Abstract
During the year 2020–2021, a disease syndrome very commonly observed in railway creepers (Ipomoea cairica (L.) Sweet) was taken into consideration from Gorakhpur Province (UP East region). Whitefly, a common vector for plant-related viral diseases was observed for wide transmission of disease. DNA from 17 infected leaf samples was isolated and analyzed through PCR using specific primers designed for the detection of Begomoviruses. Further amplification of isolated DNA fragments supporting a begomovirus infection with an estimated size of (2.7 kb). RCA of the isolated DNA sample was carried out using ϕ29 DNA polymerase by digesting it through a set of restriction endonucleases (such as BamHI, Kpn1, HindIII, EcoRI) obtaining the best result through KpnI. The amplified segment was cloned into pUC 18vectors. The obtained sequences were matched using the NCBI BLAST database showing the highest sequence similarity of 98.7% with ToLCNDV of snake gourd (Accession no. KY780199), isolates of CP genes sequence in Varanasi. ToLCNDV, a begomovirus of bipartite nature was first reported to be from Tomato (Solanaceae), later affecting certain members of the Cucurbitaceae family in India and adjacent countries. The obtained DNA sequence was submitted at NCBI with the name ToLCNDV-IP (GenBank Accession no. OM777194). The phylogenetic analysis clubbed the current isolate ToLCNDV-IP with Asian isolates. All European isolates were clubbed in separate clades indicating two distinct groups of ToLCNDV isolates. ToLCNDV-IP isolate was found to be an intralineage recombinant between two Asian isolates viz ToLCNDV isolate from Papaya (India) and ToLCNDV isolate from Tomato (Pakistan). This study shows the association of recombinant ToLCNDV infection in a new host Ipomoea cairica for the first time in India.
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Data availability
The complete nucleotide sequence of ToLCNDV have been deposited in NCBI under accession number OM777194.
References
Ansar M, Agnihotri AK, Ranjan T, Karn M, Srinivasaraghavan A, Kumar RR, Phagat A (2021) Nightshade (Solanum nigrum), an intermediate host between tomato and cucurbits of Tomato leaf curl New Delhi virus. Phytopathol Mediterr 60(3):409–419. https://doi.org/10.36253/phyto-12745
Austin DF, Huaman Z (1996) A synopsis of Ipomoea (Convolvulaceae) in the Americas. Taxon 45(5):231
Bora A, Gogoi HK, Kalita MC (2016) Use of RCA PCR assay for detection of begomovirus infection in Bhut Jolokia (Capsicum assamicum) in Tezpur region of Assam, India. South Asian J Exper Biol 6(2):64–69
Borah BK, Dasgupta I (2012) PCR-RFLP analysis indicates that recombination might be a common occurrence among the cassava infecting begomoviruses in India. Virus Genes 45:327–332
Briddon RW, Patil BL, Bagewadi B, Nawaz-ul-Rehman MS, Fauquet CM (2010) Distinct evolutionary histories of the DNA-A and DNA-B components of bipartite begomoviruses. BMC Evol Biol 8(10):97. https://doi.org/10.1186/1471-2148-10-97.PMID:20377896;PMCID:PMC2858149
Brown JK (1994) Current status of Bemisia tabaci as a plant pest and virus vector in agro-ecosystems worldwide. FAO Plant Protection Bulletin (FAO); Bulletin Phytosanitaire de la FAO (FAO); Boletin Fitosanitario de la FAO (FAO).
Dean FB, Nelson JR, Giesler TL, Lasken RS (2001) Rapid amplification of plasmid and phage DNA using Phi29 DNA polymerase and multiply primed rolling circle amplification. Genome Res 11:1095–1099
Dry IB, Rigden JE, Krake LR, Mullineaux PM, Rezaian MA (1993) Nucleotide sequence and genome organization of tomato leaf curl geminivirus. J Gen Virol 74:147–147
Fauquet CM, Briddon RW, Brown JK, Moriones E, Stanley J, Zerbini M, Zhou X (2008) Geminivirus strain demarcation and nomenclature. Adv Virol 153:783–821
Olivé F et al (2021) ICTV Virus Taxonomy Profile: Geminiviridae. J General Virol. 102:001696
Gibbs MJ, Armstrong JS, Gibbs AJ (2000) Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16:573–582. https://doi.org/10.1093/bioinformatics/16.7.573
Haible D, Kober S, Jeske H (2006) Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses. J Virol Met 135:9–16
Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT: 95–98.
Hussain M, Mansoor S, Iram S, Zafar Y, Briddon RW (2004) First report of Tomato leaf curl New Delhi virus affecting chilli pepper in Pakistan. Plant Pathol 53:794–794
Ito T, Sharma P, Kittipakorn K, Ikegami M (2008) Complete nucleotide sequence of a new isolate of tomato leaf curl New Delhi virus infecting cucumber, bottle gourd and muskmelon in Thailand. Adv Virol 153:611–613
Jerom G, Schenk TC, Bottex B, Delbianco A, Vos S (2020) Pest survey card on tomato leaf curl New Delhi virus. EFSA Supporting Publications. https://doi.org/10.2903/sp.efsa.2020.EN-1904,17,7
Juárez M, Tovar R, Fiallo-Olivé E, Aranda MA, Gosálvez B, Castillo P, Moriones E, Navas-Castillo J (2014) First detection of tomato leaf curl new delhi virus infecting zucchini in Spain. Plant Dis 98(6):857
Martin DP, Murrell B, Golden M, Khoosal A, Muhire B (2021) RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol. 1:3
Moffat AS (1999) Geminiviruses emerge as serious crop threat. Science 286:1835–1835
Padidam M, Beachy RN, Fauquet CM (1995) Tomato leaf curl geminivirus from India has a bipartite genome and coat protein is not essential for infectivity. J Gen Virol 76(Pt 1):25–35
Pant V, Gupta D, Choudhury NR, Malathi VG, Varma A, Mukherjee SK (2001) Molecular characterization of the Rep protein of the blackgram isolate of Indian mungbean yellow mosaic virus. J Gen Virol 82:2559–2567
Patil BL, Fauquet CM (2009) Cassava mosaic geminiviruses: actual knowledge and perspectives. Mol Plant Pathol 10:685–701
Patil BL, Rajasubramaniam S, Bagchi C, Dasgupta I (2005) Both Indian cassava mosaic virus and Sri Lankan cassava mosaic virus are found in India and exhibit high variability as assessed by PCRRFLP. Arch Virol 150:389–397
Posada D, Crandall KA (2001) Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci USA 98:13757–13762. https://doi.org/10.1073/pnas.241370698
Pratap D, Kumar S, Raj SK, Sharma AK (2011) Agrobacterium-mediated transformation of eggplant (Solanum melongena L.) using cotyledon explants and coat protein gene of Cucumber mosaic virus. Indian J Biotechnol 10:19–24
Qureshi MA, Lal A, Nawaz-ul-Rehman MS, Vo TTB, Sanjaya GNPW, Ho PT, Nattanong B, Kil E-J, Jahan SMH, Lee K-Y, Tsai C-W, Dao HT, Hoat TX, Aye T-T, Win NK, Lee J, Kim S-M, Lee S (2022) Emergence of Asian endemic begomoviruses as a pandemic threat. Front Plant Sci 13:970941. https://doi.org/10.3389/fpls.2022.970941
Raj SK, Snehi SK, Khan MS, Singh R, Khan AA (2008) Molecular evidence for association of Tomato leaf curl New Delhi virus with leaf curl disease of papaya (Carica papaya L.) in India. Australas Plant Dis Notes 3:152–155
Salminen MO, Carr JK, Burke DS, Mccutchan FE (1995) Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. AIDS Res Hum Retroviruses 11:1423–1425. https://doi.org/10.1089/aid.1995.11.1423
Sawyer S (1999) GENECONV: A computer package for the statistical detection of gene conversion. Department of Mathematics, Washington University in St. Louis. Available at: http://www.math.wustl.edu/%7Esawyer/geneconv/
Shafiq M, Asad S, Zafar Y, Briddon RW, Mansoor S (2010) Pepper leaf curl Lahore virus requires the DNA B component of Tomato leaf curl New Delhi virus to cause leaf curl symptoms. Virol J 13(7):367
Smith J (1992) Analyzing the mosaic structure of genes. J Mol Evol 34:126–129. https://doi.org/10.1007/BF00182389
Srivastava D, Rauniyar N (2020) Medicinal Plants of Genus Ipomoea. Lambert Academic Publishing, Beau Bassin Mauritius, LAP
Stanley J (1983) Infectivity of the cloned geminivirus genome requires sequences from both DNAs. Nature 305(59):643–645
Tahir M, Haider MS (2005) First report of Tomato leaf curl New Delhi virus infecting bitter gourd in Pakistan. Plant Pathol 54:807–807
Tamura K, Stecher G, Kumar S (2021) MEGA11: Molecular evolutionary genetics analysis version 11. Mol Biol Evol 38:3022–3027. https://doi.org/10.1093/molbev/msab120
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties, and weight matrix choice. Nucleic Acids Res 22:4673–4680
Usharani KS, Surendranath B, Paul-Khurana SM, Garg ID, Malathi VG (2004) Potato leaf curl-a new disease of potato in northern India caused by a strain of Tomato leaf curl New Delhi virus. Plant Pathol 53:235–235
Vo TTB, Lal A, Ho PT, Troiano E, Parrella G, Kil EJ, Lee S (2022) Different Infectivity of Mediterranean and Southern Asian Tomato Leaf Curl New Delhi Virus Isolates in Cucurbit Crops. Plants (basel). 11(5):704
Zaidi SSS, Martin DP, Amin I, Farooq M, Mansoor S (2016) Tomato leaf curl New Delhi virus: A widespread bipartite begomovirus in the territory of monopartite Begomoviruses. Mol Plant Pathol 18:901–911
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The author would like to thank Prof V.K Baranwal, Principal Scientist, Division of Plant Pathology, IARI, New Delhi for their constant support and help in carrying out these labs related work.
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NR carried out the research work communicated in this paper and was helped by DD in the same. PS has carried out the bioinformatics analysis.DS and VKB has conceived the work, provided the guidance and did manuscript editing. Authors NR, PS and DD have contributed in shaping the manuscript.
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Rauniyar, N., Singhal, P., Diksha, D. et al. Characterization of a recombinant tomato leaf curl New Delhi Virus (ToLCNDV) in a perennial medicinal climber host (Ipomoea cairica (L.) Sweet). 3 Biotech 13, 3 (2023). https://doi.org/10.1007/s13205-022-03418-6
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DOI: https://doi.org/10.1007/s13205-022-03418-6