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Identification, genetic diversity and recombination analysis of Watermelon Mosaic Virus isolates

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Abstract

Watermelon mosaic virus (WMV) is an important virus causing adverse effects on cucurbits throughout the world. In this study, we recorded WMV infection in the watermelon (Citrullus lanatus)-growing area of Alwar and Sikar in districts of Rajasthan, India. The RT-PCR-based detection was performed to confirm the presence of WMV, by using potyvirus-degenerated coat protein primers. Further, the complete genome sequences of two WMV isolates were compared with previously reported genome sequences. The complete genome of each isolate was 10,030 nt long, excluding the poly-A tails. Phylogeny relationships of the WMV isolates in the present study revealed the presence of uneven evolutionary pressure among the different WMV viral genomic segments. The analysis revealed that all the WMV isolates were divided into three clusters and the Indian WMV isolates cluster together with the French isolate. Recombination analysis of WMV exhibited significant recombination hotspots in the P1, NIa-Pro and Nib-CP regions. Our finding highlights the importance of genetic variability and recombination analysis to provide a better understanding of WMV molecular diversity.

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Acknowledgements

The authors are thankful to the Department of Biotechnology, GOI, India (BT/PR14902/BRB/10/889/2010‏), for financial support. The authors are also thankful to Dr. Govind P. Rao, Principal Scientist, Indian Agricultural Research Institute, Pusa Campus, New Delhi, India, for his critical review and suggestions during the manuscript preparation.

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Authors and Affiliations

  1. School of Liberal Arts and Sciences, Mody University, Lakshmangarh, Sikar, Rajasthan, 332311, India

    Rakesh Kumar Verma & Megha Mishra

  2. Department of Biotechnology, Mohanlal Sukhadia University, Vigyan Bhawan-Block B, New Campus, Udaipur, Rajasthan, 313001, India

    Avinash Marwal

  3. Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, UP, India

    R. K. Gaur

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  1. Rakesh Kumar Verma
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Contributions

RKV, MM and AM did the experimental work and RKG did the experiment design and manuscript editing.

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Correspondence to R. K. Gaur.

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13205_2020_2248_MOESM1_ESM.docx

Table S1: Recombination Break points in watermelon mosaic virus (WMV) geographical isolates calculated by different algorithms implemented in RDP.4.0 (DOCX 32 kb)

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Verma, R.K., Mishra, M., Marwal, A. et al. Identification, genetic diversity and recombination analysis of Watermelon Mosaic Virus isolates. 3 Biotech 10, 257 (2020). https://doi.org/10.1007/s13205-020-02248-8

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