] [Indexed: 10/28/2022]
Abstract
Tobacco viruses including Tobacco mosaic virus (TMV), Cucumber mosaic virus (CMV), Tobacco etch virus (TEV), Potato virus Y (PVY) and Tobacco vein banding mosaic virus (TVBMV) are major viruses infecting tobacco and can cause serious crop losses. A multiplex reverse transcription polymerase chain reaction assay was developed to detect simultaneously and differentiate all five viruses. The system used specific primer sets for each virus producing five distinct fragments 237, 273, 347, 456 and 547 bp, representing TMV, CMV subgroup I, TEV, PVY(O) and TVBMV, respectively. These primers were used for detection of the different viruses by single PCR and multiplex PCR and the results were confirmed by DNA sequencing analysis. The protocol was used to detect viruses from different parts of China. The simultaneous and sensitive detection of different viruses using the multiplex PCR is more efficient and economical than other conventional methods for tobacco virus detection. This multiplex PCR provides a rapid and reliable method for the detection and identification of major tobacco viruses, and will be useful for epidemiological studies.
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Affiliation(s)
- Jin Dai
- State Key Laboratory of Crop Stress Biology in Arid Areas and Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, 712100, China
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Stainton D, Kraberger S, Walters M, Wiltshire EJ, Rosario K, Halafihi M, Lolohea S, Katoa I, Faitua TH, Aholelei W, Taufa L, Thomas JE, Collings DA, Martin DP, Varsani A. Evidence of inter-component recombination, intra-component recombination and reassortment in banana bunchy top virus. J Gen Virol 2012; 93:1103-1119. [PMID: 22278830 DOI: 10.1099/vir.0.040337-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Banana bunchy top virus (BBTV; family Nanoviridae, genus Babuvirus) is a multi-component, ssDNA virus, which causes widespread banana crop losses throughout tropical Africa and Australasia. We determined the full genome sequences of 12 BBTV isolates from the Kingdom of Tonga and analysed these together with previously determined BBTV sequences to show that reassortment and both inter- and intra-component recombination have all been relatively frequent occurrences during BBTV evolution. We found that whereas DNA-U3 components display evidence of complex inter- and intra-component recombination, all of the South Pacific DNA-R components have a common intra-component recombinant origin spanning the replication-associated protein gene. Altogether, the DNA-U3 and DNA-M components display a greater degree of inter-component recombination than the DNA-R, -S, -C and -M components. The breakpoint distribution of the inter-component recombination events reveals a primary recombination hotspot around the 5' side of the common region major and, in accordance with recombination hotspots detectable in related ssDNA viruses, a secondary recombination hotspot near the origin of virion-strand replication.
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Affiliation(s)
- Daisy Stainton
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Simona Kraberger
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Matthew Walters
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Elizabeth J Wiltshire
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Karyna Rosario
- College of Marine Science, University of South Florida, St Petersburg, FL 33701, USA
| | - Mana'ia Halafihi
- Ministry of Agriculture and Food, Forests and Fisheries, Nuku'alofa, Tongatapu, Kingdom of Tonga
| | | | - Ika Katoa
- Ministry of Agriculture and Food, Forests and Fisheries, Nuku'alofa, Tongatapu, Kingdom of Tonga
| | | | - Waikato Aholelei
- Ministry of Agriculture and Food, Forests and Fisheries, Nuku'alofa, Tongatapu, Kingdom of Tonga
| | - Luseane Taufa
- Ministry of Agriculture and Food, Forests and Fisheries, Nuku'alofa, Tongatapu, Kingdom of Tonga
| | - John E Thomas
- The University of Queensland, Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, Ecosciences Precinct, PO Box 46, Brisbane QLD 4001, Australia
| | - David A Collings
- Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand.,School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arvind Varsani
- Electron Microscope Unit, University of Cape Town, Rondebosch 7701, Cape Town, South Africa.,Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand.,School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
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Abstract
Cucumber mosaic virus (CMV) is an important virus because of its agricultural impact in the Mediterranean Basin and worldwide, and also as a model for understanding plant-virus interactions. This review focuses on those areas where most progress has been made over the past decade in our understanding of CMV. Clearly, a deep understanding of the role of the recently described CMV 2b gene in suppression of host RNA silencing and viral virulence is the most important discovery. These findings have had an impact well beyond the virus itself, as the 2b gene is an important tool in the studies of eukaryotic gene regulation. Protein 2b was shown to be involved in most of the steps of the virus cycle and to interfere with several basal host defenses. Progress has also been made concerning the mechanisms of virus replication and movement. However, only a few host proteins that interact with viral proteins have been identified, making this an area of research where major efforts are still needed. Another area where major advances have been made is CMV population genetics, where contrasting results were obtained. On the one hand, CMV was shown to be prone to recombination and to show high genetic diversity based on sequence data of different isolates. On the other hand, populations did not exhibit high genetic variability either within plants, or even in a field and the nearby wild plants. The situation was partially clarified with the finding that severe bottlenecks occur during both virus movement within a plant and transmission between plants. Finally, novel studies were undertaken to elucidate mechanisms leading to selection in virus population, according to the host or its environment, opening a new research area in plant-virus coevolution.
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Koundal V, Haq QMR, Praveen S. Characterization, genetic diversity, and evolutionary link of Cucumber mosaic virus strain New Delhi from India. Biochem Genet 2010; 49:25-38. [PMID: 20978836 DOI: 10.1007/s10528-010-9382-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 06/29/2010] [Indexed: 11/30/2022]
Abstract
The genome of Cucumber mosaic virus New Delhi strain (CMV-ND) from India, obtained from tomato, was completely sequenced and compared with full genome sequences of 14 known CMV strains from subgroups I and II, for their genetic diversity. Sequence analysis suggests CMV-ND shares maximum sequence identity at the nucleotide level with a CMV strain from Taiwan. Among all 15 strains of CMV, the encoded protein 2b is least conserved, whereas the coat protein (CP) is most conserved. Sequence identity values and phylogram results indicate that CMV-ND belongs to subgroup I. Based on the recombination detection program result, it appears that CMV is prone to recombination, and different RNA components of CMV-ND have evolved differently. Recombinational analysis of all 15 CMV strains detected maximum recombination breakpoints in RNA2; CP showed the least recombination sites.
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Affiliation(s)
- Vikas Koundal
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
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