1
|
Venkataravanappa V, Ashwathappa KV, Hiremath S, Manjunatha L, Shankarappa KS, Krishna Reddy M, Lakshminarayana Reddy CN. Begomovirus and DNA-satellites association with mosaic and leaf curl disease of Solanum nigrum and Physalis minima: the new hosts for chilli leaf curl virus. Virusdisease 2023; 34:504-513. [PMID: 38046062 PMCID: PMC10686937 DOI: 10.1007/s13337-023-00850-x] [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: 07/05/2023] [Accepted: 11/03/2023] [Indexed: 12/05/2023] Open
Abstract
The numerous plants of Solanum nigrum L, and Physalis minima L, well-known weeds with medicinal properties in agriculture and horticulture crops exhibiting severe mosaic, enation and leaf curl symptoms, were collected from the Varanasi and Mirzapur districts of Uttar Pradesh, India. The begomovirus infection in S. nigrum and P. minima was validated by PCR using virus-specific primers. The whole genome of the represented isolate of S. nigrum (SN1), P. minima (PM1), and beta satellite was amplified, cloned and sequenced. The SDT analysis showed that the DNA-A of PM1 and SN1 isolate showed the highest nt identity of 87.4 to 99.1%, with several chilli leaf curl virus (ChiLCuV) isolates from India and Oman, respectively. The betasatellite sequence (PM1β) obtained from the PM1 isolate showed a very low identity of 83.1-84.5%. A demarcation threshold of 91% for betasatellite species delineation has led to identifying a new betasatellite in the PM1 sample. This unique betasatellite has been named "physalis minima leaf curl betasatellite," indicating its novelty with the plant. Whereas, betasatellite sequence (SN1β) obtained from the SN1 sample showed 86.8-91.2% nucleotide identity with ChiLCB isolates infecting several crops in Indian subcontinents. The RDP analysis of the viral genome and betasatellite of SN1 and PM1 isolates revealed recombination in substantial portions of their genetic makeup, which appeared to have originated from pre-existing begomoviruses known to infect diverse host species. The present research also highlights the potential role of these plants as significant reservoir hosts for ChiLCuV in chili plants. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-023-00850-x.
Collapse
Affiliation(s)
- V. Venkataravanappa
- Division of Crop Protection, Central Horticultural Experimental Station (CHES), ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Chettalli, Madikeri District, Bengaluru, Karnataka 560089 India
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, GKVK, Bengaluru, Karnataka 560065 India
| | - K. V. Ashwathappa
- Division of Crop Protection, Central Horticultural Experimental Station (CHES), ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Chettalli, Madikeri District, Bengaluru, Karnataka 560089 India
| | - Shridhar Hiremath
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, GKVK, Bengaluru, Karnataka 560065 India
- Centre for Infectious Diseases, CSIR- North East Institute of Science and Technology, Jorhat, Assam 785006 India
| | - L. Manjunatha
- Crop Protection, Indian Institute of Horticultural Research, Bangalore, India
| | - K. S. Shankarappa
- Department of Plant Pathology, College of Horticulture, Bengaluru, 560 065 India
- University of Horticultural Sciences, Bagalkot, Karnataka India
| | - M. Krishna Reddy
- Division of Crop Protection, Central Horticultural Experimental Station (CHES), ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Chettalli, Madikeri District, Bengaluru, Karnataka 560089 India
| | - C. N. Lakshminarayana Reddy
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, GKVK, Bengaluru, Karnataka 560065 India
| |
Collapse
|
2
|
Venkataravanappa V, Ashwathappa KV, Kallingappa P, Shridhar H, Hemachandra Reddy P, Reddy MK, Reddy CNL. Diversity and phylogeography of begomoviruses and DNA satellites associated with the leaf curl and mosaic disease complex of eggplant. Microb Pathog 2023; 180:106127. [PMID: 37119939 DOI: 10.1016/j.micpath.2023.106127] [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: 01/12/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/01/2023]
Abstract
Eggplant is one of the important vegetable crops grown across the world, and its production is threatened by both biotic and abiotic stresses. Diseases caused by viruses are becoming major limiting factors for its successful cultivation. A survey for begomovirus-like symptoms in 72 eggplant fields located in six different Indian states revealed a prevalence of disease ranging from 5.2 to 40.2%, and the symptoms recorded were mosaic, mottling, petiole bending, yellowing, and upward curling, vein thickening, and enation of the leaves, and stunting of plants. The causal agent associated with these plants was transmitted from infected leaf samples to healthy eggplant seedlings via grafting and whiteflies (Bemisia tabaci). The presence of begomovirus was confirmed in 72 infected eggplant samples collected from the surveyed fields exhibiting leaf curl and mosaic disease by PCR using begomovirus specifc primers (DNA-A componet), which resulted in an expected amplicon of 1.2 kb. The partial genome sequence obtained from amplified 1.2 kb from all samples indicated that they are closely related begomovirus species, tomato leaf Karnataka virus (ToLCKV, two samples), tomato leaf curl Palampur virus (ToLCPalV, fifty eggplant samples), and chilli leaf curl virus (ChLCuV, twenty samples). Based on the partial genome sequence analysis, fourteen representative samples were selected for full viral genome amplification by the rolling circle DNA amplification (RCA) technique. Analyses of fourteen eggplant isolates genome sequences using the Sequence Demarcation Tool (SDT) indicated that one isolate had the maximum nucleotide (nt) identity with ToLCKV and eight isolates with ToLCPalV. Whereas, four isolates four isolates (BLC1-CH, BLC2-CH, BLC3-CH, BLC4-CH) are showing nucleotide identity of less than 91% with chilli infecting viruses begomoviruses with chilli infecting begomoviruses and as per the guidelines given by the ICTV study group for the classification of begomoviruses these isolates are considered as one novel begomovirus species, for which name, Eggplant leaf curl Chhattisgarh virus (EgLCuChV) is proposed. For DNA-B component, seven eggplant isolates had the highest nt identity with ToLCPalV infecting other crops. Further, DNA satellites sequence analysis indicated that four betasatellites identified shared maximum nucleotide identity with the tomato leaf curl betasatellite and five alphasatellites shared maximum nucleotide identity with the ageratum enation alphasatellite. Recombination and GC plot analyses indicated that the bulk of begomovirus genome and associated satellites presumably originated from of previously known mono and bipartite begomoviruses and DNA satellites. To the best of our knowledge, this is India's first report of ToLCKV and a noval virus, eggplant leaf curl Chhattisgarh virus associated with eggplant leaf curl disease.
Collapse
Affiliation(s)
- V Venkataravanappa
- Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, 560089, Karnataka, India.
| | - K V Ashwathappa
- Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, 560089, Karnataka, India
| | | | - Hiremath Shridhar
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, GKVK, Bengaluru, 560 065, Karnataka, India
| | - P Hemachandra Reddy
- Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, 560089, Karnataka, India
| | - M Krishna Reddy
- Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, 560089, Karnataka, India
| | - C N Lakshminarayana Reddy
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, GKVK, Bengaluru, 560 065, Karnataka, India.
| |
Collapse
|
3
|
Mishra M, Verma RK, Pandey V, Srivastava A, Sharma P, Gaur R, Ali A. Role of Diversity and Recombination in the Emergence of Chilli Leaf Curl Virus. Pathogens 2022; 11:pathogens11050529. [PMID: 35631050 PMCID: PMC9146097 DOI: 10.3390/pathogens11050529] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/16/2022] [Accepted: 04/27/2022] [Indexed: 02/01/2023] Open
Abstract
Chilli leaf curl virus (ChiLCV), (Genus Begomovirus, family Geminiviridae) and associated satellites pose a serious threat to chilli production, worldwide. This study highlights the factors accountable for genetic diversity, recombination, and evolution of ChiLCV, and associated chilli leaf curl alphasatellite (ChiLCA) and chilli leaf curl betasatellite (ChiLCB). Phylogenetic analysis of complete genome (DNA-A) sequences of 132 ChiLCV isolates from five countries downloaded from NCBI database clustered into three major clades and showed high population diversity. The dN/dS ratio and Tajima D value of all viral DNA-A and associated betasatellite showed selective control on evolutionary relationships. Negative values of neutrality tests indicated purified selection and an excess of low-frequency polymorphism. Nucleotide diversity (π) for C4 and Rep genes was higher than other genes of ChiLCV with an average value of π = 18.37 × 10−2 and π = 17.52 × 10−2 respectively. A high number of mutations were detected in TrAP and Rep genes, while ChiLCB has a greater number of mutations than ChiLCA. In addition, significant recombination breakpoints were detected in all regions of ChiLCV genome, ChiLCB and, ChiLCA. Our findings indicate that ChiLCV has the potential for rapid evolution and adaptation to a range of geographic conditions and could be adopted to infect a wide range of crops, including diverse chilli cultivars.
Collapse
Affiliation(s)
- Megha Mishra
- Department of Biosciences, School of Liberal Arts and Sciences, Mody University of Science and Technology, Lakshmangarh, Sikar 332311, Rajasthan, India; (M.M.); (R.K.V.)
| | - Rakesh Kumar Verma
- Department of Biosciences, School of Liberal Arts and Sciences, Mody University of Science and Technology, Lakshmangarh, Sikar 332311, Rajasthan, India; (M.M.); (R.K.V.)
| | - Vineeta Pandey
- Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur 273006, Uttar Pradesh, India; (V.P.); (A.S.)
| | - Aarshi Srivastava
- Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur 273006, Uttar Pradesh, India; (V.P.); (A.S.)
| | - Pradeep Sharma
- Department of Biotechnology, ICAR—Indian Institute of Wheat & Barley Research, Agarsain Road, Karnal 132001, Haryana, India;
| | - Rajarshi Gaur
- Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur 273006, Uttar Pradesh, India; (V.P.); (A.S.)
- Correspondence: (R.G.); (A.A.); Tel.: +1-918-631-2018 (A.A.)
| | - Akhtar Ali
- Department of Biological Science, The University of Tulsa, 800 S Tucker Drive, Tulsa, OK 74104-3189, USA
- Correspondence: (R.G.); (A.A.); Tel.: +1-918-631-2018 (A.A.)
| |
Collapse
|
4
|
Gupta K, Rishishwar R, Khan ZA, Dasgupta I. Agrobacterium-mediated co-inoculation of okra plants with cloned okra enation leaf curl virus DNA and bhendi yellow vein mosaic beta-satellite DNA furthers Koch's postulates for enation leaf curl disease. J Virol Methods 2021; 300:114413. [PMID: 34902462 DOI: 10.1016/j.jviromet.2021.114413] [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: 08/19/2020] [Revised: 10/31/2021] [Accepted: 12/08/2021] [Indexed: 10/19/2022]
Abstract
The enation leaf curl disease (ELCuD) is one of the several viral diseases affecting the cultivation of okra (Abelmoschus esculentus L.) in the Indian subcontinent. Several begomoviruses and satellites are associated with ELCuD. However, to date, there are no reports of the re-introduction of any cloned ELCuD-associated viral DNA back into okra to cause ELCuD-like symptoms. Okra enation leaf curl virus (OELCuV) and various satellites, which includes bhendi yellow vein mosaic beta-satellite (BYVMB) have earlier been reported to be associated with ELCuD and with other okra diseases such as bhendi yellow vein mosaic disease. In this report, it is shown that agrobacterium-mediated inoculation of a cloned DNA of OELCuV and BYVMB to the shoot apex of virus-free okra plants led to symptoms resembling ELCuD. The OELCuV and the BYVMB DNAs could be PCR- amplified from the symptomatic leaves of the agro-inoculated plants. Full-length OELCuV DNA could also be amplified from the same symptomatic leaves, part of whose DNA sequence matched with that of the DNA which was inoculated. Hence, this work is an important step towards the fulfilment of Koch's postulates for ELCuD.
Collapse
Affiliation(s)
- Kanika Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Rashmi Rishishwar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Zainul A Khan
- 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.
| |
Collapse
|
5
|
Singh AK, Yadav BK, Krishna R, Kumar RV, Mishra GP, Karkute SG, Krishnan N, Seth T, Kumari S, Singh B, Singh PM, Singh J. Bhendi Yellow Vein Mosaic Virus and Bhendi Yellow Vein Mosaic Betasatellite Cause Enation Leaf Curl Disease and Alter Host Phytochemical Contents in Okra. PLANT DISEASE 2021; 105:2595-2600. [PMID: 33393356 DOI: 10.1094/pdis-12-20-2655-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Whitefly (Bemisia tabaci)-transmitted begomoviruses cause severe diseases in numerous economically important dicotyledonous plants. Okra enation leaf curl disease (OELCuD) has emerged as a serious threat to okra (Abelmoschus esculentus L. Moench) cultivation in the Indian subcontinent. This study reports the association of a monopartite begomovirus (bhendi yellow vein mosaic virus; BYVMV) and betasatellite (bhendi yellow vein mosaic betasatellite; BYVB) with OELCuD in the Mau region of Uttar Pradesh, India. The BYVMV alone inoculated Nicotiana benthamiana and A. esculentus cv. Pusa Sawani plants developed mild symptoms. Co-inoculation of BYVMV and BYVB resulted in a reduced incubation period, an increased symptom severity, and an enhanced BYVMV accumulation by Southern hybridization and quantitative real-time PCR. This is the first study that satisfies Koch's postulates for OELCuD in its natural host. Activities of various antioxidative enzymes were significantly increased in the virus-inoculated okra plants. Differential responses in various biochemical components (such as photosynthetic pigments, phenol, proline, and sugar) in diseased okra plants were observed. This change in phytochemical responses is significant in understanding its impact on virus pathogenesis and disease development.
Collapse
Affiliation(s)
- Achuit K Singh
- Indian Council of Agricultural Research, Indian Institute of Vegetable Research, Varanasi 221 305, Uttar Pradesh, India
| | - Brijesh K Yadav
- Indian Council of Agricultural Research, Indian Institute of Vegetable Research, Varanasi 221 305, Uttar Pradesh, India
| | - Ram Krishna
- Indian Council of Agricultural Research, Indian Institute of Vegetable Research, Varanasi 221 305, Uttar Pradesh, India
| | - R Vinoth Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067, Delhi, India
| | - Gyan P Mishra
- Indian Council of Agricultural Research, Indian Institute of Vegetable Research, Varanasi 221 305, Uttar Pradesh, India
| | - Suhas G Karkute
- Indian Council of Agricultural Research, Indian Institute of Vegetable Research, Varanasi 221 305, Uttar Pradesh, India
| | - Nagendran Krishnan
- Indian Council of Agricultural Research, Indian Institute of Vegetable Research, Varanasi 221 305, Uttar Pradesh, India
| | - Tania Seth
- Indian Council of Agricultural Research, Indian Institute of Vegetable Research, Varanasi 221 305, Uttar Pradesh, India
| | - Shweta Kumari
- Indian Council of Agricultural Research, Indian Institute of Vegetable Research, Varanasi 221 305, Uttar Pradesh, India
| | - Bijendra Singh
- Indian Council of Agricultural Research, Indian Institute of Vegetable Research, Varanasi 221 305, Uttar Pradesh, India
| | - Prabhakar M Singh
- Indian Council of Agricultural Research, Indian Institute of Vegetable Research, Varanasi 221 305, Uttar Pradesh, India
| | - Jagdish Singh
- Indian Council of Agricultural Research, Indian Institute of Vegetable Research, Varanasi 221 305, Uttar Pradesh, India
| |
Collapse
|
6
|
Emmanuel CJ, Manohara S, Shaw MW. Molecular characterization of begomovirus-betasatellite-alphasatellite complex associated with okra enation leaf curl disease in Northern Sri Lanka. 3 Biotech 2020; 10:506. [PMID: 33184593 PMCID: PMC7642014 DOI: 10.1007/s13205-020-02502-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/20/2020] [Indexed: 10/23/2022] Open
Abstract
Okra enation leaf curl is a newly emerging disease in commercial okra cultivation fields in Northern Sri Lanka. The present study aimed to identify and characterize the causative begomovirus and associated satellites. Okra plants showing the enation leaf curl disease symptoms were collected from Vavuniya and Jaffna districts of Northern Province. The PCR diagnostic and genome sequencing revealed that the symptomatic okra plants are associated with begomovirus, betasatellite, and alphasatellite complex. The begomovirus isolates shared 98.2-99.7% nucleotide identity with Okra enation leaf curl virus. The betasatellites showed 96-98.8% nucleotide identity with Bhendi yellow vein mosaic betasatellite which is usually associated with Bhendi yellow vein mosaic disease. Two distinct alphasatellite species, Okra leaf curl alphasatellite and Bhendi yellow vein mosaic alphasatellite, were identified in leaf samples with enation leaf curl disease. The disease was transmitted by whiteflies from diseased plants to healthy plants. Hybrid varieties were more susceptible to the disease compared to cultivated varieties.
Collapse
Affiliation(s)
| | - Sharmya Manohara
- Department of Botany, Faculty of Science, University of Jaffna, Jaffna, 40000 JA Sri Lanka
| | - Michael Warren Shaw
- School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6BZ UK
| |
Collapse
|
7
|
Mishra M, Verma RK, Marwal A, Sharma P, Gaur RK. Biology and Interaction of the Natural Occurrence of Distinct Monopartite Begomoviruses Associated With Satellites in Capsicum annum From India. Front Microbiol 2020; 11:512957. [PMID: 33117300 PMCID: PMC7575687 DOI: 10.3389/fmicb.2020.512957] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 09/03/2020] [Indexed: 01/29/2023] Open
Abstract
Chili (Capsicum annuum L.) is an important vegetable and spice crop of tropical and sub-tropical regions. Chili plants showing upward leaf curling, leaf crinkling, and leaf yellowing symptoms, collected from Sikar district of Rajasthan, India, were found to be associated with begomovirus and satellite molecules. The presence of virus was confirmed by PCR using virus-specific primer. The full-length genomic DNA-A of three begomovirus (MM-1, CS-1 and RV-1) and two satellites (MM-2 and MM-3) were cloned which was identified from single symptomatic chili plant. The genome organization of isolated three viruses is similar to those of other Old World monopartite begomoviruses. The comparison of the sequences and closest phylogenetic relationships for the begomoviruses, betasatellite and alphasatellite DNAs revealed that MM-1 was designated as DNA-A of Chili leaf curl virus (ChiLCV), CS-1 is considered to be a new distinct species of Tomato leaf curl Gujrat virus (ToLCGV) whereas RV-1 as a new strain of Cotton leaf curl Multan virus (CLCuMuV). The DNA-A component of ChiLCV showed 8.6%, ToLCGV of 16.6% and CLCuMuV of 7.7% average evolutionary divergence, concomitantly, the betasatellite and alphasatellite molecule had 9.9% and 5.9% overall sequence divergence, respectively. Interestingly, most of the begomoviruses were found to be intra-species recombinants. The dN/dS ratio and Tajima D value of all viral DNA-A component and their associated betasatellite showed their selective control on evolutionary relationships. The nucleotide substitution rates were determined for the DNA-A genomes of ChiLCV (7.22 × 10–4 substitutions site–1 year–1), CLCuMuV (1.49 × 10–4 substitutions site–1 year–1), ToLCGV (7.47 × 10–4 substitutions site–1 year–1), the genome of associated ChiLCB (4.20 × 10–4 substitutions site–1 year–1) and CLCuMuA (1.49 × 10–4 substitutions site–1 year–1). Agro-inoculation studies indicate that the presence of DNA betasatellite induce severe symptoms in N. benthamiana and chili, suggesting prerequisite association for typical disease development.
Collapse
Affiliation(s)
- Megha Mishra
- Department of Biosciences, School of Liberal Arts and Sciences, Mody University of Science and Technology, Sikar, India
| | - Rakesh Kumar Verma
- Department of Biosciences, School of Liberal Arts and Sciences, Mody University of Science and Technology, Sikar, India
| | - Avinash Marwal
- Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, India
| | - Pradeep Sharma
- Biotechnology Unit, ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - R K Gaur
- Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur, India
| |
Collapse
|
8
|
Mubin M, Ijaz S, Nahid N, Hassan M, Younus A, Qazi J, Nawaz-Ul-Rehman MS. Journey of begomovirus betasatellite molecules: from satellites to indispensable partners. Virus Genes 2019; 56:16-26. [PMID: 31773493 DOI: 10.1007/s11262-019-01716-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 11/17/2019] [Indexed: 12/21/2022]
Abstract
Betasatellites are a group of circular, single-stranded DNA molecules that are frequently found to be associated with monopartite begomoviruses of the family Geminiviridae. Betasatellites require their helper viruses for replication, movement, and encapsidation and they are often essential for induction of typical disease symptoms. The βC1 protein encoded by betasatellites is multifunctional that participates in diverse cellular events. It interferes with several cellular processes like normal development, chloroplasts, and innate immune system of plants. Recent research has indicated βC1 protein interaction with cellular proteins and its involvement in modulation of the host's cell cycle and symptom determination. This article focuses on the functional mechanisms of βC1 and its interactions with other viral and host proteins.
Collapse
Affiliation(s)
- Muhammad Mubin
- Virology Lab, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Sehrish Ijaz
- Virology Lab, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Nazia Nahid
- Department of Bioinformatics and Biotechnology, GC University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Hassan
- Virology Lab, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Ayesha Younus
- Laser Matter Interaction and Nano-sciences Lab, Department of Physics, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Javaria Qazi
- Department of Biotechnology, Quaid e Azam University, Islamabad, Pakistan
| | | |
Collapse
|
9
|
Venkataravanappa V, Reddy CNL, Shankarappa KS, Reddy MK. Association of Tomato Leaf Curl New Delhi Virus, Betasatellite, and Alphasatellite with Mosaic Disease of Spine Gourd ( Momordica dioica Roxb. Willd) in India. IRANIAN JOURNAL OF BIOTECHNOLOGY 2019; 17:e2134. [PMID: 31457044 PMCID: PMC6697862 DOI: 10.21859/ijb.2134] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Background Spine gourd (Momordica dioica Roxb. Willd) is one of the important cucurbitaceous crops grown across the world for vegetable and medicinal purposes. Diseases caused by the DNA viruses are becoming the limiting factors for the production of spine gourd reducing its potential yield. For the commercial cultivation of the spine gourd, propagation material used by most of the growers is tuberous roots and stem cuttings, which in turn results in an increased occurrence of the mosaic disease. There is a need for understanding the causal agent; through characterization of which will lead to the designing management strategies for the spine gourd mosaic disease control. Objectives Characterization of a begomovirus and its satellites associated with mosaic disease on spine gourd. Materials and Methods Total DNA was extracted from spine gourd samples exhibiting symptoms typical to the begomoviruses infection (mosaic mottling, leaf curl) and was tested by PCR using begomovirus specific primers. Furthermore, the complete genome of begomo viruses (DNA A, DNA B, alpha satellite, and beta satellite) was amplified by rolling circle amplification (RCA) method. Results The full-length sequences of DNA A, DNA B, alpha satellite, and beta satellite isolated from symptomatic spine gourd were determined. The full length genomes (DNA A and DNA B) of the Tomato leaf curl New Delhi Virus (ToLCNDV) infecting spine gourd were compared with the other begomovirus genomes available in the data base. The sequence analysis has revealed that DNA A and DNA B components of the begomovirus infecting spine gourd share 95.4-96.2 and 86.7-91.2% identical sequence (i.e., nucleotide (nt) identity) with that of ToLCNDV infecting potato and cucurbits in the Indian subcontinent isolates reported earlier (available in GenBank), respectively. Further, alpha satellite and beta satellite were also detected in the begomovirus infected spine gourd samples. The recombination analysis of the DNA A, DNA B, beta satellite, and alpha satellite of the begomovirus infecting spine gourd showed the associated begomovirus and satellite DNAs were driven from the different begomoviruses, leading to emergence as a new variant of the begomovirus infecting spine gourd. Conclusions The commercial cultivation of the spine gourd by most growers depends on the tuberous roots and stem cutting. The occurrence of begomovirus in spine gourd gives an alarming signal against utilization of such infected plant materials in the crop breeding and improvement programs. Using the clean virus-free vegetative propagation material is considered as one of the most important methods for controlling viral diseases. The study is highly useful for detection of the begomovirus infecting spine gourd in the detection of the virus infection in the clonally propagated planting material.
Collapse
Affiliation(s)
- V Venkataravanappa
- Central Horticultural Experiment Station (CHES), Chettalli, Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bengaluru, India
| | - C N Lakshminarayana Reddy
- Department of Plant Pathology, College of Agriculture, GKVK, University of Agricultural Sciences, Bangalore, Karnataka, India
| | - K S Shankarappa
- Department of Plant Pathology, College of Horticulture, Bengaluru, University of Horticultural Sciences, Bagalkot, Karnataka, India
| | - M Krishna Reddy
- Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, Karnataka, India
| |
Collapse
|
10
|
Venkataravanappa V, Kodandaram MH, Lakshminarayana Reddy CN, Shankarappa KS, Krishna Reddy M. Comparative transmission of Bhendi yellow vein mosaic virus by two cryptic species of the whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae). 3 Biotech 2017; 7:331. [PMID: 28955628 PMCID: PMC5603454 DOI: 10.1007/s13205-017-0970-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 09/11/2017] [Indexed: 10/18/2022] Open
Abstract
The leaf sample from okra plants showing prominent yellow vein mosaic symptoms and healthy plant without any virus symptoms were collected from farmer's field. The presence of begomovirus in the infected sample was confirmed by polymerase chain reaction (PCR) and the amplicons were cloned and sequenced. The genome analysis showed that the isolate in the present study had 99% nucleotide identity with Bhendi yellow vein mosaic virus (BYVMV) revealing it as BYVMV variant. The genetic species of Bemisia tabaci collected from fields were identified as Asia-1 and MEAM-1 genetic species based on silver leaf assay, sequence characterized amplified region marker, and mtCOI gene sequence. The comparative virus-vector relationship of both genetic species of B. tabaci indicates a minimum of two and three B. tabaci in MEAM-1 and Asia-1 genetic species, respectively, per plant were required to transmit the disease. The minimum acquisition access period and inoculation access period of 15 (MEAM-1) and 20 min (Asia-1) were required to transmit the YVMD; it was further confirmed by nucleic acid hybridization using coat protein gene-specific probe of BYVMV. With respect to the sex, the female B. tabaci were more efficient in transmitting the disease as compared to male ones in both the genetic species of B. tabaci. The MEAM-1 to transmit the BYVMV more efficiently than Asia-1 genetic species of B. tabaci.
Collapse
Affiliation(s)
- V. Venkataravanappa
- Division of Plant Pathology, Central Horticultural Experimental Station, ICAR-Institute of Horticultural Research, Hessaraghatta Lake PO, Chettalli, Bangalore, 571248 India
| | - M. H. Kodandaram
- ICAR-Indian Institute of Vegetable Research, Varanasi, 221305 Uttar Pradesh India
| | - C. N. Lakshminarayana Reddy
- Department of Plant Pathology, College of Sericulture, University of Agricultural Sciences, Chintamani, Bangalore, 563125 Karnataka India
| | - K. S. Shankarappa
- Department of Plant Pathology, College of Horticulture, University of Horticultural Sciences, Bagalkot, Bengaluru, 560065 Karnataka India
| | - M. Krishna Reddy
- Division of Plant Pathology, Plant Virology Laboratory, ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, 560089 Karnataka India
| |
Collapse
|
11
|
Wang IN, Yeh WB, Lin NS. Phylogeography and Coevolution of Bamboo Mosaic Virus and Its Associated Satellite RNA. Front Microbiol 2017; 8:886. [PMID: 28588562 PMCID: PMC5440514 DOI: 10.3389/fmicb.2017.00886] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/02/2017] [Indexed: 11/17/2022] Open
Abstract
Bamboo mosaic virus (BaMV), a plant potexvirus, has been found only in infected bamboo species. It is frequently associated with a large, linear single-stranded satellite RNA (satBaMV) that encodes a non-structural protein. Decades of collecting across a wide geographic area in Asia have accumulated a sizable number of BaMV and satBaMV isolates. In this study, we reconstructed the BaMV phylogeny and satBaMV phylogeny with partial coat protein gene sequences and partial genomic sequences, respectively. The evolutionary relationships allowed us to infer the phylogeography of BaMV and satBaMV on the Asian continent and its outlying islands. The BaMV phylogeny suggests that the BaMV isolates from Taiwan, unsurprisingly, are most likely derived from China. Interestingly, the newly available satBaMV isolates from China were found to be most closely related to the previously established Clade III, which is found in India. The general pattern of clustering along the China/India and Taiwan divide led us to hypothesize that the Taiwan Strait has been a physical barrier to gene flow in the past evolutionary history of both BaMV and satBaMV. Lastly, cophylogeny analyses revealed a complex association pattern between BaMV and satBaMV isolates from China. In general, closely related BaMV sequences tend to carry closely related satBaMV sequences as well; but instances of mismatching with distantly related satBaMV isolates were also found. We hypothesize plausible scenarios of infection and superinfection of bamboo hosts that may be responsible for the observed association pattern. However, a more systematic sampling throughout the geographic distribution of various bamboo species is needed to unambiguously establish the origin, movement, and evolution of BaMV and satBaMV.
Collapse
Affiliation(s)
- Ing-Nang Wang
- Department of Biological Sciences, University at Albany, AlbanyNY, United States
| | - Wen-Bin Yeh
- Department of Entomology, National Chung Hsin UniversityTaichung, Taiwan
| | - Na-Sheng Lin
- Institute of Plant and Microbial Biology, Academia SinicaTaipei, Taiwan
| |
Collapse
|
12
|
Mishra GP, Singh B, Seth T, Singh AK, Halder J, Krishnan N, Tiwari SK, Singh PM. Biotechnological Advancements and Begomovirus Management in Okra ( Abelmoschus esculentus L.): Status and Perspectives. FRONTIERS IN PLANT SCIENCE 2017; 8:360. [PMID: 28367155 PMCID: PMC5355441 DOI: 10.3389/fpls.2017.00360] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 03/01/2017] [Indexed: 05/24/2023]
Abstract
Despite the importance of okra, as one of the important vegetable crop, very little attention has been paid to its genetic improvement using advanced biotechnological tools. The exploitation of marker assisted breeding in okra is often limited due to the availability of a few molecular markers, the absence of molecular genetic-map(s), and other molecular tools. Chromosome linkage-groups were not yet constructed for this crop and reports on marker development are very scanty and mostly hovering around cultivar characterization. Besides, very little progress has been observed for transgenic development. However, high throughput biotechnological tools like chromosome engineering, RNA interference (RNAi), marker-assisted recurrent selection (MARS), genome-wide selection (GWS), targeted gene replacement, next generation sequencing (NGS), and nanobiotechnology can provide a rapid way for okra improvement. Further, the etiology of many deadly viral diseases like the yellow vein mosaic virus (YVMV) and okra enation leaf curl virus (OELCV) in okra is broadly indistinct and has been shown to be caused by various begomovirus species. These diseases cause systemic infections and have a very effective mode of transmission; thus, preventing their spread has been very complicated. Biotechnological interventions have the potential to enhance okra production even under different viral-stress conditions. In this background, this review deals with the biotechnological advancements in okra per se along with the begomoviruses infecting okra, and special emphasis has been laid on the exploitation of advanced genomic tools for the development of resistant varieties.
Collapse
Affiliation(s)
- Gyan P. Mishra
- Department of Biotechnology, ICAR-Indian Institute of Vegetable ResearchVaranasi, India
| | | | | | | | | | | | | | | |
Collapse
|
13
|
Molecular genetic analysis and evolution of begomoviruses and betasatellites causing yellow mosaic disease of bhendi. Virus Genes 2016; 53:275-285. [DOI: 10.1007/s11262-016-1414-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 11/22/2016] [Indexed: 01/08/2023]
|
14
|
First report of an alphasatellite associated with Okra enation leaf curl virus. Virus Genes 2013; 46:585-7. [PMID: 23475199 DOI: 10.1007/s11262-013-0898-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 03/01/2013] [Indexed: 12/17/2022]
Abstract
An alphasatellite DNA associated with Okra enation leaf curl virus (OELCuV) which causes enation and leaf curling in okra (Abelmoschus esculentus) plants was characterized. The full-length DNA comprises 1,350 nucleotides and shows typical genome organization of an alphasatellite. It shows the highest nucleotide sequence identity (79.7 %) to Hollyhock yellow vein virus-associated symptomless alphasatellite (HoYVSLA). This is the first report of the association of an alphasatellite with OELCuV from India.
Collapse
|
15
|
Kumar J, Gunapati S, Singh SP, Kumar A, Lalit A, Sharma NC, Puranik R, Tuli R. A new betasatellite associated with cotton leaf curl Burewala virus infecting tomato in India: influence on symptoms and viral accumulation. Arch Virol 2013; 158:1349-53. [PMID: 23361863 DOI: 10.1007/s00705-013-1613-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 12/08/2012] [Indexed: 11/29/2022]
Abstract
A begomovirus and its associated alpha- and betasatellite were detected in tomato plants affected with leaf curl disease. Based on a nucleotide sequence identity of 99 %, this begomovirus was designated an isolate of cotton leaf curl Burewala virus (CLCuBuV). The alphasatellite exhibited 93 % sequence identity to cotton leaf curl Burewala alphasatellite (CLCuBuA) and is hence referred to here as a variant of CLCuBuA. The detected betasatellite was recombinant in nature and showed 70 % sequence identity to the known betasatellites. Inoculation of healthy tomato with CLCuBuV plus betasatellite, either in the presence or the absence of alphasatellite, led to typical leaf curling, while inoculation with CLCuBuV in the absence of betasatellite resulted in mild symptoms. This confirmed the role of the betasatellite in expression of disease symptoms. We propose to name the newly detected betasatellite tomato leaf curl Hajipur betasatellite (ToLCHJB).
Collapse
Affiliation(s)
- Jitendra Kumar
- National Agri-Food Biotechnology Institute, Mohali, 160071 Punjab, India.
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Abstract
Begomoviruses are numerous and geographically widespread viruses that cause devastating diseases in many crops. Monopartite begomoviruses are frequently associated with betasatellites or alphasatellites. Both betasatellite and alphasatellite DNA genomes are approximately half the size of begomovirus DNA genomes. Betasatellites are essential for induction of typical disease symptoms. The βC1 genes encoded by the betasatellites have important roles in symptom induction, in suppression of transcriptional and posttranscriptional gene silencing, and they can affect jasmonic acid responsive genes. Host plants of begomoviruses have evolved diverse innate defense mechanisms against the βC1 protein to counter these challenges. Alphasatellites have been identified mainly in monopartite begomoviruses that associate with betasatellites and have no known contributions to pathogenesis of begomovirus-betasatellite disease complexes. Applications of current molecular tools are facilitating viral diagnosis and the discovery of novel species of geminiviruses and satellite DNAs and are also advancing our understanding of the global diversity and evolution of satellite DNAs.
Collapse
Affiliation(s)
- Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
17
|
Venkataravanappa V, Lakshminarayana Reddy CN, Jalali S, Krishna Reddy M. Molecular characterization of distinct bipartite begomovirus infecting bhendi (Abelmoschus esculentus L.) in India. Virus Genes 2012; 44:522-35. [PMID: 22447131 DOI: 10.1007/s11262-012-0732-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 02/24/2012] [Indexed: 11/28/2022]
Abstract
Yellow vein mosaic disease of okra is a whitefly transmitted begomovirus causing heavy economic loss in different parts of India. The okra isolate (OY131) of this virus from a bhendi plant [(Abelmoschus esculentus L.) Moench] showing yellow vein mosaic, vein twisting, reduced leaves, and a bushy appearance in the Palem region, New Delhi, India, was characterized in the present study. The complete DNA-A and DNA-B sequences have been determined and are comprised of 2,746 and 2,703 nucleotides, respectively. The betasatellite (DNA-β) component was absent in the sample. The genome organization was typically of biparite begomoviruses, which were characterized earlier. Comparison of DNA-A component with other known begomoviruses suggest that this virus, being only distantly related (<85.9% similarity with its nearest relative, BYVMV) to other known begomoviruses, is a new species. We have tentatively assigned the genome to a novel geminivirus species Bhendi yellow vein mosaic Delhi virus [BYVDV-IN (India: Delhi: okra)]. DNA-B showed highest sequence identity (87.8% identical) to that of a ToLCNDV (AY158080). The phylogenetic analysis of the present isolate is distinct from all other viruses; however clusters with ToLCNDV group infect different crops. The recombination analysis revealed that this isolate has sequences originated from ToLCNDV. This is the first known bhendi yellow vein mosaic disease associated bipartite begomovirus from India.
Collapse
Affiliation(s)
- V Venkataravanappa
- Division of Plant Pathology, Plant Virology Laboratory, Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, 560 089, India
| | | | | | | |
Collapse
|