Genetic variability of tomato leaf curl new delhi virus infecting cucumber in sub-Himalayan plains in Eastern India

Article Sidebar

PDF
Published: Mar 15, 2021
Keywords:
Cucumis sativus ToLCNDV PCR Sub-Himalayan plains Phylogenetic analysis

Main Article Content

Karmakar, A.
Department of Botany, University of North Bengal, Siliguri-734013, India; 2Department of Biotechnology, University of North Bengal, Siliguri-734013, India
Sarkar, T.
Department of Botany, University of North Bengal, Siliguri-734013, India
Chakraborty, P.
Department of Botany, University of North Bengal, Siliguri-734013, India
Biswas, K. K.
Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi-110012, India
Saha, A.
Department of Botany, University of North Bengal, Siliguri-734013
Saha, D.
Department of Biotechnology, University of North Bengal, Siliguri-734013, India

Abstract

Cucumber (Cucumis sativus, Cucurbitaceae) is a vegetable crop widely cultivated in India.Disease survey was conducted from December, 2016 to March, 2017in different locations of sub-Himalayan plains in Eastern India. During survey, leaf curl disease of cucumber was found to be one of the most serious threats in cucumber production. Based on disease symptoms, thirty infected and five healthy leaf samples were collected. Twenty out of thirty infected samples were found positive for begomovirus infection upon PCR with begomovirus specific universal primers. Amplified products were cloned, sequenced and four representative sequences (one from each location) were submitted to GenBank. BLAST analysis of the isolates showed 97-99% nucleotide identity with Tomato leaf curl New Delhi virus (ToLCNDV) infecting cucumber from Bangladesh. A phylogenetic tree was constructed and a two-dimensional colour-coded sequence identity matrix was generated to find out the relationship between present ToLCNDV isolates and other isolates of India and neighboring countries. From the present study it was evident that the present isolates were closely related to Bangladeshi isolates rather than other Indian isolates.This might becorrelated to different factors like-availability of vectors, weather condition and agricultural practices in this area are similar with the neighbor country Bangladesh

Article Details

How to Cite
Karmakar, A., Sarkar, T., Chakraborty, P., Biswas, K. K., Saha, A., & Saha, D. (2021). Genetic variability of tomato leaf curl new delhi virus infecting cucumber in sub-Himalayan plains in Eastern India. International Journal of Agricultural Technology, 17(2), 535–544. retrieved from https://li04.tci-thaijo.org/index.php/IJAT/article/view/5994
Issue
Vol. 17 No. 2 (2021): March
Section
Original Study
Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

References

Bandaranayake, W. M. E. K., Wickramarachchi, W. A. R. T., Wickramasinghe, H. A. M., Rajapakshe, R. G. A. S. and Dissanayake, D. M. K. K. (2016). Molecular detection and characterization of bipartite begomoviruses associated with cucurbitaceae vegetables in Sri Lanka. Journal of the National Science Foundation of Sri Lanka, 42:265-271.

Brown, J., Zerbini, F. M., Navas-Castillo, J., Moriones, E., Ramos-Sobrinho, R., Silva, J. C., Fiallo-Olivé, E., Briddon, R., Hernández-Zepeda, C., Idris, A.,Malathi, V. G., Martin, D. P., Rivera-Bustamante, R., Ueda, S. and Varsani, A. (2015). Revision of Begomovirus taxonomy based on pairwise sequence comparisons. Archives of Virology, 160:1593-1619.

Dharmendra, P., Kashikar, A. R. and Mukherjee, S. K. (2011). Molecular characterization and infectivity of a tomato leaf curl New Delhi virus variant associated with newly emerging yellow mosaic disease of egg plant in India. Virology Journal, 8:305.

Fauquet, C. M. and Stanley, J. (2003). Geminivirus classification and nomenclature: progress and problems. Annals of Applied Biology, 142:165-189.

Fortes, I. M., Sánchez-Campos, S., Fiallo-Olivé, E., Díaz-Pendón, J. A., Navas-Castillo, J. and Moriones, E. (2016). A novel strain of Tomato Leaf Curl New Delhi Virus has spread to the mediterranean Basin.Viruses, 8:307.

Government of India. Horticulture Statistics Division, Department of Agriculture, Horticultural Statistics at a Glance (2017).Available at http://www.indiaenvironmentportal.org.in/files/file/Horticulture%20At%20a%20Glance%202017.pdf.Accessed on September 21, 2018.

Haible, D., Kober, S. and Jeske, H. (2006). Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses. Journal of Virology Methods, 135:9-16.

Hamilton, D. (2000). Solanaceous crop begomoviruses: Additions to EPPO List. European and Mediterranean Plant Protection Organization Report for March 2000. European and Mediterranean Plant Protection Organization, Paris, France.

Ito, T., Sharma, P., Kittipakorn, K. and 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. Archives of Virology, 153:611-613.

Mizutani, T., Daryono, B. S., Ikegami, M. and Natsuaki, K. T. (2011).First report of Tomato leaf curl New Delhi virus infecting cucumber in Central Java, Indonesia. Plant Disease, 95:1485.

Muhire, B. M, Varsani, A. and Martin, D. P. (2014). SDT: A virus classification tool based on pairwise sequence alignment and identity calculation. PLoS ONE, 9:e108277.

Mukherjee, P. K., Nema, N. K., Maity, N. and Sarkar, B. K. (2013). Phytochemical and therapeutic potential of cucumber. Fitoterapia, 84:227-236.

Phaneendra, C., Rao, K. R. S. S., Jain, R. K. and Mandal, B. (2012). Tomato leaf curl New Delhi virus is associated with pumpkin leaf curl: A new disease in northern India. Indian Journal of Virology, 23:42-45.

Raj, S. K.and Singh, B. P. (1996). Association of geminivirus infection with yellow green mosaic disease of Cucumissativus:Diagnosis by nucleic acid probes. Indian Journal of Experimental Biology, 34:603-605.

Raj, S. K., Snehi, S. K., Khan, M. S., Tiwari, A. K. and Rao, G. P. (2010).First report of Pepper leaf curl Bangladesh virus affecting M. charantia in India. Australasian Plant Disease Notes, 5:14-16.

Raj, S. K., Snehi, S. K., Khan, M. S., Tiwari, A. K. and Rao, G. P. (2011). First molecular characterization of Ageratum enation virus associated with mosaic disease of pointed gourd (TrichosanthesdioicaRoxb.) in India. Phytoparasitica, 39:497-502.

Reddy, R. V. C., Colvin, J., Muniyappa, U. and Seal, S. (2005). Diversity and distribution of Begomovirusesinfecting tomato in India. Archives of Virology, 150:845-867.

Reddy, A. B., Patti, M. S., Reddy, K. M. and Venkataravanappa, V. (2011). Detection and diagnosis of tomato leaf curl virus infecting tomato in Northern Karnataka. African Journal of Agricultural Research, 6:1051-1057.

Saha, A., Saha, B. and Saha, D. (2014). Molecular detection and partial characterization of a begomovirus causing leaf curl disease of potato in sub-Himalayan West Bengal, India.Journal of Environmental Biology, 35:601-606.

Sambrook, J. and Russel, D. W. (2001). Molecular cloning: A laboratory manual, 2nd Edn. USA. Cold Spring Harbour, Laboratory Press.

Singh, R., Raj, S. K. and Prasad, V. (2007). Molecular identification of a new strain of Squash leaf curl China virus infecting Cucurbita maxima in India. Journal of Phytopathology, 156:222-228.

Sohrab, S. S., Mandal, B., Ali, A. and Varma, A. (2006). Molecular diagnosis of emerging begomoviruses in cucurbits occurring in northern India. Indian Journal of Virology, 17:88-95.

Sohrab, S. S., Yasir, M. and Ali El-Kafrawy, S. (2017). Begomovirus infection on cucumber in Saudi Arabia. Plant Omics Journal, 10:7-14.

Sohrab, S. S., Mandal, B., Ali, A. and Varma, A. (2010). Chlorotic Curly Stunt: A Severe Begomovirusdisease of bottle gourd in Northern India. Virus Disease, 21:56-63.

Suresh, L. M., Malathi, V. G. and Shivanna, M. B. (2013). Molecular detection of begomoviruses associated with a new yellow leaf crumple disease of cucumber in Maharashtra, India. Indian Phytopathology, 66:294-301.

Tamura, K., Stecher, G., Peterson, D., Filipski, A. and Kumar, S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution, 30:2725-2729.

Thompson, J. D., Higgins, D. G. and Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22:4673-4680.

Tiwari, A. K., Sharma, P. K., Khan, M. S., Snehi, S. K, Raj, S. K. and Rao, G. P. (2010). Molecular detection and identification of Tomato leaf curl New Delhi virus isolate causing yellow mosaic disease in Bitter gourd (Momordicacharantia), a medicinally important plant in India. Medicinal Plants, 2:117-123.

Tiwari, A. K., Snehi, S. K., Khan, M. S., Sharma, P. K., Raj, S. K. and Rao, G. P. (2012). Molecular detection and identification of Tomato leaf curl New Delhi virus associated with yellow mosaic and leaf curling disease of Luffa cylindrica crops in India. Indian Phytopathology, 65:48-55.

Tiwari, A. K., Snehi, S. K., Rao, G. P. and Raj, S. K. (2008). Begomovirus: A major problem for cucurbitaceous crops in eastern Uttar Pradesh. Indian Journal of Virology, 19:123.

Venkataravanappa, V., Reddy, C. N. L., Shankarappa, K. S., Jayappa, J., Pandey, S. and Reddy, M. K. (2019). Characterization of Tomato leaf curl New Delhi virus and DNA- Satellites Association with Mosaic Disease of Cucumber. International Journal of Biotechnology and Bioengineering, 5:93-109.

Yazdani-Khameneh, S., Aboutorabi, S., Shoori, M., Aghazadeh, A., Jahanshahi, P., Golnaraghi, A. and Maleki, M. (2016). Natural Occurrence of Tomato leaf curl New Delhi virus in Iranian Cucurbit Crops. Plant Pathology Journal, 32:201-208.

Zaidi, SS-e-A., Shafiq, M., Amin, I., Scheffler, B. E., Scheffler, J. A., Briddon, R. W. and Mansoor, S. (2016). Frequent occurrence of Tomato Leaf Curl New Delhi Virus in cotton leaf curl disease affected cotton in Pakistan. PLoS ONE, 11:e0155520.

Zaidi, S. S. E. A., Martin, D. P., Amin, I., Farooq, M. and Mansoor, S. (2017). Tomato leaf curl New Delhi virus: a widespread bipartite begomovirus in the territory of monopartitebegomoviruses. Molecular Plant Pathology, 18:901-911.