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Naresh M, Purkayastha A, Dasgupta I. P4 protein of an Indian isolate of rice tungro bacilliform virus modulates gene silencing. Virus Genes 2024; 60:55-64. [PMID: 38055154 DOI: 10.1007/s11262-023-02039-2] [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: 07/29/2023] [Accepted: 11/09/2023] [Indexed: 12/07/2023]
Abstract
Plant hosts and their viral pathogens are engaged in a constant cycle of defense and counter-defense as part of a molecular arms race, principal among them being the plant RNAi defense and the viral RNAi suppressor counter-defense. Rice tungro bacilliform virus (RTBV), member of the family Caulimoviridae, genus Tungrovirus, species Tungrovirus oryzae, infects rice in South- and Southeast Asia and causes severe symptoms of stunting, yellow-orange discoloration and twisting of leaf tips. To better understand the possible counter-defensive roles of RTBV against the host RNAi defense system, we explored the ability of the P4 protein of an Indian isolate of RTBV to act as a possible modulator of RNAi. Using a transient silencing and silencing suppression assay in Nicotiana benthamiana, we show that P4 not only displays an RNAi suppressor function, but also potentially enhances RNAi. The results also suggests that the N-terminal 168 amino acid residues of P4 are sufficient to maintain RNAi suppressor activity. Taken together with the earlier reports this work strengthens the view that the P4 protein carries out RNAi suppressor and a potential RNAi enhancer function.
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Affiliation(s)
- Madhvi Naresh
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Arunima Purkayastha
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Indranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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2
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Ishwara Bhat A, Selvarajan R, Balasubramanian V. Emerging and Re-Emerging Diseases Caused by Badnaviruses. Pathogens 2023; 12:pathogens12020245. [PMID: 36839517 PMCID: PMC9963457 DOI: 10.3390/pathogens12020245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
New and emerging plant diseases are caused by different pathogens including viruses that often cause significant crop losses. Badnaviruses are pararetroviruses that contain a single molecule of ds DNA genome of 7 to 9 kb in size and infect a large number of economically important crops such as banana and plantains, black pepper, cacao, citrus, grapevine, pineapple, sugarcane, sweet potato, taro, and yam, causing significant yield losses. Many of the species in the genus have a restricted host range and several of them are known to infect a single crop. Combined infections of different virus species and strains offer conditions that favor the development of new strains via recombination, especially in vegetatively propagated crops. The primary spread of badnaviruses is through vegetative propagating materials while for the secondary spread, they depend on insects such as mealybugs and aphids. Disease emerges as a consequence of the interactions between host and pathogens under favorable environmental conditions. The viral genome of the pararetroviruses is known to be integrated into the chromosome of the host and a few plants with integrants when subjected to different kinds of abiotic stress will give rise to episomal forms of the virus and cause disease. Attempts have been made to develop management strategies for badnaviruses both conventionally and using precision breeding techniques such as genome editing. Until 2016 only 32 badnavirus species infecting different crops were known, but in a span of six years, this number has gone up to 68. The current review highlights the emerging disease problems and management options for badnaviruses infecting economically important crops.
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Affiliation(s)
- Alangar Ishwara Bhat
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Kozhikode 673012, Kerala, India
| | - Ramasamy Selvarajan
- Division of Crop Protection, ICAR-National Research Centre for Banana, Trichy 620102, Tamil Nadu, India
| | - Velusamy Balasubramanian
- Division of Crop Protection, ICAR-National Research Centre for Banana, Trichy 620102, Tamil Nadu, India
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3
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Janiga PK, Nithya K, Viswanathan R. Dynamics of Genetic Diversity Among Indian Sugarcane Bacilliform Virus Species and Implications of Associated Recombination Events in the Virus. SUGAR TECH 2022. [DOI: 10.1007/s12355-022-01224-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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4
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Grapevine Badnavirus 1: Detection, Genetic Diversity, and Distribution in Croatia. PLANTS 2022; 11:plants11162135. [PMID: 36015438 PMCID: PMC9416389 DOI: 10.3390/plants11162135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022]
Abstract
Grapevine badnavirus 1 (GBV-1) was recently discovered in grapevine using high throughput sequencing. In order to carry out large-scale testing that will allow for better insights into virus distribution, conventional and real-time PCR assays were developed using sequences both from previously known, and four newly characterized isolates. Throughout the growing season and dormancy, GBV-1 can be detected by real-time PCR using available tissue, with the possibility of false-negative results early in vegetation growth. GBV-1 real-time PCR analysis of 4302 grapevine samples from the Croatian continental and coastal wine-growing regions revealed 576 (~13.4%) positive vines. In the continental wine-growing region, virus incidence was confirmed in only two collection plantations, whereas in the coastal region, infection was confirmed in 30 commercial vineyards and one collection plantation. Infection rates ranged from 1.9 to 96% at the different sites, with predominantly autochthonous grapevine cultivars infected. Conventional PCR products obtained from 50 newly discovered GBV-1 isolates, containing the 375 nucleotides long portion of the reverse transcriptase gene, showed nucleotide and amino acid identities ranging from 94.1 to 100% and from 92.8 to 100%, respectively. The reconstructed phylogenetic tree positioned the GBV-1 isolates taken from the same vineyard close to each other indicating a possible local infection event, although the tree nodes were generally not well supported.
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Shahzad GIR, Passera A, Maldera G, Casati P, Marcello I, Bianco PA. Biocontrol Potential of Endophytic Plant-Growth-Promoting Bacteria against Phytopathogenic Viruses: Molecular Interaction with the Host Plant and Comparison with Chitosan. Int J Mol Sci 2022; 23:6990. [PMID: 35805989 PMCID: PMC9266900 DOI: 10.3390/ijms23136990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/16/2022] Open
Abstract
Endophytic plant-growth-promoting bacteria (ePGPB) are interesting tools for pest management strategies. However, the molecular interactions underlying specific biocontrol effects, particularly against phytopathogenic viruses, remain unexplored. Herein, we investigated the antiviral effects and triggers of induced systemic resistance mediated by four ePGPB (Paraburkholderia fungorum strain R8, Paenibacillus pasadenensis strain R16, Pantoea agglomerans strain 255-7, and Pseudomonas syringae strain 260-02) against four viruses (Cymbidium Ring Spot Virus-CymRSV; Cucumber Mosaic Virus-CMV; Potato Virus X-PVX; and Potato Virus Y-PVY) on Nicotiana benthamiana plants under controlled conditions and compared them with a chitosan-based resistance inducer product. Our studies indicated that ePGPB- and chitosan-treated plants presented well-defined biocontrol efficacy against CymRSV and CMV, unlike PVX and PVY. They exhibited significant reductions in symptom severity while promoting plant height compared to nontreated, virus-infected controls. However, these phenotypic traits showed no association with relative virus quantification. Moreover, the tested defense-related genes (Enhanced Disease Susceptibility-1 (EDS1), Non-expressor of Pathogenesis-related genes-1 (NPR1), and Pathogenesis-related protein-2B (PR2B)) implied the involvement of a salicylic-acid-related defense pathway triggered by EDS1 gene upregulation.
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Affiliation(s)
| | | | | | | | - Iriti Marcello
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroecology, University of Milan, 20133 Milan, Italy; (G.-i.-R.S.); (A.P.); (G.M.); (P.C.); (P.A.B.)
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6
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Liu B, Zhang G, Song D, Wang Q, Li H, Gu A, Bai J. Complete genome sequence of a novel virus belonging to the genus Badnavirus in jujube (Ziziphus jujuba Mill.) in China. Arch Virol 2022; 167:1885-1888. [DOI: 10.1007/s00705-022-05482-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/10/2022] [Indexed: 11/29/2022]
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7
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Silva G, Bömer M, Turaki AA, Nkere CK, Kumar PL, Seal SE. Homing in on Endogenous Badnaviral Elements: Development of Multiplex PCR-DGGE for Detection and Rapid Identification of Badnavirus Sequences in Yam Germplasm. FRONTIERS IN PLANT SCIENCE 2022; 13:846989. [PMID: 35620696 PMCID: PMC9127665 DOI: 10.3389/fpls.2022.846989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
Viruses of the genus Badnavirus (family Caulimoviridae) are double-stranded DNA-reverse transcribing (dsDNA-RT) plant viruses and have emerged as serious pathogens of tropical and temperate crops globally. Endogenous badnaviral sequences are found integrated in the genomes of several economically important plant species. Infection due to activation of replication-competent integrated copies of the genera Badnavirus, Petuvirus and Cavemovirus has been described. Such endogenous badnaviral elements pose challenges to the development of nucleic acid-based diagnostic methods for episomal virus infections and decisions on health certification for international movement of germplasm and seed. One major food security crop affected is yam (Dioscorea spp.). A diverse range of Dioscorea bacilliform viruses (DBVs), and endogenous DBV (eDBV) sequences have been found to be widespread in yams cultivated in West Africa and other parts of the world. This study outlines the development of multiplex PCR-dependent denaturing gradient gel electrophoresis (PCR-DGGE) to assist in the detection and analysis of eDBVs, through the example of analysing yam germplasm from Nigeria and Ghana. Primers targeting the three most prevalent DBV monophyletic species groups in West Africa were designed to improve DGGE resolution of complex eDBV sequence fingerprints. Multiplex PCR-DGGE with the addition of a tailor-made DGGE sequence marker enables rapid comparison of endogenous badnaviral sequence diversity across germplasm, as illustrated in this study for eDBV diversity in yam.
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Affiliation(s)
- Gonçalo Silva
- Natural Resources Institute, University of Greenwich, Chatham Maritime, United Kingdom
| | - Moritz Bömer
- Natural Resources Institute, University of Greenwich, Chatham Maritime, United Kingdom
| | - Aliyu A. Turaki
- Kebbi State University of Science and Technology Aliero, Birnin Kebbi, Nigeria
| | - Chukwuemeka K. Nkere
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- Department of Crop Protection and Environmental Biology (CPEB), University of Ibadan, Ibadan, Nigeria
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | - P. Lava Kumar
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Susan E. Seal
- Natural Resources Institute, University of Greenwich, Chatham Maritime, United Kingdom
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Coordinated Action of RTBV and RTSV Proteins Suppress Host RNA Silencing Machinery. Microorganisms 2022; 10:microorganisms10020197. [PMID: 35208652 PMCID: PMC8875415 DOI: 10.3390/microorganisms10020197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/30/2021] [Accepted: 01/05/2022] [Indexed: 11/17/2022] Open
Abstract
RNA silencing is as an adaptive immune response in plants that limits the accumulation or spread of invading viruses. Successful virus infection entails countering the RNA silencing machinery for efficient replication and systemic spread in the host. The viruses encode proteins with the ability to suppress or block the host silencing mechanism, resulting in severe pathogenic symptoms and diseases. Tungro is a viral disease caused by a complex of two viruses and it provides an excellent system to understand the host and virus interactions during infection. It is known that Rice tungro bacilliform virus (RTBV) is the major determinant of the disease while Rice tungro spherical virus (RTSV) accentuates the symptoms. This study brings to focus the important role of RTBV ORF-IV in disease manifestation, by acting as both the victim and silencer of the RNA silencing pathway. The ORF-IV is a weak suppressor of the S-PTGS or stable silencing, but its suppression activity is augmented in the presence of specific RTSV proteins. Among these, RTBV ORF-IV and RTSV CP3 proteins interact with each other. This interaction may lead to the suppression of localized silencing as well as the spread of silencing in the host plants. The findings present a probable mechanistic glimpse of the requirement of the two viruses in enhancing tungro disease.
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Smith WK, Ma Y, Yu J, Cheng YY, Zhang P, Han TT, Lu QY. Characterization of a strong constitutive promoter from paper mulberry vein banding virus. Arch Virol 2022; 167:163-170. [PMID: 34826001 DOI: 10.1007/s00705-021-05310-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/10/2021] [Indexed: 10/19/2022]
Abstract
Paper mulberry vein banding virus (PMVBV), a member of the genus Badnavirus in the family Caulimoviridae, infects paper mulberry (Broussonetia papyrifera), a dicotyledonous plant. Putative promoter regions in the PMVBV genome were tested using recombinant plant expression vectors, revealing that the promoter activity of three genome fragments was about 1.5-fold higher than that of the 35S promoter of cauliflower mosaic virus in Nicotiana benthamiana. In transformed transgenic Arabidopsis thaliana plants, these promoter constructs showed constitutive expression. Based on the activity and gene expression patterns of these three promoter constructs, a fragment of 384 bp (named PmVP) was deduced to contain the full-length promoter of the PMVBV genome. The results suggest that the PMVBV-derived promoter can be used for the constitutive expression of transgenes in dicotyledonous plants.
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Affiliation(s)
- William K Smith
- College of Biotechnology, Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018, Jiangsu, China
| | - Yu Ma
- College of Biotechnology, Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018, Jiangsu, China
| | - Jing Yu
- College of Biotechnology, Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018, Jiangsu, China
| | - Yong-Yuan Cheng
- College of Biotechnology, Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018, Jiangsu, China
| | - Peng Zhang
- College of Biotechnology, Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018, Jiangsu, China
| | - Tao-Tao Han
- College of Biotechnology, Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018, Jiangsu, China
| | - Quan-You Lu
- College of Biotechnology, Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018, Jiangsu, China.
- Key Laboratory of Genetic Improvement of Silkworm and Mulberry, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212018, Jiangsu, China.
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10
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Oberemok V, Laikova K, Golovkin I, Kryukov L, Kamenetsky-Goldstein R. Biotechnology of virus eradication and plant vaccination in phytobiome context. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:3-8. [PMID: 34569131 DOI: 10.1111/plb.13338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
A plant's associated biota plays an integral role in its metabolism, nutrient uptake, stress tolerance, pathogen resistance and other physiological processes. Although a virome is an integral part of the phytobiome, a major contradiction exists between the holobiont approach and the practical need to eradicate pathogens from agricultural crops. In this review, we discuss grapevine virus control, but the issue is also relevant for numerous other crops, including potato, cassava, citrus, cacao and other species. Grapevine diseases, especially viral infections, cause main crop losses. Methods have been developed to eliminate viruses and other microorganisms from plant material, but elimination of viruses from plant material does not guarantee protection from future reinfection. Elimination of viral particles in plant material could create genetic drift, leading in turn to an increase in the occurrence of pathogenic strains of viruses. A possible solution may be a combination of virus elimination and plant propagation in tissue culture with in vitro vaccination. In this context, possible strategies to control viral infections include application of plant resistance inducers, cross protection and vaccination using siRNA, dsRNA and viral replicons during plant 'cleaning' and in vitro propagation. The experience and knowledge accumulated in human immunization can help plant scientists to develop and employ new methods of protection, leading to more sustainable and healthier crop production.
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Affiliation(s)
- V Oberemok
- V.I. Vernadsky Crimean Federal University, Simferopol, Russia
- Nikita Botanical Gardens - National Scientific Centre Russian Academy of Sciences, Yalta, Russia
| | - K Laikova
- V.I. Vernadsky Crimean Federal University, Simferopol, Russia
- Research Institute of Agriculture of Crimea, Simferopol, Russia
| | - I Golovkin
- V.I. Vernadsky Crimean Federal University, Simferopol, Russia
| | - L Kryukov
- V.I. Vernadsky Crimean Federal University, Simferopol, Russia
- Lobachevsky State University of Nizhni Novgorod, Nizhni Novgorod, Russia
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11
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Vadlamudi T, Kaldis A, Divi VSG, Patil BL, Voloudakis AE. The Citrus yellow mosaic badnavirus ORFI functions as a RNA-silencing suppressor. Virus Genes 2021; 57:469-473. [PMID: 34379307 DOI: 10.1007/s11262-021-01863-8] [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: 02/26/2021] [Accepted: 07/27/2021] [Indexed: 11/27/2022]
Abstract
Citrus yellow mosaic badnavirus (CMBV) causes mosaic disease in all economically important citrus cultivars of India, with losses reaching up to 70%. CMBV belongs to the genus Badnavirus, family Caulimoviridae, possessing a circular double-stranded (ds) DNA genome with six open reading frames (ORFs I to VI), whose functions are yet to be deciphered. The RNA-silencing suppressor (RSS) activity has not been assigned to any CMBV ORF as yet. In the present study, it was found that ORFI exhibited RSS activity among all the six CMBV ORFs tested. Studies were done by employing the well-established Agrobacterium-mediated transient assay based on the transgenic Nicotiana benthamiana 16c plant line expressing the green fluorescent protein (GFP). The RSS activity of ORFI was confirmed by the analysis of the GFP visual expression in the agroinfiltrated leaves, further supported by quantification of GFP expression by RT-PCR. Based on the GFP visual expression, the CMBV ORFI was a weak RSS when compared to the p19 protein of tomato bushy stunt virus. In contrast, the ORFII, ORFIV, ORFV, ORFVI, and CP gene did not exhibit any RSS activity. Hence, ORFI is the first ORF of CMBV to be identified with RNA-silencing suppression activity.
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Affiliation(s)
- Tharanath Vadlamudi
- Laboratory of Plant Breeding and Biometry, Faculty of Crop Science, Agricultural University of Athens, 11855, Athens, Greece
- Department of Virology, Sri Venkateswara University, Tirupati, Andhra Pradesh, 517502, India
| | - Athanasios Kaldis
- Laboratory of Plant Breeding and Biometry, Faculty of Crop Science, Agricultural University of Athens, 11855, Athens, Greece
| | | | - Basavaprabhu L Patil
- ICAR-Indian Institute of Horticultural Research, Bengaluru, Karnataka, 560089, India
| | - Andreas E Voloudakis
- Laboratory of Plant Breeding and Biometry, Faculty of Crop Science, Agricultural University of Athens, 11855, Athens, Greece.
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12
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Rumbou A, Vainio EJ, Büttner C. Towards the Forest Virome: High-Throughput Sequencing Drastically Expands Our Understanding on Virosphere in Temperate Forest Ecosystems. Microorganisms 2021; 9:microorganisms9081730. [PMID: 34442809 PMCID: PMC8399312 DOI: 10.3390/microorganisms9081730] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/22/2022] Open
Abstract
Thanks to the development of HTS technologies, a vast amount of genetic information on the virosphere of temperate forests has been gained in the last seven years. To estimate the qualitative/quantitative impact of HTS on forest virology, we have summarized viruses affecting major tree/shrub species and their fungal associates, including fungal plant pathogens, mutualists and saprotrophs. The contribution of HTS methods is extremely significant for forest virology. Reviewed data on viral presence in holobionts allowed us a first attempt to address the role of virome in holobionts. Forest health is dependent on the variability of microorganisms interacting with the host tree/holobiont; symbiotic microbiota and pathogens engage in a permanent interplay, which influences the host. Through virus–virus interplays synergistic or antagonistic relations may evolve, which may drastically affect the health of the holobiont. Novel insights of these interplays may allow practical applications for forest plant protection based on endophytes and mycovirus biocontrol agents. The current analysis is conceived in light of the prospect that novel viruses may initiate an emergent infectious disease and that measures for the avoidance of future outbreaks in forests should be considered.
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Affiliation(s)
- Artemis Rumbou
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, 14195 Berlin, Germany;
- Correspondence:
| | - Eeva J. Vainio
- Natural Resources Institute Finland, Forest Health and Biodiversity, Latokartanonkaari 9, 00790 Helsinki, Finland;
| | - Carmen Büttner
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, 14195 Berlin, Germany;
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Balan S, Nithya K, Cherian KA, Viswanathan R. True Seed Transmission of Sugarcane bacilliform virus (SCBV) in Sugarcane. SUGAR TECH 2021. [DOI: 10.1007/s12355-021-01031-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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14
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Ashraf F, Ashraf MA, Hu X, Zhang S. A novel computational approach to the silencing of Sugarcane Bacilliform Guadeloupe A Virus determines potential host-derived MicroRNAs in sugarcane ( Saccharum officinarum L.). PeerJ 2020; 8:e8359. [PMID: 31976180 PMCID: PMC6964690 DOI: 10.7717/peerj.8359] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 12/05/2019] [Indexed: 01/24/2023] Open
Abstract
Sugarcane Bacilliform Guadeloupe A Virus (SCBGAV, genus Badnavirus, family Caulimoviridae) is an emerging, deleterious pathogen of sugarcane which presents a substantial barrier to producing high sugarcane earnings. Sugarcane bacilliform viruses (SCBVs) are one of the main species that infect sugarcane. During the last 30 years, significant genetic changes in SCBV strains have been observed with a high risk of disease incidence associated with crop damage. SCBV infection may lead to significant losses in biomass production in susceptible sugarcane cultivars. The circular, double-stranded (ds) DNA genome of SCBGAV (7.4 Kb) is composed of three open reading frames (ORFs) on the positive strand that replicate by a reverse transcriptase. SCBGAV can infect sugarcane in a semipersistent manner via the insect vectors sugarcane mealybug species. In the current study, we used miRNA target prediction algorithms to identify and comprehensively analyze the genome-wide sugarcane (Saccharum officinarum L.)-encoded microRNA (miRNA) targets against the SCBGAV. Mature miRNA target sequences were retrieved from the miRBase (miRNA database) and were further analyzed for hybridization to the SCBGAV genome. Multiple computational approaches—including miRNA-target seed pairing, multiple target positions, minimum free energy, target site accessibility, maximum complementarity, pattern recognition and minimum folding energy for attachments—were considered by all algorithms. Among them, sof-miR396 was identified as the top effective candidate, capable of targeting the vital ORF3 of the SCBGAV genome. miRanda, RNA22 and RNAhybrid algorithms predicted hybridization of sof-miR396 at common locus position 3394. The predicted sugarcane miRNAs against viral mRNA targets possess antiviral activities, leading to translational inhibition by mRNA cleavage. Interaction network of sugarcane-encoded miRNAs with SCBGAV genes, created using Circos, allow analyze new targets. The finding of the present study acts as a first step towards the creation of SCBGAV-resistant sugarcane through the expression of the identified miRNAs.
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Affiliation(s)
- Fakiha Ashraf
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Muhammad Aleem Ashraf
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.,Department of Plant Breeding and Genetics, University College of Agriculture and Environmental Sciences, Islamia University of Bahawalpur, Baghdad-Ul-Jadeed Campus, Bahwalpur, Pakistan
| | - Xiaowen Hu
- Zhanjiang Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guandong, China
| | - Shuzhen Zhang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
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15
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Mechanisms of Plant Tolerance to RNA Viruses Induced by Plant-Growth-Promoting Microorganisms. PLANTS 2019; 8:plants8120575. [PMID: 31817560 PMCID: PMC6963434 DOI: 10.3390/plants8120575] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/29/2019] [Accepted: 12/04/2019] [Indexed: 12/25/2022]
Abstract
Plant viruses are globally responsible for the significant crop losses of economically important plants. All common approaches are not able to eradicate viral infection. Many non-conventional strategies are currently used to control viral infection, but unfortunately, they are not always effective. Therefore, it is necessary to search for efficient and eco-friendly measures to prevent viral diseases. Since the genomic material of 90% higher plant viruses consists of single-stranded RNA, the best way to target the viral genome is to use ribonucleases (RNase), which can be effective against any viral disease of plants. Here, we show the importance of the search for endophytes with protease and RNase activity combined with the capacity to prime antiviral plant defense responses for their protection against viruses. This review discusses the possible mechanisms used to suppress a viral attack as well as the use of local endophytic bacteria for antiviral control in crops.
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Yusop MSM, Saad MFM, Talip N, Baharum SN, Bunawan H. A Review on Viruses Infecting Taro ( Colocasia esculenta (L.) Schott). Pathogens 2019; 8:E56. [PMID: 31027164 PMCID: PMC6630990 DOI: 10.3390/pathogens8020056] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/08/2019] [Accepted: 04/08/2019] [Indexed: 02/08/2023] Open
Abstract
Taro is an important crop in parts of the world, especially in the Pacific Islands. Like all plants, it is also susceptible to virus infections that could result in diseases, which negatively affects the source of food and trade revenue. Understanding the biology of taro viruses could improve current knowledge regarding the relationship between viruses and taro, thus allowing for a better approach towards the management of the diseases that are associated with them. By compiling and discussing the research on taro and its four major viruses (Dasheen mosaic virus, Taro bacilliform virus, Colocasia bobone disease virus, and Taro vein chlorosis virus) and a relatively new one (Taro bacilliform CH virus), this paper explores the details of each virus by examining their characteristics and highlighting information that could be used to mitigate taro infections and disease management.
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Affiliation(s)
| | - Mohd Faiz Mat Saad
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi Selangor, Malaysia.
| | - Noraini Talip
- School of Environmental and Natural Resource Sciences, Universiti Kebangsaan Malaysia, 43600 Bangi Selangor, Malaysia.
| | - Syarul Nataqain Baharum
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi Selangor, Malaysia.
| | - Hamidun Bunawan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi Selangor, Malaysia.
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17
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Lan P, Tian T, Pu L, Rao W, Li F, Li R. Characterization and detection of a new badnavirus infecting Epiphyllum spp. Arch Virol 2019; 164:1837-1841. [DOI: 10.1007/s00705-019-04237-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/07/2019] [Indexed: 01/28/2023]
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18
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Wainaina JM, Ateka E, Makori T, Kehoe MA, Boykin LM. A metagenomic study of DNA viruses from samples of local varieties of common bean in Kenya. PeerJ 2019; 7:e6465. [PMID: 30891366 PMCID: PMC6422016 DOI: 10.7717/peerj.6465] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 01/16/2019] [Indexed: 11/20/2022] Open
Abstract
Common bean (Phaseolus vulgaris L.) is the primary source of protein and nutrients in the majority of households in sub-Saharan Africa. However, pests and viral diseases are key drivers in the reduction of bean production. To date, the majority of viruses reported in beans have been RNA viruses. In this study, we carried out a viral metagenomic analysis on virus symptomatic bean plants. Our virus detection pipeline identified three viral fragments of the double-stranded DNA virus Pelargonium vein banding virus (PVBV) (family, Caulimoviridae, genus Badnavirus). This is the first report of the dsDNA virus and specifically PVBV in legumes to our knowledge. In addition two previously reported +ssRNA viruses the bean common mosaic necrosis virus (BCMNVA) (Potyviridae) and aphid lethal paralysis virus (ALPV) (Dicistroviridae) were identified. Bayesian phylogenetic analysis of the Badnavirus (PVBV) using amino acid sequences of the RT/RNA-dependent DNA polymerase region showed the Kenyan sequence (SRF019_MK014483) was closely matched with two Badnavirus viruses: Dracaena mottle virus (DrMV) (YP_610965) and Lucky bamboo bacilliform virus (ABR01170). Phylogenetic analysis of BCMNVA was based on amino acid sequences of the Nib region. The BCMNVA phylogenetic tree resolved two clades identified as clade (I and II). Sequence from this study SRF35_MK014482, clustered within clade I with other Kenyan sequences. Conversely, Bayesian phylogenetic analysis of ALPV was based on nucleotide sequences of the hypothetical protein gene 1 and 2. Three main clades were resolved and identified as clades I-III. The Kenyan sequence from this study (SRF35_MK014481) clustered within clade II, and nested within a sub-clade; comprising of sequences from China and an earlier ALPV sequences from Kenya isolated from maize (MF458892). Our findings support the use of viral metagenomics to reveal the nascent viruses, their viral diversity and evolutionary history of these viruses. The detection of ALPV and PVBV indicate that these viruses have likely been underreported due to the unavailability of diagnostic tools.
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Affiliation(s)
- James M. Wainaina
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Elijah Ateka
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Timothy Makori
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Monica A. Kehoe
- Diagnostic Laboratory Service, Plant Pathology, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Laura M. Boykin
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
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Petersen SM, Keith C, Austin K, Howard S, Su L, Qiu W. A Natural Reservoir and Transmission Vector of Grapevine Vein Clearing Virus. PLANT DISEASE 2019; 103:571-577. [PMID: 30484754 DOI: 10.1094/pdis-06-18-1073-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Grapevine vein clearing virus (GVCV) is associated with a vein-clearing and vine-decline disease. In this study, we surveyed wild Ampelopsis cordata from the Vitaceae family and found that 31% (35 of 113) of native A. cordata plants are infected with GVCV. The full-length genome sequence of one GVCV isolate from A. cordata shared 99.8% identical nucleotides with an isolate from a nearby cultivated 'Chardonel' grapevine, suggesting the occurrence of an insect vector. To identify a vector, we collected Aphis illinoisensis (common name: grape aphids) from wild A. cordata plants and detected GVCV in the aphid populations. We found that A. illinoisensis is capable of transmitting GVCV from infected A. cordata to Chardonel grapevines in the greenhouse. Upon transmission, GVCV caused severe symptoms on the infected Chardonel 45 days post transmission. We conclude that wild GVCV isolates from A. cordata are capable of inducing a severe disease on cultivated grapevines once they spread from native A. cordata to vineyards via grape aphids. The discovery of a natural reservoir and an insect vector of GVCV provides timely knowledge for disease management in vineyards and critical clues on viral evolution and epidemiology.
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Affiliation(s)
- Sylvia M Petersen
- Center for Grapevine Biotechnology, William H. Darr College of Agriculture, Missouri State University, Mountain Grove, MO 65711
| | - Cory Keith
- Center for Grapevine Biotechnology, William H. Darr College of Agriculture, Missouri State University, Mountain Grove, MO 65711
| | - Kaylie Austin
- Center for Grapevine Biotechnology, William H. Darr College of Agriculture, Missouri State University, Mountain Grove, MO 65711
| | - Susanne Howard
- Center for Grapevine Biotechnology, William H. Darr College of Agriculture, Missouri State University, Mountain Grove, MO 65711
| | - Li Su
- Center for Grapevine Biotechnology, William H. Darr College of Agriculture, Missouri State University, Mountain Grove, MO 65711
| | - Wenping Qiu
- Center for Grapevine Biotechnology, William H. Darr College of Agriculture, Missouri State University, Mountain Grove, MO 65711
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Sukal AC, Kidanemariam DB, Dale JL, Harding RM, James AP. Assessment and optimization of rolling circle amplification protocols for the detection and characterization of badnaviruses. Virology 2019; 529:73-80. [PMID: 30665100 DOI: 10.1016/j.virol.2019.01.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 01/13/2019] [Accepted: 01/13/2019] [Indexed: 11/15/2022]
Abstract
The genus Badnavirus is characterized by members that are genetically and serologically heterogeneous which presents challenges for their detection and characterization. The presence of integrated badnavirus-like sequences in some host species further complicates detection using PCR-based protocols. To address these challenges, we have assessed and optimized various RCA protocols including random-primed RCA (RP-RCA), primer-spiked random-primed RCA (primer-spiked RP-RCA), directed RCA (D-RCA) and specific-primed RCA (SP-RCA). Using Dioscorea bacilliform AL virus (DBALV) as an example, we demonstrate that viral DNA amplified using the optimized D-RCA and SP-RCA protocols showed an 85-fold increase in badnavirus NGS reads compared with RP-RCA. The optimized RCA techniques described here were used to detect a range of badnaviruses infecting banana, sugar cane, taro and yam demonstrating the utility of RCA for detection of diverse badnaviruses infecting a variety of host plant species.
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Affiliation(s)
- Amit C Sukal
- Centre for Tropical Crops and Biocommodities (CTCB), Faculty of Science and Engineering (SEF), Queensland University of Technology (QUT), Brisbane 4001, Australia; Centre for Pacific Crops and Trees (CePaCT), Land Resource Division (LRD), Pacific Community (SPC), Suva, Fiji
| | - Dawit B Kidanemariam
- Centre for Tropical Crops and Biocommodities (CTCB), Faculty of Science and Engineering (SEF), Queensland University of Technology (QUT), Brisbane 4001, Australia
| | - James L Dale
- Centre for Tropical Crops and Biocommodities (CTCB), Faculty of Science and Engineering (SEF), Queensland University of Technology (QUT), Brisbane 4001, Australia
| | - Robert M Harding
- Centre for Tropical Crops and Biocommodities (CTCB), Faculty of Science and Engineering (SEF), Queensland University of Technology (QUT), Brisbane 4001, Australia.
| | - Anthony P James
- Centre for Tropical Crops and Biocommodities (CTCB), Faculty of Science and Engineering (SEF), Queensland University of Technology (QUT), Brisbane 4001, Australia
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21
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Development of Quantitative Real-Time PCR Assays for Rapid and Sensitive Detection of Two Badnavirus Species in Sugarcane. BIOMED RESEARCH INTERNATIONAL 2018; 2018:8678242. [PMID: 30175148 PMCID: PMC6106854 DOI: 10.1155/2018/8678242] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/11/2018] [Accepted: 07/15/2018] [Indexed: 11/30/2022]
Abstract
Sugarcane-infecting badnaviruses (sugarcane bacilliform viruses, SCBVs) represent a genetically heterogeneous species complex, posing a serious threat to the yield and quality of sugarcane in all major producing regions. SCBVs are commonly transmitted across regions by the exchange of sugarcane germplasm. In this study, we develop two quick, sensitive, and reliable protocols for real-time quantitative PCR (qPCR) of Sugarcane bacilliform MO virus (SCBMOV) and Sugarcane bacilliform IM virus (SCBIMV) using two sets of TaqMan probes and primers targeting the reverse transcriptase/ribonuclease H (RT/RNase H) region. The two assays had a detection limit of 100 copies of plasmid DNA and were 100 times more sensitive than conventional PCR. High specificity of the two assays was observed with respect to SCBIMV and SCBMOV. A total of 176 sugarcane leaf tissue samples from Fujian and Yunnan provinces were collected and analyzed in parallel by conventional PCR, SCBIMV-qPCR, and SCBMOV-qPCR. The SCBIMV-qPCR and SCBMOV-qPCR assays indicated that 50% (88/176) and 47% (83/176) samples tested positive, respectively, whereas only 29% (51/176) tested positive with conventional PCR with the primer pairs SCBV-F and SCBV-R. We demonstrate for the first time that SCBIMV and SCBMOV occur in China and reveal coinfection of both Badnavirus species in 29% (51/176) of tested leaf samples. Our findings supply sensitive and reliable qPCR assays for the detection and quantitation of SCBV in sugarcane quarantine programs.
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Verchot J, Thapa A, Wijayasekara D, Hoyt PR. Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes. J Vis Exp 2018. [PMID: 30102276 DOI: 10.3791/57855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
This metagenome approach is used to identify plant viruses with circular DNA genomes and their transcripts. Often plant DNA viruses that occur in low titers in their host or cannot be mechanically inoculated to another host are difficult to propagate to achieve a greater titer of infectious material. Infected leaves are ground in a mild buffer with optimal pH and ionic composition recommended for purifying most bacilliform Para retroviruses. Urea is used to break up inclusion bodies that trap virions and to dissolve cellular components. Differential centrifugation provides further separation of virions from plant contaminants. Then proteinase K treatment removes the capsids. Then the viral DNA is concentrated and used for next-generation sequencing (NGS). The NGS data are used to assemble contigs which are submitted to NCBI-BLASTn to identify a subset of virus sequences in the generated dataset. In a parallel pipeline, RNA is isolated from infected leaves using a standard column-based RNA extraction method. Then ribosome depletion is carried out to enrich for a subset of mRNA and virus transcripts. Assembled sequences derived from RNA sequencing (RNA-seq) were submitted to NCBI-BLASTn to identify a subset of virus sequences in this dataset. In our study, we identified two related full-length badnavirus genomes in the two datasets. This method is preferred to another common approach which extracts the aggregate population of small RNA sequences to reconstitute plant virus genomic sequences. This latter metagenomic pipeline recovers virus related sequences that are retro-transcribing elements inserted into the plant genome. This is coupled to biochemical or molecular assays to further discern the actively infectious agents. The approach documented in this study, recovers sequences representative of replicating viruses that likely indicate active virus infection.
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Affiliation(s)
| | - Aastha Thapa
- Noble Research Center, Oklahoma State University
| | - Dulanjani Wijayasekara
- Department of Biology, College of Engineering and Natural Sciences, The University of Tulsa
| | - Peter R Hoyt
- Bioinformatics and Genomics Core Facility, Department of Biochemistry and Molecular Biology, Oklahoma State University
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Rumbou A, Candresse T, Marais A, Theil S, Langer J, Jalkanen R, Büttner C. A novel badnavirus discovered from Betula sp. affected by birch leaf-roll disease. PLoS One 2018; 13:e0193888. [PMID: 29494687 PMCID: PMC5833271 DOI: 10.1371/journal.pone.0193888] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 02/20/2018] [Indexed: 01/26/2023] Open
Abstract
In declining birches (Betula sp.) from different European stands affected by the “birch leaf-roll disease” (BLRD) a novel virus is identified by means of RNA-Seq virome analysis. The virus represents a new member in the genus Badnavirus, family Caulimoviridae, tentatively named Birch leaf roll-associated virus (BLRaV) and it is the first badnavirus found to infect birch. Complete genome sequences (7,862–7,864 nucleotides) of three viral isolates of Finnish and German origin have been determined. The virus sequences show a typical badnavirus organization with three major open reading frames (ORFs) and a fourth potential ORF overlapping with the end of ORF3. ORFs 1-2-3 show low level of amino acid identity to the corresponding proteins encoded by other badnaviruses, reaching a maximum of 44% identity (ORF3). Grapevine vein-clearing virus appears as the closest badnavirus when considering the polymerase region. So far, we can exclude evidence for presence of endogenous BLRaV elements in the birch genome, while evidence for the episomal activity of BLRaV is provided. The viral population holds significant haplotype diversity, while co-infection by different BLRaV variants are observed in single hosts. BLRaV presence is associated with the BLRD in both silver (B. pendula) and downy birch (B. pubescens). These results challenge the earlier hypothesis of a causal role of Cherry leaf roll virus in BLRD. Further work is now needed to finally prove that BLRaV is the causal agent for the BLRD.
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Affiliation(s)
- Artemis Rumbou
- Division Phytomedicine, Albrecht Daniel Thaer-Institute, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
- * E-mail:
| | - Thierry Candresse
- Equipe Virologie, UMR 1332 BFP, French National Institute for Agricultural Research (INRA), Villenave d'Ornon Cedex, France
| | - Armelle Marais
- Equipe Virologie, UMR 1332 BFP, French National Institute for Agricultural Research (INRA), Villenave d'Ornon Cedex, France
| | - Sebastien Theil
- Equipe Virologie, UMR 1332 BFP, French National Institute for Agricultural Research (INRA), Villenave d'Ornon Cedex, France
| | - Juliane Langer
- Division Phytomedicine, Albrecht Daniel Thaer-Institute, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Risto Jalkanen
- Rovaniemi Unit, Finnish Forest Research Institute (Metla), Natural Resources Institute, Luke, Rovaniemi, Finland
| | - Carmen Büttner
- Division Phytomedicine, Albrecht Daniel Thaer-Institute, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
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24
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Molecular characterization of two badnavirus genomes associated with Canna yellow mottle disease. Virus Res 2018; 243:19-24. [PMID: 28988983 DOI: 10.1016/j.virusres.2017.10.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 11/23/2022]
Abstract
Members of the genus Badnavirus have a single non-covalently closed circular double-stranded DNA genome of 7.2-9.2kb. The genome encodes three open reading frames (ORFs) on the positive DNA strand. Canna yellow mottle virus (CaYMV) is a badnavirus that has been described as the etiological cause of yellow mottle disease in canna, although only a 565bp fragment of the genome has been previously reported from cannas. In this report, concentrated virions were recovered from infected canna plants and nucleic acids were extracted. Two full-length sequences represent two badnavirus genomes were recovered and were determined to be 6966bp and 7385bp in length. These DNAs represent a virus strain belonging to Canna yellow mottle virus and a novel species tentatively termed Canna yellow mottle associated virus. Phylogenetic analysis indicates that these two viruses are closely related to sugarcane bacilliform GD virus, pineapple bacilliform comosus virus, banana streak MY virus, and cycad leaf necrosis virus. We also showed naturally grown canna plants to be frequently co-infected by these two badnaviruses along with a potyvirus, Canna yellow streak virus.
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Chingandu N, Kouakou K, Aka R, Ameyaw G, Gutierrez OA, Herrmann HW, Brown JK. The proposed new species, cacao red vein virus, and three previously recognized badnavirus species are associated with cacao swollen shoot disease. Virol J 2017; 14:199. [PMID: 29052506 PMCID: PMC5649073 DOI: 10.1186/s12985-017-0866-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 10/11/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Cacao swollen shoot virus (CSSV), Cacao swollen shoot CD virus (CSSCDV), and Cacao swollen shoot Togo A virus (CSSTAV) cause cacao swollen shoot disease (CSSD) in West Africa. During 2000-2003, leaf and shoot-swelling symptoms and rapid tree death were observed in cacao in Cote d'Ivoire and Ghana. Molecular tests showed positive infection in only ~50-60% of symptomatic trees, suggesting the possible emergence of an unknown badnavirus. METHODS The DNA virome was determined from symptomatic cacao samples using Illumina-Hi Seq, and sequence accuracy was verified by Sanger sequencing. The resultant 14, and seven previously known, full-length badnaviral genomic and RT-RNase H sequences were analyzed by pairwise distance analysis to resolve species relationships, and by Maximum likelihood (ML) to reconstruct phylogenetic relationships. The viral coding and non-coding sequences, genome organization, and predicted conserved protein domains (CPDs) were identified and characterized at the species level. RESULTS The 21 CSSD-badnaviral genomes and RT-RNase H sequences shared 70-100% and 72-100% identity, respectively. The RT-RNase H analysis predicted four species, based on an ≥80% species cutoff. The ML genome sequence tree resolved three well-supported clades, with ≥70% bootstrap, whereas, the RT-RNase H phylogeny was poorly resolved, however, both trees grouped CSSD isolates within one large clade, including the newly discovered Cacao red vein virus (CRVV) proposed species. The genome arrangement of the four species consists of four, five, or six predicted open reading frames (ORFs), and the CPDs have similar architectures. By comparison, two New World cacao-infecting badnaviruses encode four ORFs, and harbor CPDs like the West African species. CONCLUSIONS Three previously recognized West African cacao-infecting badnaviral species were identified, and a fourth, previously unidentified species, CRVV, is described for the first time. The CRVV is a suspect causal agent of the rapid decline phenotype, however Koch's Postulates have not been proven. To reconcile viral evolutionary with epidemiology considerations, more detailed information about CSSD-genomic variability is essential. Also, the functional basis for the multiple genome arrangements and subtly distinct CPD architectures among cacao-infecting badnaviruses is poorly understood. New knowledge about functional relationships may help explain the diverse symptomatologies observed in affected cacao trees.
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Affiliation(s)
| | - Koffie Kouakou
- Centre National de Recherche Agronomique (CNRA), Programme Cacao, Divo, Côte d’Ivoire
| | - Romain Aka
- Centre National de Recherche Agronomique (CNRA), Programme Cacao, Divo, Côte d’Ivoire
| | - George Ameyaw
- Cocoa Research Institute of Ghana, New Tafo-Akim, Ghana
| | - Osman A. Gutierrez
- USDA-ARS Subtropical Horticultural Research Station, Miami, FL 33158 USA
| | | | - Judith K. Brown
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721 USA
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PCR-DGGE Analysis: Unravelling Complex Mixtures of Badnavirus Sequences Present in Yam Germplasm. Viruses 2017; 9:v9070181. [PMID: 28696406 PMCID: PMC5537673 DOI: 10.3390/v9070181] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/29/2017] [Accepted: 07/04/2017] [Indexed: 12/19/2022] Open
Abstract
Badnaviruses (family Caulimoviridae, genus Badnavirus) have emerged as serious pathogens especially affecting the cultivation of tropical crops. Badnavirus sequences can be integrated in host genomes, complicating the detection of episomal infections and the assessment of viral genetic diversity in samples containing a complex mixture of sequences. Yam (Dioscorea spp.) plants are hosts to a diverse range of badnavirus species, and recent findings have suggested that mixed infections occur frequently in West African yam germplasm. Historically, the determination of the diversity of badnaviruses present in yam breeding lines has been achieved by cloning and sequencing of polymerase chain reaction (PCR) products. In this study, the molecular diversity of partial reverse transcriptase (RT)-ribonuclease H (RNaseH) sequences from yam badnaviruses was analysed using PCR-dependent denaturing gradient gel electrophoresis (PCR-DGGE). This resulted in the identification of complex ‘fingerprints’ composed of multiple sequences of Dioscorea bacilliform viruses (DBVs). Many of these sequences show high nucleotide identities to endogenous DBV (eDBV) sequences deposited in GenBank, and fall into six monophyletic species groups. Our findings highlight PCR-DGGE as a powerful tool in badnavirus diversity studies enabling a rapid indication of sequence diversity as well as potential candidate integrated sequences revealed by their conserved nature across germplasm.
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Du K, Liu S, Chen Z, Fan Z, Wang H, Tian G, Zhou T. Full genome sequence of jujube mosaic-associated virus, a new member of the family Caulimoviridae. Arch Virol 2017; 162:3221-3224. [DOI: 10.1007/s00705-017-3438-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 05/22/2017] [Indexed: 10/19/2022]
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Friscina A, Chiappetta L, Jacquemond M, Tepfer M. Infection of non-host model plant species with the narrow-host-range Cacao swollen shoot virus. MOLECULAR PLANT PATHOLOGY 2017; 18:293-297. [PMID: 27010241 PMCID: PMC6638213 DOI: 10.1111/mpp.12404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/11/2016] [Accepted: 03/21/2016] [Indexed: 05/20/2023]
Abstract
Cacao swollen shoot virus (CSSV) is a major pathogen of cacao (Theobroma cacao) in Africa, and long-standing efforts to limit its spread by the culling of infected trees have had very limited success. CSSV is a particularly difficult virus to study, as it has a very narrow host range, limited to several tropical tree species. Furthermore, the virus is not mechanically transmissible, and its insect vector can only be used with difficulty. Thus, the only efficient means to infect cacao plants that have been experimentally described so far are by particle bombardment or the agroinoculation of cacao plants with an infectious clone. We have genetically transformed three non-host species with an infectious form of the CSSV genome: two experimental hosts widely used in plant virology (Nicotiana tabacum and N. benthamiana) and the model species Arabidopsis thaliana. In transformed plants of all three species, the CSSV genome was able to replicate, and, in tobacco, CSSV particles could be observed by immunosorbent electron microscopy, demonstrating that the complete virus cycle could be completed in a non-host plant. These results will greatly facilitate the preliminary testing of CSSV control strategies using plants that are easy to raise and to transform genetically.
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Affiliation(s)
- Arianna Friscina
- Plant Virology Group, ICGEB Biosafety OutstationCa' Tron di Roncade31056Italy
| | - Laura Chiappetta
- Plant Virology Group, ICGEB Biosafety OutstationCa' Tron di Roncade31056Italy
| | | | - Mark Tepfer
- Plant Virology Group, ICGEB Biosafety OutstationCa' Tron di Roncade31056Italy
- Station de Pathologie Végétale UR407, BP 94F‐84143Montfavet cedexFrance
- Institut Jean‐Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris‐Saclay78026Versailles cedexFrance
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Beach S, Kovens M, Hubbert L, Honesty S, Guo Q, Pap D, Dai R, Kovacs L, Qiu W. Genetic and Phenotypic Characterization of Grapevine vein clearing virus from Wild Vitis rupestris. PHYTOPATHOLOGY 2017; 107:138-144. [PMID: 27577962 DOI: 10.1094/phyto-04-16-0173-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Grapevine vein clearing virus (GVCV), a new member of the genus Badnavirus in the family Caulimoviridae, is associated with a vein clearing and vine decline disease that severely affects grape production and berry quality in commercial vineyards in the Midwest region of the United States. In this paper, the genetic and phenotypic characteristics of GVCV-VRU1 and GVCV-VRU2, two isolates from wild Vitis rupestris grapevines in their native habitat, are described. The GVCV-VRU1 genome is 7,755 bp long while the GVCV-VRU2 genome consists of 7,725 bp, both of which are different from the genome of the GVCV-CHA isolate (7,753 bp), which was originally discovered in the grape cultivar 'Chardonel'. The nucleotide sequence identity among GVCV-VRU1, GVCV-VRU2, and GVCV-CHA ranges from 91.6 to 93.4%, and open reading frame (ORF) II is the most divergent ORF with only 83.3 to 88.5% identity. Sequence analysis of the ORF II indicated that GVCV isolates genetically similar to GVCV-VRU1 and GVCV-VRU2 also are present in commercial vineyards. Symptoms of GVCV-VRU1- or GVCV-VRU2-infected wild V. rupestris grapevine appeared initially as translucent vein clearing on young leaves and progressed to vein necrosis on mature leaves. Inoculation of GVCV-VRU1 or GVCV-VRU2 by grafting onto grape cultivar Chardonel resulted in mild mottle and leaf distortion. The natural range of wild V. rupestris grapevines overlaps with commercial vineyards in the Midwestern United States. Therefore, the discovery of GVCV isolates in wild V. rupestris grapevines has important implications for epidemics and management of the GVCV-associated disease.
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Affiliation(s)
- Steven Beach
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - Michael Kovens
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - LeAnn Hubbert
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - Shae Honesty
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - Qiang Guo
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - Daniel Pap
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - Ru Dai
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - Laszlo Kovacs
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - Wenping Qiu
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
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Bhat AI, Hohn T, Selvarajan R. Badnaviruses: The Current Global Scenario. Viruses 2016; 8:E177. [PMID: 27338451 PMCID: PMC4926197 DOI: 10.3390/v8060177] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/18/2016] [Accepted: 05/25/2016] [Indexed: 12/16/2022] Open
Abstract
Badnaviruses (Family: Caulimoviridae; Genus: Badnavirus) are non-enveloped bacilliform DNA viruses with a monopartite genome containing about 7.2 to 9.2 kb of dsDNA with three to seven open reading frames. They are transmitted by mealybugs and a few species by aphids in a semi-persistent manner. They are one of the most important plant virus groups and have emerged as serious pathogens affecting the cultivation of several horticultural crops in the tropics, especially banana, black pepper, cocoa, citrus, sugarcane, taro, and yam. Some badnaviruses are also known as endogenous viruses integrated into their host genomes and a few such endogenous viruses can be awakened, e.g., through abiotic stress, giving rise to infective episomal forms. The presence of endogenous badnaviruses poses a new challenge for the fool-proof diagnosis, taxonomy, and management of the diseases. The present review aims to highlight emerging disease problems, virus characteristics, transmission, and diagnosis of badnaviruses.
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Affiliation(s)
| | - Thomas Hohn
- UNIBAS, Botanical Institute, 4056 Basel, Switzerland.
| | - Ramasamy Selvarajan
- ICAR-National Research Centre for Banana, Tiruchirapalli 620102, Tamil Nadu, India.
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Rajeswaran R, Golyaev V, Seguin J, Zvereva AS, Farinelli L, Pooggin MM. Interactions of Rice tungro bacilliform pararetrovirus and its protein P4 with plant RNA-silencing machinery. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:1370-8. [PMID: 25122481 DOI: 10.1094/mpmi-07-14-0201-r] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Small interfering RNA (siRNA)-directed gene silencing plays a major role in antiviral defense. Virus-derived siRNAs inhibit viral replication in infected cells and potentially move to neighboring cells, immunizing them from incoming virus. Viruses have evolved various ways to evade and suppress siRNA production or action. Here, we show that 21-, 22-, and 24-nucleotide (nt) viral siRNAs together constitute up to 19% of total small RNA population of Oryza sativa plants infected with Rice tungro bacilliform virus (RTBV) and cover both strands of the RTBV DNA genome. However, viral siRNA hotspots are restricted to a short noncoding region between transcription and reverse-transcription start sites. This region generates double-stranded RNA (dsRNA) precursors of siRNAs and, in pregenomic RNA, forms a stable secondary structure likely inaccessible to siRNA-directed cleavage. In transient assays, RTBV protein P4 suppressed cell-to-cell spread of silencing but enhanced cell-autonomous silencing, which correlated with reduced 21-nt siRNA levels and increased 22-nt siRNA levels. Our findings imply that RTBV generates decoy dsRNA that restricts siRNA production to the structured noncoding region and thereby protects other regions of the viral genome from repressive action of siRNAs, while the viral protein P4 interferes with cell-to-cell spread of antiviral silencing.
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Rybicki EP. A Top Ten list for economically important plant viruses. Arch Virol 2014; 160:17-20. [PMID: 25430908 DOI: 10.1007/s00705-014-2295-9] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/20/2014] [Indexed: 12/31/2022]
Abstract
The concept of "Top Ten" lists of plant pathogens is in vogue in recent years, and plant viruses are no exception. However, the only list available has more to do with historical and scientific worth than it has to do with economic impact on humans and their animals. This review will discuss the most important plant viruses that cause serious harm to food plants that sustain the bulk of humankind.
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Affiliation(s)
- Edward P Rybicki
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, PB Rondebosch, Cape Town, 7701, South Africa,
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Umber M, Filloux D, Muller E, Laboureau N, Galzi S, Roumagnac P, Iskra-Caruana ML, Pavis C, Teycheney PY, Seal SE. The genome of African yam (Dioscorea cayenensis-rotundata complex) hosts endogenous sequences from four distinct Badnavirus species. MOLECULAR PLANT PATHOLOGY 2014; 15:790-801. [PMID: 24605894 PMCID: PMC6638810 DOI: 10.1111/mpp.12137] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Several endogenous viral elements (EVEs) have been identified in plant genomes, including endogenous pararetroviruses (EPRVs). Here, we report the first characterization of EPRV sequences in the genome of African yam of the Dioscorea cayenensis-rotundata complex. We propose that these sequences should be termed 'endogenous Dioscorea bacilliform viruses' (eDBVs). Molecular characterization of eDBVs shows that they constitute sequences originating from various parts of badnavirus genomes, resulting in a mosaic structure that is typical of most EPRVs characterized to date. Using complementary molecular approaches, we show that eDBVs belong to at least four distinct Badnavirus species, indicating multiple, independent, endogenization events. Phylogenetic analyses of eDBVs support and enrich the current taxonomy of yam badnaviruses and lead to the characterization of a new Badnavirus species in yam. The impact of eDBVs on diagnosis, yam germplasm conservation and movement, and breeding is discussed.
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Affiliation(s)
- Marie Umber
- INRA, UR1321 ASTRO Agrosystèmes tropicaux, F-97170, Petit-Bourg, (Guadeloupe), France
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Sharma SK, Kumar PV, Baranwal VK. Immunodiagnosis of episomal Banana streak MY virus using polyclonal antibodies to an expressed putative coat protein. J Virol Methods 2014; 207:86-94. [PMID: 24977315 DOI: 10.1016/j.jviromet.2014.06.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 06/17/2014] [Accepted: 06/20/2014] [Indexed: 11/24/2022]
Abstract
A cryptic Badnavirus species complex, known as banana streak viruses (BSV) poses a serious threat to banana production and genetic improvement worldwide. Due to the presence of integrated BSV sequences in the banana genome, routine detection is largely based on serological and nucleo-serological diagnostic methods which require high titre specific polyclonal antiserum. Viral structural proteins like coat protein (CP) are the best target for in vitro expression, to be used as antigen for antiserum production. However, in badnaviruses precise CP sequences are not known. In this study, two putative CP coding regions (p48 and p37) of Banana streak MY virus (BSMYV) were identified in silico by comparison with caulimoviruses, retroviruses and Rice tungro bacilliform virus. The putative CP coding region (p37) was in vitro expressed in pMAL system and affinity purified. The purified fusion protein was used as antigen for raising polyclonal antiserum in rabbit. The specificity of antiserum was confirmed in Western blots, immunosorbent electron microscopy (ISEM) and antigen coated plate-enzyme linked immunosorbent assay (ACP-ELISA). The antiserum (1:2000) was successfully used in ACP-ELISA for specific detection of BSMYV infection in field and tissue culture raised banana plants. The antiserum was also utilized in immuno-capture PCR (IC-PCR) based indexing of episomal BSMYV infection. This is the first report of in silico identification of putative CP region of BSMYV, production of polyclonal antiserum against recombinant p37 and its successful use in immunodetection.
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Affiliation(s)
- Susheel Kumar Sharma
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - P Vignesh Kumar
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Virendra Kumar Baranwal
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India.
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Wang Y, Cheng X, Wu X, Wang A, Wu X. Characterization of complete genome and small RNA profile of pagoda yellow mosaic associated virus, a novel badnavirus in China. Virus Res 2014; 188:103-8. [PMID: 24751798 DOI: 10.1016/j.virusres.2014.04.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/06/2014] [Accepted: 04/09/2014] [Indexed: 12/16/2022]
Abstract
A new badnavirus was discovered from pagoda trees showing yellow mosaic symptoms on the leaves by high throughput sequencing of small RNAs. The complete genome of this virus was determined to comprise 7424 nucleotides, and the virus shared 40.4-45.1% identity with that of other badnaviruses. The genome encodes five open reading frames (ORFs) on the plus strand, which includes three conserved badnaviral ORFs. These results suggest that this virus is a new member of the genus Badnavirus in the family Caulimoviridae. The virus is tentatively named pagoda yellow mosaic associated virus (PYMAV). Phylogenetic analysis suggested that this virus together with gooseberry vein banding virus (GVBV) and grapevine vein-clearing virus (GVCV) forms a separate group that is distinct two other well characterized badnaviral groups. Additionally, the viral derived small RNA (vsRNA) profile of PYMAV was analyzed and compared with that of viruses within the same family. Results showed that the most abundant PYMAV vsRNAs were 21-nt, whereas other viruses in the same family have a predominance of 22- or 24-nt vsRNA. The percentage of sense PYMAV vsRNA was almost equal to that of antisense vsRNA, whereas vsRNAs of other viruses in the family display preferences toward the sense strand of their genome. Furthermore, PYMAV vsRNAs were symmetrically distributed along the genome with no obvious vsRNA generating hotspots.
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Affiliation(s)
- Yilun Wang
- College of Agricultural and Food Science, Zhejiang Agricultural and Forestry University, Lin'an 311300, Zhejiang, PR China
| | - Xiaofei Cheng
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, Zhejiang, PR China; Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London N5V 4T3, Ontario, Canada
| | - Xiaoxia Wu
- College of Agriculture, Northeast Agricultural University, Key Laboratory of Soybean Biology, Ministry of Education, Harbin 150030, Heilongjiang, PR China
| | - Aiming Wang
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London N5V 4T3, Ontario, Canada
| | - Xiaoyun Wu
- College of Agricultural and Food Science, Zhejiang Agricultural and Forestry University, Lin'an 311300, Zhejiang, PR China.
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The common evolutionary history of badnaviruses and banana. INFECTION GENETICS AND EVOLUTION 2013; 21:83-9. [PMID: 24184704 DOI: 10.1016/j.meegid.2013.10.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 10/13/2013] [Accepted: 10/15/2013] [Indexed: 12/12/2022]
Abstract
Recent plant genome sequencing efforts have revealed myriad viral sequences suggesting a cryptic interaction between both partners. Interestingly, no integration step has ever been reported as an obligatory step in the life cycle of plant viruses. Circular dsDNA viruses belonging to the family Caulimoviridae are the most abundant among integrated plant viral sequences. In this review, we describe how this hitherto hidden interaction could inform the evolutionary history of both partners badnaviruses and banana plants.
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