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Venkataravanappa V, Madhu GS, Muralidhara BM, Hiremath S, Reddy MK. Molecular characterization of recombinant citrus yellow mosaic badnavirus infecting Coorg mandarin exhibiting yellow mosaic disease symptoms in high humid tropic region of Western Ghats. Virusdisease 2024; 35:310-320. [PMID: 39071877 PMCID: PMC11269539 DOI: 10.1007/s13337-024-00864-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/22/2024] [Indexed: 07/30/2024] Open
Abstract
The citrus yellow mosaic badnavirus (CMBV) is one of the most important viruses causing yellowing and declining in different Citrus species. The Coorg mandarin, pomelo and grapefruit showing the yellow mosaic disease symptoms were collected from different famers field during the survey. Further viral pathogenicity was confirmed through grafting on Rangpur lime as root stock. To confirm the identity of the pathogen, total genomic DNA was extracted from Coorg mandarin, Pomelo and grapefruit were subjected to PCR amplification using ORF III specific primers. Further the complete genome of CMBV amplified using different sets of specific primers were cloned and sequenced. The sequence analysis showed that CMBV from the Coorg mandarin showed maximum nt identity of 94.5% with CMBV-AL infecting acid lime. Recombination and GC plot analysis showed that the recombination occurred at in low GC content regions of genome of the CMBV and are derived from the previously reported Badnaviruses infecting different Citrus species. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-024-00864-z.
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Affiliation(s)
- V. Venkataravanappa
- Division of Plant Pathology, ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, Karnataka 560089 India
- CHES, ICAR-Indian Institute of Horticultural Research Chettalli, Madikeri District, Karnataka India
| | - G. S. Madhu
- CHES, ICAR-Indian Institute of Horticultural Research Chettalli, Madikeri District, Karnataka India
| | - B. M. Muralidhara
- CHES, ICAR-Indian Institute of Horticultural Research Chettalli, Madikeri District, Karnataka India
| | - Shridhar Hiremath
- Centre for Infectious Diseases, CSIR-North East Institute of Science and Technology, Jorhat, Assam 785006 India
| | - M. Krishna Reddy
- Division of Plant Pathology, ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, Karnataka 560089 India
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Yang Z, Chen Z, Bakht F, Li S, Zi S, Li X, Zhao X, Wen G, Zhao M. Complete genome sequence of a novel badnavirus infecting Fatsia japonica in China. Arch Virol 2024; 169:97. [PMID: 38619640 DOI: 10.1007/s00705-024-06023-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 03/11/2024] [Indexed: 04/16/2024]
Abstract
The complete genome sequence of a novel badnavirus, tentatively named "fatsia badnavirus 1" (FaBV1, OM540428), was identified in Fatsia japonica. The infected plant displayed virus-like symptoms on leaves, including yellowing and chlorosis. The genome of FaBV1 is 7313 bp in length and similar in size and organization to other members of the genus Badnavirus (family Caulimoviridae), containing four open reading frames (ORFs), three of which are found in all known badnaviruses, and the other of which is only present in some badnaviruses. The virus has the genome characteristics of badnaviruses, including a tRNAMet binding site (5'-TCTGAATTTATAGCGCTA-3') and two cysteine-rich domains (C-X-C-2X-C-4X-H-4X-C and C-2X-C-11X-C-2X-C-4X-C-2X-C). Pairwise sequence comparisons of the RT+RNase H region indicated that FaBV1 shares 61.4-71.2% nucleotide (nt) sequence identity with other known badnaviruses, which is below the threshold (80% nt sequence identity in the RT+RNase H region) used for species demarcation in the genus Badnavirus. Phylogenetic analysis revealed that FaBV1, ivy ringspot-associated virus (IRSaV, MN850490.1), and cacao mild mosaic virus (CMMV, KX276640.1) together form a separate clade within the genus Badnavirus, suggesting that FaBV1 is a new member of the genus Badnavirus in the family Caulimoviridae. To our knowledge, this is the first report of a badnavirus infecting F. japonica.
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Affiliation(s)
- Zefen Yang
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Zeli Chen
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
- Quality Standard and Testing Technology Research Institute, Yunnan Academy of Agricultural Sciences, No. 2238, Beijing Road, Kunming, 650205, Yunnan, China
| | - Faryal Bakht
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Pakistan
| | - Shangyun Li
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Shaomei Zi
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Xin Li
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Xiyan Zhao
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Guosong Wen
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Mingfu Zhao
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.
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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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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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Infectivity of an Infectious Clone of Banana Streak CA Virus in A-Genome Bananas ( Musa acuminata ssp.). Viruses 2021; 13:v13061071. [PMID: 34199911 PMCID: PMC8226583 DOI: 10.3390/v13061071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/17/2022] Open
Abstract
We have characterized the complete genome sequence of an Australian isolate of banana streak CA virus (BSCAV). A greater-than-full-length, cloned copy of the virus genome was assembled and agroinoculated into five tissue-cultured plants of nine different Musa acuminata banana accessions. BSCAV was highly infectious in all nine accessions. All five inoculated plants from eight accessions developed symptoms by 28 weeks post-inoculation, while all five plants of M. acuminata AA subsp. zebrina remained symptomless. Symptoms were mild in six accessions but were severe in Khae Phrae (M. acuminata subsp. siamea) and the East African Highland banana accession Igisahira Gisanzwe. This is the first full-length BSCAV genome sequence reported from Australia and the first report of the infectivity of an infectious clone of banana streak virus.
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Zheng Q, Wang X, Zhou J, Ma Y. Complete genome sequence of a new member of the genus Badnavirus from red pitaya (Hylocereus polyrhizus). Arch Virol 2020; 165:749-752. [PMID: 32034473 DOI: 10.1007/s00705-019-04503-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 11/25/2019] [Indexed: 11/25/2022]
Abstract
Here, we report a circular double-stranded DNA virus from red pitaya (Hylocereus polyrhizus). The complete genome sequence is 7,837 nt in length and shares 98.7% nucleotide sequence identity with epiphyllum mottle-associated virus (EpMoaV) and 40.4-54.6% with other members of the genus Badnavirus. It has four open reading frames (ORFs), encoding putative proteins of 19.9, 14.8, 225.7 and 14.2 kDa, respectively. The reverse transcriptase (RT)-ribonuclease H (RNase H) region exhibits less than 70.5% nucleotide sequence identity to RT-RNase H of other badnaviruses, and 99.7% to that of EpMoaV. Phylogenetic analysis revealed that the virus from this study and EpMoaV form a single group. Consequently, we propose this virus as a new member of the genus Badnavirus in the family Caulimoviridae and have named it "pitaya badnavirus 1" (PiBV1). PiBV1 and EpMoaV should be considered two isolates of a badnavirus that infects members of the family Cactaceae.
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Affiliation(s)
- Qianming Zheng
- Institute of Pomology Science, Guizhou Provincial Academy of Agricultural Sciences, Huaxi District, Jinzhu Town, Guiyang, 550006, Guizhou, China
| | - Xiaoke Wang
- Institute of Pomology Science, Guizhou Provincial Academy of Agricultural Sciences, Huaxi District, Jinzhu Town, Guiyang, 550006, Guizhou, China
| | - Junliang Zhou
- Institute of Pomology Science, Guizhou Provincial Academy of Agricultural Sciences, Huaxi District, Jinzhu Town, Guiyang, 550006, Guizhou, China
| | - Yuhua Ma
- Institute of Pomology Science, Guizhou Provincial Academy of Agricultural Sciences, Huaxi District, Jinzhu Town, Guiyang, 550006, Guizhou, China.
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Genomic, Morphological and Biological Traits of the Viruses Infecting Major Fruit Trees. Viruses 2019; 11:v11060515. [PMID: 31167478 PMCID: PMC6631394 DOI: 10.3390/v11060515] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 11/17/2022] Open
Abstract
Banana trees, citrus fruit trees, pome fruit trees, grapevines, mango trees, and stone fruit trees are major fruit trees cultured worldwide and correspond to nearly 90% of the global production of woody fruit trees. In light of the above, the present manuscript summarizes the viruses that infect the major fruit trees, including their taxonomy and morphology, and highlights selected viruses that significantly affect fruit production, including their genomic and biological features. The results showed that a total of 163 viruses, belonging to 45 genera classified into 23 families have been reported to infect the major woody fruit trees. It is clear that there is higher accumulation of viruses in grapevine (80/163) compared to the other fruit trees (each corresponding to less than 35/163), while only one virus species has been reported infecting mango. Most of the viruses (over 70%) infecting woody fruit trees are positive-sense single-stranded RNA (+ssRNA), and the remainder belong to the -ssRNA, ssRNA-RT, dsRNA, ssDNA and dsDNA-RT groups (each corresponding to less than 8%). Most of the viruses are icosahedral or isometric (79/163), and their diameter ranges from 16 to 80 nm with the majority being 25-30 nm. Cross-infection has occurred in a high frequency among pome and stone fruit trees, whereas no or little cross-infection has occurred among banana, citrus and grapevine. The viruses infecting woody fruit trees are mostly transmitted by vegetative propagation, grafting, and root grafting in orchards and are usually vectored by mealybug, soft scale, aphids, mites or thrips. These viruses cause adverse effects in their fruit tree hosts, inducing a wide range of symptoms and significant damage, such as reduced yield, quality, vigor and longevity.
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Abstract
Mealybug wilt of pineapple (MWP) is a disease of pineapple that has a long history in Hawaii, but is present throughout the world where pineapples are grown in tropical regions. The disease has an interesting etiology that is poorly understood but involves an association with virus particles, mealybug vectors, and ants which spread the mealybug vectors. Several distinct pineapple mealybug wilt-associated virus (PMWaV) species have been identified thus far with potential further member species yet to be characterized. Pineapple mealybug wilt-associated viruses are member species of the Ampelovirus genus of the Closteroviridae family. Ampeloviruses are split into two subgroups, subgroup I and subgroup II. PMWaV-2 is a subgroup II member, and these have a longer and more complex genome with additional genes on the 3’ terminus of the RNA genome compared to subgroup I ampeloviruses. PMWaV-2, along with the presence of mealybug vectors, have been shown to be necessary factors in symptom development in Hawaii. Some of these extra genes in the 3’ of PMWaV-2 have recently been shown to function as silencing suppressors, and may play a role in the virulence of PMWaV-2 and symptom development. In other regions of the world, reports of symptomatic plants without PMWaV-2 infection, but with PMWaV-1, -3 or some combination, contradict the requirement of PMWaV-2 for symptom development in MWP. It is possible that further, uncharacterized PMWaVs may be present in symptomatic pineapple plants that test negative for PMWaV-2, explaining the inconsistency in symptom development. More research is necessary to explore the confusing etiology of the MWP disease, and to perhaps shed light upon the symptom development.
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Motghare M, Dhar AK, Kokane A, Warghane A, Kokane S, Sharma AK, Reddy MK, Ghosh DK. Quantitative distribution of Citrus yellow mosaic badnavirus in sweet orange (Citrus sinensis) and its implication in developing disease diagnostics. J Virol Methods 2018; 259:25-31. [PMID: 29859966 DOI: 10.1016/j.jviromet.2018.05.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/14/2018] [Accepted: 05/30/2018] [Indexed: 10/14/2022]
Abstract
Citrus yellow mosaic badnavirus (CMBV) is the etiologic agent of citrus yellow mosaic disease, which has caused serious economic losses to Indian citrus industry. CMBV is a quarantined pathogen that is geographically restricted to India. To prevent unintentional movement of the virus to other major citrus-growing countries in fruits, root stocks or grafted citrus plants and facilitate trade, a sensitive, validated diagnostic tool is needed. In the present study, we developed a SYBR Green real-time PCR-based method to detect and quantify CMBV in different tissues of infected Mosambi sweet orange (Citrus sinensis) and compared its sensitivity to conventional PCR protocols. Primers were designed to recognize a portion of the CMBV capsid protein gene. Conventional and real-time PCR were performed on several different tissues: shoot tips, leaves displaying typical CMBV symptoms, asymptomatic leaves, senescent leaves, thorns, green stems and feeder roots. The detection limit of CMBV by conventional PCR was 2.5 × 104 copies per 5 ng of total genomic DNA, while the detection limit of real-time PCR was found to be 4.6 × 102 virus copies per 5 ng of viral DNA. The viral load varied between different tissues. The highest concentration occurred in feeder roots (3.5 × 108 copies per 5 ng of total genomic DNA) and the lowest in thorns (1 × 106 copies per 5 ng of total genomic DNA). The variation in viral load within different tissues suggests movement of the virus within an infected plant that follows the path of photo-assimilates via the phloem. In symptomatic leaves, the CMBV concentration was highest in the lamella followed by midrib and petiole, suggesting that virus resides inside these sections of a leaf and side by side symptoms develop. On the other hand, in asymptomatic leaves, the petiole contained higher virus load than the lamella and midrib suggesting that the pathogen gets established from the stem through the phloem into petiole then infects the lamella and midrib. In addition to information on virus movement, the distribution of CMBV in different tissues helps with the selection of tissues with relatively higher viral load to sample for early and sensitive diagnosis of the disease, which will be useful for better management of the disease in endemic areas.
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Affiliation(s)
- Manali Motghare
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur 440033, Maharashtra, India
| | - Arun Kumar Dhar
- Aquaculture Pathology Laboratory, School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona 8572, USA
| | - Amol Kokane
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur 440033, Maharashtra, India
| | - Ashish Warghane
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur 440033, Maharashtra, India
| | - Sunil Kokane
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur 440033, Maharashtra, India
| | - Ashwani Kumar Sharma
- Department of Biotechnology, Indian Institute of Technology, Roorkee 247667, India
| | - M Krishna Reddy
- Plant Virology Laboratory, ICAR-Indian Institute of Horticulture, Bangalore 560089, India
| | - Dilip Kumar Ghosh
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur 440033, Maharashtra, India.
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Characterization of an Australian isolate of taro bacilliform virus and development of an infectious clone. Arch Virol 2018; 163:1677-1681. [PMID: 29488119 DOI: 10.1007/s00705-018-3783-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/14/2018] [Indexed: 01/28/2023]
Abstract
The badnavirus taro bacilliform virus (TaBV) has been reported to infect taro (Colocasia esculenta L.) and other edible aroids in several South Pacific island countries, but there are no published reports from Australia. Using PCR and RCA, we identified and characterized an Australian TaBV isolate. A terminally redundant cloned copy of the TaBV genome was generated and shown to be infectious in taro following agro-inoculation. This is the first report of TaBV from Australia and also the first report of an infectious clone for this virus.
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Kumar PV, Sharma SK, Rishi N, Baranwal VK. Efficient immunodiagnosis of Citrus yellow mosaic virus using polyclonal antibodies with an expressed recombinant virion-associated protein. 3 Biotech 2018; 8:39. [PMID: 29291152 DOI: 10.1007/s13205-017-1063-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/21/2017] [Indexed: 11/30/2022] Open
Abstract
Citrus yellow mosaic virus (CYMV) is a member of genus Badnavirus of the family Caulimoviridae. It is the causal agent of citrus yellow mosaic disease in citrus and causes reduction in yield. As the virus is vegetative propagated by grafting, development of high-throughput diagnosis methods based on serological techniques is a prerequisite for production of healthy virus-free planting material. The current study describes the development of polyclonal antibodies raised in rabbits against purified recombinant virion-associated protein (rVAP) encoded by ORF-II of CYMV. The specificity of developed antiserum was evaluated in immunosorbent electron microscopy (ISEM), antigen-coated plate-enzyme linked immunosorbent assay (ACP-ELISA) and immunocapture PCR (IC-PCR). The antiserum specifically reacted up to a dilution of 1:2000 in ACP-ELISA for detection of CYMV-infected plants. The antiserum was validated by screening CYMV-infected plants maintained in the glass house through ACP-ELISA. To the best for our knowledge, this is the first report on production of polyclonal antiserum using recombinant virion-associated protein as fusion protein, which could be used for screening CYMV-infected plants by ELISA and IC-PCR. These immunodiagnostic methods can be effectively employed in routine indexing of citrus and in quarantine process.
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Affiliation(s)
- P Vignesh Kumar
- Division of Plant Pathology, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | | | - Narayan Rishi
- Amity Institute of Virology and Immunology, Amity University, Noida, 201303 India
| | - Virendra Kumar Baranwal
- Division of Plant Pathology, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
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Abstract
Promoters regulate gene expression, and are essential biotechnology tools. Since its introduction in the mid-1990s, biotechnology has greatly enhanced maize productivity primarily through the development of insect control and herbicide tolerance traits. Additional biotechnology applications include improving seed nutrient composition, industrial protein production, therapeutic production, disease resistance, abiotic stress resistance, and yield enhancement. Biotechnology has also greatly expanded basic research into important mechanisms that govern plant growth and reproduction. Many novel promoters have been developed to facilitate this work, but only a few are widely used. Transgene optimization includes a variety of strategies some of which effect promoter structure. Recent reviews examine the state of the art with respect to transgene design for biotechnology applications. This chapter examines the use of transgene technology in maize, focusing on the way promoters are selected and used. The impact of new developments in genomic technology on promoter structure is also discussed.
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Li Y, Deng C, Qiao Y, Zhao X, Zhou Q. Characterization of a new badnavirus from Wisteria sinensis. Arch Virol 2017; 162:2125-2129. [PMID: 28299484 DOI: 10.1007/s00705-017-3322-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 03/02/2017] [Indexed: 11/26/2022]
Abstract
The complete genome sequence of a previously undescribed badnavirus isolated from a wisteria plant exhibiting mosaic and crinkle symptoms in Beijing, China, was determined. The circular double-stranded DNA genome of this virus was 7362 bp in size with four open reading frames (ORFs 1 to 4) on the plus strand. Sequence analysis showed that this virus shared the highest (69%) nucleotide (nt) sequence identity with pagoda yellow mosaic associated virus (PYMAV). In the RT-RNase H region of the ORF-3 encoded polyprotein, this virus shared 74% nt sequence identity with PYMAV. Phylogenetic analysis provided further evidence that the virus identified in this study is a member of a new species in the genus Badnavirus. The name wisteria badnavirus 1 (WBV1) is proposed for this new virus.
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Affiliation(s)
- Yongqiang Li
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China.
| | - Congliang Deng
- Plant Laboratory of Beijing Entry-Exit Inspection and Quarantine Bureau, Beijing, 100026, China
| | - Yan Qiao
- Beijing Plant Protection Station, Beijing, 100029, China
| | - Xiaoli Zhao
- Plant Laboratory of Beijing Entry-Exit Inspection and Quarantine Bureau, Beijing, 100026, China
| | - Qi Zhou
- Chinese Society of Inspection and Quarantine, Beijing, 101312, China.
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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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Kazmi SA, Yang Z, Hong N, Wang G, Wang Y. Characterization by Small RNA Sequencing of Taro Bacilliform CH Virus (TaBCHV), a Novel Badnavirus. PLoS One 2015. [PMID: 26207896 PMCID: PMC4514669 DOI: 10.1371/journal.pone.0134147] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
RNA silencing is an antiviral immunity that regulates gene expression through the production of small RNAs (sRNAs). In this study, deep sequencing of small RNAs was used to identify viruses infecting two taro plants. Blast searching identified five and nine contigs assembled from small RNAs of samples T1 and T2 matched onto the genome sequences of badnaviruses in the family Caulimoviridae. Complete genome sequences of two isolates of the badnavirus determined by sequence specific amplification comprised of 7,641 nucleotides and shared overall nucleotide similarities of 44.1%‒55.8% with other badnaviruses. Six open reading frames (ORFs) were identified on the plus strand, showed amino acid similarities ranging from 59.8% (ORF3) to 10.2% (ORF6) to the corresponding proteins encoded by other badnaviruses. Phylogenetic analysis also supports that the virus is a new member in the genus Badnavirus. The virus is tentatively named as Taro bacilliform CH virus (TaBCHV), and it is the second badnavirus infecting taro plants, following Taro bacilliform virus (TaBV). In addition, analyzes of viral derived small RNAs (vsRNAs) from TaBCHV showed that almost equivalent number of vsRNAs were generated from both strands and the most abundant vsRNAs were 21 nt, with uracil bias at 5' terminal. Furthermore, TaBCHV vsRNAs were asymmetrically distributed on its entire circular genome at both orientations with the hotspots mainly generated in the ORF5 region.
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Affiliation(s)
- Syeda Amber Kazmi
- State Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zuokun Yang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ni Hong
- State Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- * E-mail:
| | - Guoping Wang
- State Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yanfen Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
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Bhat AI, Sasi S, Revathy KA, Deeshma KP, Saji KV. Sequence diversity among badnavirus isolates infecting black pepper and related species in India. Virusdisease 2015; 25:402-7. [PMID: 25674613 DOI: 10.1007/s13337-014-0221-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 05/07/2014] [Indexed: 10/25/2022] Open
Abstract
The badnavirus, piper yellow mottle virus (PYMoV) is known to infect black pepper (Piper nigrum), betelvine (P. betle) and Indian long pepper (P. longum) in India and other parts of the world. Occurrence of PYMoV or other badnaviruses in other species of Piper and its variability is not reported so far. We have analysed sequence variability in the conserved putative reverse transcriptase (RT)/ribonuclease H (RNase H) coding region of the virus using specific badnavirus primers from 13 virus isolates of black pepper collected from different cultivars and regions and one isolate each from 23 other species of Piper. Of these, four species failed to produce expected amplicon while amplicon from four other species showed more similarities to plant sequences than to badnaviruses. Of the remaining, isolates from black pepper, P. argyrophyllum, P. attenuatum, P. barberi, P. betle, P. colubrinum, P. galeatum, P. longum, P. ornatum, P. sarmentosum and P. trichostachyon showed an identity of >85 % at the nucleotide and >90 % at the amino acid level with PYMoV indicating that they are isolates of PYMoV. On the other hand high sequence variability of 21-43 % at nucleotide and 17-46 % at amino acid level compared to PYMoV was found among isolates infecting P. bababudani, P. chaba, P. peepuloides, P. mullesua and P. thomsonii suggesting the presence of new badnaviruses. Phylogenetic analyses showed close clustering of all PYMoV isolates that were well separated from other known badnaviruses. This is the first report of occurrence of PYMoV in eight Piper spp and likely occurrence of four new species in five Piper spp.
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Affiliation(s)
- A I Bhat
- Division of Crop Protection, Indian Institute of Spices Research, Marikunnu PO, Kozhikode, 673 012 Kerala India
| | - Shina Sasi
- Division of Crop Protection, Indian Institute of Spices Research, Marikunnu PO, Kozhikode, 673 012 Kerala India
| | - K A Revathy
- Division of Crop Protection, Indian Institute of Spices Research, Marikunnu PO, Kozhikode, 673 012 Kerala India
| | - K P Deeshma
- Division of Crop Protection, Indian Institute of Spices Research, Marikunnu PO, Kozhikode, 673 012 Kerala India
| | - K V Saji
- Division of Crop Protection, Indian Institute of Spices Research, Marikunnu PO, Kozhikode, 673 012 Kerala India
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Zhang Y, Angel CA, Valdes S, Qiu W, Schoelz JE. Characterization of the promoter of Grapevine vein clearing virus. J Gen Virol 2015; 96:165-169. [PMID: 25281563 DOI: 10.1099/vir.0.069286-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Grapevine vein clearing virus (GVCV) is a recently discovered DNA virus in grapevine that is closely associated with the grapevine vein clearing syndrome observed in vineyards in Missouri and surrounding states. The genome sequence of GVCV indicates that it belongs to the genus Badnavirus in the family Caulimoviridae. To identify the GVCV promoter, we cloned portions of the GVCV large intergenic region in front of a GFP gene present in an Agrobacterium tumefaciens binary vector. GFP expression was assessed by ELISA 3 days after agroinfiltration of Nicotiana benthamiana leaves. We found that the GVCV DNA segment between nts 7332 and 7672 directed expression of GFP and this expression was stronger than expression using the Cauliflower mosaic virus 35S promoter. It was revealed by 5' and 3' RACE that transcription was initiated predominantly at nt 7571 and terminated at nt 7676.
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Affiliation(s)
- Y Zhang
- Division of Plant Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - C A Angel
- Division of Plant Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - S Valdes
- Division of Plant Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - W Qiu
- Center for Grapevine Biotechnology, William H. Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711, USA
| | - J E Schoelz
- Division of Plant Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA
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Abstract
Citrus is thought to have originated in Southeast Asia and horticulturally desirable clonal selections have been clonally cultivated for hundreds of years. While some citrus species have nucellar embryony, most cultivation of citrus has been by clonal propagation to ensure that propagated plants have the same traits as the parent selection. Clonal propagation also avoids juvenility, and the propagated plants produce fruit sooner. Because of the clonal propagation of citrus, citrus has accumulated a large number of viruses; many of these viruses are asymptomatic until a susceptible rootstock and/or scion is encountered. The viruses reported to occur in citrus will be summarized in this review. Methods of therapy to clean selected clones from viruses will be reviewed; the use of quarantine, clean stock, and certification programs for control of citrus viruses and other strategies to control insect spread citrus viruses, such as mild strain cross-protection and the use of pest management areas will be discussed.
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Complete genome sequencing of Piper yellow mottle virus infecting black pepper, betelvine, and Indian long pepper. Virus Genes 2014; 50:172-5. [PMID: 25331343 DOI: 10.1007/s11262-014-1134-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
Abstract
The complete genome of the Piper yellow mottle virus (PYMoV), a Badnavirus belonging to the family Caulimoviridae, was sequenced from three naturally infected hosts namely, black pepper, betelvine, and Indian long pepper. The genome length of the three virus strains (one from each of the three host species) varied from 7,559 to 7,584 nucleotides, and all the three strains possessed four open reading frames (ORFs) I to IV that potentially encode proteins of 15.67, 17.08, 218.6, and 17.22 kDa, respectively. ORF III encodes a polyprotein consisting of viral movement protein, trimeric dUTPase, zinc finger, aspartic protease, reverse transcriptase, and RNase H whereas ORF I, II, and IV encode proteins of unknown functions. The complete genome sequences at the nucleotide level were 89-99 % identical with one available sequence of PYMoV and 39-56 % identical with other badnaviruses, indicating that all three are strains of PYMoV. Nucleotide and amino acid sequences of ORF I-IV and of the intergenic region (IR) were 80-100 % identical among PYMoV strains. Phylogenetic analysis of ORF III amino acid sequences showed the PYMoV strains forming a distinct cluster well separated from other badnaviruses. Among other badnaviruses, Fig badnavirus 1 (FBV-1) was the one most closely related to PYMoV.
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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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Lin YY, Fang MM, Lin PC, Chiu MT, Liu LY, Lin CP, Lin SS. Improving initial infectivity of the Turnip mosaic virus (TuMV) infectious clone by an mini binary vector via agro-infiltration. BOTANICAL STUDIES 2013; 54:22. [PMID: 28510872 PMCID: PMC5432745 DOI: 10.1186/1999-3110-54-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 12/05/2012] [Indexed: 05/21/2023]
Abstract
BACKGROUND The in vivo infectious clone of Turnip mosaic virus (TuMV), p35S-TuMV, was used on plant pathology research for many years. To activate p35S-TuMV, the plasmid was mechanically introduced to the local lesion host Chenopodium quinoa. However, low infectivity occurred when the TuMV from C. quinoa was transferred to the systemic host Nicotiana benthamiana. RESULTS To increase the efficiency of initial infectivity on N. benthamiana, the expression of the TuMV infectious clone by a binary vector that directly activates viral RNA through agro-infiltration is considered to be a good alternative. The size of the binary vector by agro-infiltration is usually large and its backbone has numerous restriction sites that increase difficulty for construction. In this study, we attempted to construct a mini binary vector (pBD003) with less restriction sites. The full-length cDNA of TuMV genome, with or without green fluorescence protein, was inserted in pBD003 to generate pBD-TuMV constructs, which were then individually introduced to N. benthamiana plants by agro-infiltration. Symptom development and ELISA positivity with TuMV antiserum indicated that the pBD-TuMV constructs are infectious. Moreover, the initial infectivity of a mild strain TuMV-GK, which contains an R182K mutation on HC-Pro, constructed in the pBD003 vector was significantly increased by agro-infiltration. CONCLUSION Thus, we concluded that the newly constructed mini binary vector provides a more feasible tool for TuMV researches in areas, such as creating a mild strain for cross-protection, or a viral vector for foreign gene expression. In addition, the multiple cloning sites will be further cloned in pBD003 for convenience in constructing other viral infectious clones.
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Affiliation(s)
- Yen-Yu Lin
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, 81, Chang-Xing ST.,, Taipei, 106 Taiwan
- Department of Plant Pathology and Microbiology, College of Bioresources and Agriculture, National Taiwan University, 1, Sec. 4, Roosevelt Rd.,, Taipei, 106 Taiwan
| | - Meng-Mei Fang
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, 81, Chang-Xing ST.,, Taipei, 106 Taiwan
| | - Pin-Chun Lin
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, 81, Chang-Xing ST.,, Taipei, 106 Taiwan
| | - Ming-Tzu Chiu
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, 81, Chang-Xing ST.,, Taipei, 106 Taiwan
- Department of Plant Pathology and Microbiology, College of Bioresources and Agriculture, National Taiwan University, 1, Sec. 4, Roosevelt Rd.,, Taipei, 106 Taiwan
| | - Li-Yu Liu
- Department of Agronomy, National Taiwan University, 1, Sec. 4, Roosevelt Rd.,, Taipei, 106 Taiwan
| | - Chan-Pin Lin
- Department of Plant Pathology and Microbiology, College of Bioresources and Agriculture, National Taiwan University, 1, Sec. 4, Roosevelt Rd.,, Taipei, 106 Taiwan
| | - Shih-Shun Lin
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, 81, Chang-Xing ST.,, Taipei, 106 Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, 1, Sec. 4, Roosevelt Rd.,, Taipei, 106 Taiwan
- Agriculture Biotechnology Research Center, Academia Sinica, 128, Sec. 2, Academia Rd.,, Taipei, 115 Taiwan
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Borah BK, Sharma S, Kant R, Johnson AMA, Saigopal DVR, Dasgupta I. Bacilliform DNA-containing plant viruses in the tropics: commonalities within a genetically diverse group. MOLECULAR PLANT PATHOLOGY 2013; 14:759-71. [PMID: 23763585 PMCID: PMC6638767 DOI: 10.1111/mpp.12046] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
UNLABELLED Plant viruses, possessing a bacilliform shape and containing double-stranded DNA, are emerging as important pathogens in a number of agricultural and horticultural crops in the tropics. They have been reported from a large number of countries in African and Asian continents, as well as from islands from the Pacific region. The viruses, belonging to two genera, Badnavirus and Tungrovirus, within the family Caulimoviridae, have genomes displaying a common plan, yet are highly variable, sometimes even between isolates of the same virus. In this article, we summarize the current knowledge with a view to revealing the common features embedded within the genetic diversity of this group of viruses. TAXONOMY Virus; order Unassigned; family Caulimoviridae; genera Badnavirus and Tungrovirus; species Banana streak viruses, Bougainvillea spectabilis chlorotic vein banding virus, Cacao swollen shoot virus, Citrus yellow mosaic badnavirus, Dioscorea bacilliform viruses, Rice tungro bacilliform virus, Sugarcane bacilliform viruses and Taro bacilliform virus. MICROBIOLOGICAL PROPERTIES Bacilliform in shape; length, 60-900 nm; width, 35-50 nm; circular double-stranded DNA of approximately 7.5 kbp with one or more single-stranded discontinuities. HOST RANGE Each virus generally limited to its own host, including banana, bougainvillea, black pepper, cacao, citrus species, Dioscorea alata, rice, sugarcane and taro. DISEASE SYMPTOMS Foliar streaking in banana and sugarcane, swelling of shoots in cacao, yellow mosaic in leaves and stems in citrus, brown spot in the tubers in yam and yellow-orange discoloration and stunting in rice. USEFUL WEBSITES http://www.dpvweb.net.
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Affiliation(s)
- Basanta K Borah
- Department of Plant Molecular Biology, Delhi University South Campus, New Delhi 110021, India
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Kalischuk ML, Fusaro AF, Waterhouse PM, Pappu HR, Kawchuk LM. Complete genomic sequence of a Rubus yellow net virus isolate and detection of genome-wide pararetrovirus-derived small RNAs. Virus Res 2013; 178:306-13. [PMID: 24076299 DOI: 10.1016/j.virusres.2013.09.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 09/12/2013] [Accepted: 09/16/2013] [Indexed: 12/29/2022]
Abstract
Rubus yellow net virus (RYNV) was cloned and sequenced from a red raspberry (Rubus idaeus L.) plant exhibiting symptoms of mosaic and mottling in the leaves. Its genomic sequence indicates that it is a distinct member of the genus Badnavirus, with 7932bp and seven ORFs, the first three corresponding in size and location to the ORFs found in the type member Commelina yellow mottle virus. Bioinformatic analysis of the genomic sequence detected several features including nucleic acid binding motifs, multiple zinc finger-like sequences and domains associated with cellular signaling. Subsequent sequencing of the small RNAs (sRNAs) from RYNV-infected R. idaeus leaf tissue was used to determine any RYNV sequences targeted by RNA silencing and identified abundant virus-derived small RNAs (vsRNAs). The majority of the vsRNAs were 22-nt in length. We observed a highly uneven genome-wide distribution of vsRNAs with strong clustering to small defined regions distributed over both strands of the RYNV genome. Together, our data show that sequences of the aphid-transmitted pararetrovirus RYNV are targeted in red raspberry by the interfering RNA pathway, a predominant antiviral defense mechanism in plants.
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Affiliation(s)
- Melanie L Kalischuk
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-106, United States; Agriculture and Agri-Food Canada, P.O. Box 3000, Lethbridge, Alberta T1J 4B1, Canada
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24
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Karuppaiah R, Viswanathan R, Kumar VG. Genetic diversity of Sugarcane bacilliform virus isolates infecting Saccharum spp. in India. Virus Genes 2013; 46:505-16. [PMID: 23430710 DOI: 10.1007/s11262-013-0890-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 02/05/2013] [Indexed: 02/05/2023]
Abstract
Sugarcane bacilliform virus (SCBV), which causes leaf freckle in sugarcane, is a member of the genus Badnavirus. Studies were conducted to characterize SCBV in Saccharum officinarum germplasm and cultivated varieties in India by sequencing the complete genomes of five isolates. Genome lengths ranged from 7,553 to 7,884 nucleotides. Duplications in ORF3 and insertions in the RNase H-domain in some of the isolates were found to contribute to the large size of their genomes. The Indian SCBV isolates share identities of 69-85 % for the complete genomic sequence, indicating wide genetic diversity among them, and share 70-82 % identity with Sugarcane bacilliform Ireng Maleng virus (SCBIMV) and Sugarcane bacilliform Morocco virus (SCBMV), as well as 43-46 % identity with Banana streak virus (BSV) and BSV-related SCBV species from Guadeloupe, indicating that the Indian SCBV isolates are distinct from SCBV isolates reported to date. Irrespective of the region compared, SCBV isolates from India, Australia, and Morocco clustered together. BSV and BSV-related SCBV isolates from Guadeloupe formed another cluster. A phylogenetic analysis based on the partial RT/RNase H-sequence separated SCBV and BSV-related SCBV sequences into 11 SCBV groups viz. SCBV-A to -K. Among the 11 groups, the SCBV sequences separated under H, I, J, and K are newly identified in this study, representing three new species and are tentatively named as SCBBBV, SCBBOV, and SCBBRV. Thus, the PASC and phylogenetic analyses evidenced that the symptoms associated with badnaviruses in sugarcane in India are caused by at least three new species, SCBBBV, SCBBOV, and SCBBRV, besides SCBIMV and SCBMV represented by SCBV-BT and SCBV-Iscam, respectively.
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Affiliation(s)
- R Karuppaiah
- Plant Pathology Section, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, 641007, India
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25
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Sether DM, Melzer MJ, Borth WB, Hu JS. Pineapple bacilliform CO virus: Diversity, Detection, Distribution, and Transmission. PLANT DISEASE 2012; 96:1798-1804. [PMID: 30727278 DOI: 10.1094/pdis-08-11-0718-re] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Members of the genus Badnavirus (family Caulimovirdae) have been identified in dicots and monocots worldwide. The genome of a pineapple badnavirus, designated Pineapple bacilliform CO virus-HI1 (PBCOV-HI1), and nine genomic variants (A through H) were isolated and sequenced from pineapple, Ananas comosus, in Hawaii. The 7,451-nucleotide genome of PBCOV-HI1 possesses three open reading frames (ORFs) encoding putative proteins of 20 (ORF1), 15 (ORF2), and 211 (ORF3) kDa. ORF3 encodes a polyprotein that includes a putative movement protein and viral aspartyl proteinase, reverse transcriptase, and RNase H regions. Three distinct groups of putative endogenous pineapple pararetroviral sequences and Metaviridae-like retrotransposons encoding long terminal repeat, reverse-transcriptase, RNase H, and integrase regions were also identified from the pineapple genome. Detection assays were developed to distinguish PBCOV-HI1 and genomic variants, putative endogenous pararetrovirus sequences, and Ananas Metaviridae sequences also identified in pineapple. PBCOV-HI1 incidences in two commercially grown pineapple hybrids, PRI 73-114 and PRI 73-50, was 34 to 68%. PBCOV-HI1 was transmitted by gray pineapple mealybugs, Dysmicoccus neobrevipes, to pineapple.
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Affiliation(s)
- D M Sether
- University of Hawaii at Manoa, Department of Plant and Environmental Protection Sciences, Honolulu 96822-2232
| | - M J Melzer
- University of Hawaii at Manoa, Department of Plant and Environmental Protection Sciences, Honolulu 96822-2232
| | - W B Borth
- University of Hawaii at Manoa, Department of Plant and Environmental Protection Sciences, Honolulu 96822-2232
| | - J S Hu
- University of Hawaii at Manoa, Department of Plant and Environmental Protection Sciences, Honolulu 96822-2232
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26
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Anthony Johnson AM, Borah BK, Sai Gopal DVR, Dasgupta I. Analysis of full-length sequences of two Citrus yellow mosaic badnavirus isolates infecting Citrus jambhiri (Rough Lemon) and Citrus sinensis L. Osbeck (Sweet Orange) from a nursery in India. Virus Genes 2012; 45:600-5. [PMID: 22926812 DOI: 10.1007/s11262-012-0808-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Accepted: 08/10/2012] [Indexed: 10/28/2022]
Abstract
Citrus yellow mosaic badna virus (CMBV), a member of the Family Caulimoviridae, Genus Badnavirus is the causative agent of mosaic disease among Citrus species in southern India. Despite its reported prevalence in several citrus species, complete information on clear functional genomics or functional information of full-length genomes from all the CMBV isolates infecting citrus species are not available in publicly accessible databases. CMBV isolates from Rough Lemon and Sweet Orange collected from a nursery were cloned and sequenced. The analysis revealed high sequence homology of the two CMBV isolates with previously reported CMBV sequences implying that they represent new variants. Based on computational analysis of the predicted secondary structures, the possible functions of some CMBV proteins have been analyzed.
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27
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Molecular analysis of the complete genomic sequences of four isolates of Gooseberry vein banding associated virus. Virus Genes 2011; 43:130-7. [PMID: 21533750 DOI: 10.1007/s11262-011-0614-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 04/12/2011] [Indexed: 10/18/2022]
Abstract
The presence of Gooseberry vein banding associated virus (GVBaV), a badnavirus in the family Caulimoviridae, is strongly correlated with gooseberry vein banding disease in Ribes spp. In this study, full-length genomic sequences of four GVBaV isolates from different hosts and geographic regions were determined to be 7649-7663 nucleotides. These isolates share identities of 96.4-97.3% for the complete genomic sequence, indicating low genetic diversity among them. The GVBaV genome contains three open reading frames (ORFs) on the plus strand that potentially encode proteins of 26, 16, and 216 kDa. The size and organization of GVBaV ORFs 1-3 are similar to those of most other badnaviruses. The putative amino acid sequence of GVBaV ORF 3 contained motifs that are conserved among badnavirus proteins including aspartic protease, reverse transcriptase, and ribonuclease H. The highly conserved putative plant tRNA(met)-binding site is also present in the 935-bp intergenic region of GVBaV. The identities of the genomic sequences of GVBaV and other badnaviruses range from 49.1% (Sugarcane bacilliform Mor virus) to 51.7% (Pelargonium vein banding virus, PVBV). Phylogenetic analysis using the amino acid sequence of the ORF 3 putative protein shows that GVBaV groups most closely to Dioscorea bacilliform virus, PVBV, and Taro bacilliform virus. These results confirm that GVBaV is a pararetrovirus of the genus Badnavirus in the family Caulimoviridae.
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Purkayastha A, Mathur S, Verma V, Sharma S, Dasgupta I. Virus-induced gene silencing in rice using a vector derived from a DNA virus. PLANTA 2010; 232:1531-40. [PMID: 20872012 DOI: 10.1007/s00425-010-1273-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Accepted: 09/02/2010] [Indexed: 05/08/2023]
Abstract
Virus-induced gene silencing (VIGS) is a method of rapid and transient gene silencing in plants using viral vectors. A VIGS vector for gene silencing in rice has been developed from Rice tungro bacilliform virus (RTBV), a rice-infecting virus containing DNA as the genetic material. A full-length RTBV DNA cloned as a partial dimer in a binary plasmid accumulated in rice plants when inoculated through Agrobacterium (agroinoculation) within 2 weeks and produced detectable levels of RTBV coat protein. Deletion of two of the four viral ORFs did not compromise the ability of the cloned RTBV DNA to accumulate in rice plants. To modify the cloned RTBV DNA as a VIGS vector (pRTBV-MVIGS), the tissue-specific RTBV promoter was replaced by the constitutively expressed maize ubiquitin promoter, sequences comprising the tRNA-binding site were incorporated to ensure reverse transcription-mediated replication, sequences to ensure optimal context for translation initiation of the viral genes were added and a multi-cloning site for the ease of cloning DNA fragments was included. The silencing ability of pRTBV-MVIGS was tested using the rice phytoene desaturase (pds) gene on rice. More than half of the agroinoculated rice plants showed white streaks in leaves within 21 days post-inoculation (dpi), which continued to appear in all emerging leaves till approximately 60-70 dpi. Compared to control samples, real-time PCR showed only 10-40% accumulation of pds transcripts in the leaves showing the streaks. This is the first report of the construction of a VIGS vector for rice which can be introduced by agroinoculation.
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Affiliation(s)
- Arunima Purkayastha
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
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Borah BK, Johnson AMA, Sai Gopal DVR, Dasgupta I. Sequencing and computational analysis of complete genome sequences of Citrus yellow mosaic badna virus from acid lime and pummelo. Virus Genes 2009; 39:137-40. [DOI: 10.1007/s11262-009-0367-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Accepted: 04/29/2009] [Indexed: 11/24/2022]
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Eni AO, Hughes JD, Asiedu R, Rey MEC. Sequence diversity among badnavirus isolates infecting yam (Dioscorea spp.) in Ghana, Togo, Benin and Nigeria. Arch Virol 2008; 153:2263-72. [PMID: 19030955 DOI: 10.1007/s00705-008-0258-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Accepted: 10/21/2008] [Indexed: 11/29/2022]
Abstract
We analysed the sequence diversity in the reverse transcriptase (RT)/ribonuclease H (RNaseH) coding region of 19 badnavirus isolates infecting yam (Dioscorea spp.) in Ghana, Togo, Benin, and Nigeria. Phylogenetic analysis of the deduced amino acid sequences revealed that the isolates are broadly divided into two distinct species, each clustering with Dioscorea alata bacilliform virus (DaBV) and Dioscorea sansibarensis bacilliform virus (DsBV). Fourteen isolates had 90-96% amino acid identity with DaBV, while four isolates had 83-84% amino acid identity with DsBV. One isolate from Benin, BN4Dr, was distinct and had 77 and 75% amino acid identity with DaBV and DsBV, respectively, and may be a member of a new badnavirus species infecting yam in West Africa. Viruses of the two main species were present in Ghana, Togo and Benin and were observed to infect both D. alata and D. rotundata indiscriminately. This is the first confirmed report of DsBV infection in yam in Ghana and Togo. The results of this study demonstrate that members of two distinct species of badnaviruses infect yam in the West African yam zone and suggest a putative new species, BN4Dr. We also conclude that these species are not confined to limited geographic regions or specific for yam host species. However, the three badnavirus species are serologically related. The sequence information obtained from this study can be used to develop PCR-based diagnostics to detect members of the various species and/or strains of badnaviruses infecting yam in West Africa.
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Affiliation(s)
- A O Eni
- International Institute of Tropical Agriculture, Oyo Road, Ibadan, Nigeria.
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Borah BK, Anthony Johnson AM, Sai Gopal DVR, Dasgupta I. A comparison of four DNA extraction methods for the detection of Citrus yellow mosaic badna virus from two species of citrus using PCR and dot-blot hybridization. J Virol Methods 2008; 151:321-324. [PMID: 18582956 DOI: 10.1016/j.jviromet.2008.05.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2007] [Revised: 04/10/2008] [Accepted: 05/08/2008] [Indexed: 11/25/2022]
Abstract
Nucleic acid preparations extracted using four procedures were assessed to determine the suitability of the procedure for PCR-based and DNA dot-blot-based detection of Citrus yellow mosaic badna virus (CMBV) from two citrus species, acid lime and pummelo. It was found that the success of PCR detection depended upon the procedure of DNA extraction whereas the dot-blot detection was successful with all extraction methods examined. CMBV DNA sequences amplified from two citrus species indicated high nucleotide sequence identity to the sequences reported previously from sweet orange. These results will help in choosing the correct DNA extraction procedure to be followed for efficient virus screening of citrus propagules.
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Affiliation(s)
- Basanta K Borah
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
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Pest risk assessment made by France on Citrus yellow mosaic virus or Citrus mosaic badnavirus considered by France as harmful in the French overseas departments of French Guiana, Guadeloupe, Martinique and Réunion - Scientific Opinion of the Panel on Plan. EFSA J 2008. [DOI: 10.2903/j.efsa.2008.686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Huang Q, Hartung JS. Construction of infectious clones of double-stranded DNA viruses of plants using citrus yellow mosaic virus as an example. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2008; 451:525-33. [PMID: 18370278 DOI: 10.1007/978-1-59745-102-4_35] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Double-stranded DNA (dsDNA) viruses of plants are believed to be plant pararetroviruses. Their genome is replicated by reverse transcription of a larger than unit-length terminally redundant RNA transcript of the viral genomic DNA using the virus-encoded replicase. In order to produce a cloned, infectious viral genome, the clone must be constructed in a binary vector and be longer than the full, unit-length viral genome. The clone can then be transferred by Agrobacterium-assisted inoculation into a suitable host plant to induce virus infection.
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Affiliation(s)
- Qi Huang
- Floral and Nursery Plants Research Unit, U.S. National Arboretum, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA
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Su L, Gao S, Huang Y, Ji C, Wang D, Ma Y, Fang R, Chen X. Complete genomic sequence of Dracaena mottle virus, a distinct badnavirus. Virus Genes 2007; 35:423-9. [PMID: 17497213 DOI: 10.1007/s11262-007-0102-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Accepted: 04/02/2007] [Indexed: 10/23/2022]
Abstract
The genome of Dracaena mottle virus (DrMV) was cloned from infected Dracaena sanderiana plants, and its complete nucleotide sequence was determined and analyzed. The circular DNA genome consists of 7531 base pairs (bp) and possesses seven putative open reading frames (ORFs) on the plus-strand that potentially encode proteins of 17.6, 14.9, 215.0, 11.9, 11.3, 16.1, and 11.0 kDa, respectively. ORF 3, the largest ORF, encodes a putative polyprotein that contains sequences for viral aspartyl proteinase, reverse transcriptase (RT) and ribonuclease H (RNase H), characteristic of pararetroviruses. Phylogenetic analysis based on the amino acid sequence of ORF 3 showed that DrMV is related to other badnaviruses. However, the nucleotide sequence coding for the RT and RNase H domain of DrMV shares less than 68% homology with that of any known badnaviruses. The seventh ORF of DrMV is not found in other badnaviruses described before. Our results strongly support that DrMV is a distinct species of the genus Badnavirus, family Caulimoviridae. Evidence that the DrMV sequence is integrated in the D. sanderiana genome is presented and discussed.
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Affiliation(s)
- Lei Su
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China.
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Harper G, Hart D, Moult S, Hull R, Geering A, Thomas J. The diversity of Banana streak virus isolates in Uganda. Arch Virol 2005; 150:2407-20. [PMID: 16096705 DOI: 10.1007/s00705-005-0610-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2005] [Accepted: 06/24/2005] [Indexed: 11/29/2022]
Abstract
In a study of the variation among isolates of Banana streak virus (BSV) in Uganda, 140 sequences were obtained from 49 samples by PCR across the conserved reverse transcriptase/RNaseH region of the genome. Pairwise comparison of these sequences suggested that they represented 15 different species and phylogenetic analyses showed that all species fell into three major clades based on 28% sequence difference. In addition to the Ugandan sequences, clade I also contained BSV species that are known as both integrated sequences and episomal viruses; clade II also contained integrated BSV sequences but which have not previously been identified as episomal viruses. Clade III comprised of Sugarcane bacilliform virus isolates and Ugandan BSV sequences and for which there is no evidence of integration. The possible reasons for the extraordinary levels of virus sequence variation and the potential origins and epidemiology of these viruses causing banana streak disease are discussed.
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Affiliation(s)
- G Harper
- Department of Disease and Stress Biology, John Innes Centre, Colney Lane, Norwich, UK.
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Abstract
Banana streak virus (BSV) is a badnavirus that causes a viral leaf streak disease of banana and plantain (Musa spp.). Identified in essentially all Musa growing areas of the world, it has a deleterious effect on the productivity of infected plants as well as being a major constraint to Musa breeding programmes and germplasm dissemination. Banana is a staple food in Uganda which is, per capita, one of the worlds largest banana producers and consumers. BSV was isolated from infected plants sampled across the Ugandan Musa growing area and the isolates were analysed using molecular and serological techniques. These analyses showed that BSV is very highly variable in Uganda. They suggest that the variability is, in part, due to a series of introductions of banana into Uganda, each with a different complement of infecting viruses.
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Affiliation(s)
- Glyn Harper
- Department of Disease and Stress Biology, John lnnes Centre, Colney Lane, Norwich NR4 7UH, UK.
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Baranwal VK, Majumder S, Ahlawat YS, Singh RP. Sodium sulphite yields improved DNA of higher stability for PCR detection of Citrus yellow mosaic virus from citrus leaves. J Virol Methods 2003; 112:153-6. [PMID: 12951224 DOI: 10.1016/s0166-0934(03)00188-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Citrus yellow mosaic virus (CYMV), a non-enveloped bacilliform DNA virus causes a severe mosaic disease in sweet oranges in India. CYMV is weakly immunogenic, thus serodiagnosis is not a preferred method for its detection. As an alternative a rapid and reliable detection protocol by polymerase chain reaction (PCR) was developed. However, high levels of polyphenolics and tannins in citrus leaves generally interfered with obtaining good quality DNA, and thus affected the reliable detection of virus by PCR. Consequently, we evaluated the addition of sodium sulphite to a DNA extraction protocol used previously and compared the two methods with a commercially available plant DNeasy Kit (Qiagen). The addition of sodium sulphite improved the yield, quality and stability of DNA. The CYMV DNA was not only amplified at lower template DNA concentration, but also provided better DNA yields. In addition, the sodium sulphite extracted DNA survived at various temperatures much longer than those extracted without addition of sodium sulphite or with the commercial kit. The amplified product of CYMV DNA was cloned, sequenced and found to have 89% sequence identity with the only other sequenced Indian isolate of CYMV.
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Affiliation(s)
- V K Baranwal
- Plant Virology Unit, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012, India.
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