Molecular characterization of recombinant Bipartite begomovirus associated with mosaic and leaf curl disease of Cucumber and Muskmelon

Muskmelon and cucumber are important vegetables grown in different parts of India. Leaf curl and mosaic diseases caused by begomovirus are economically important on these crops. Survey during 2012–2015 to assess the incidence of both leaf curl and mosaic in Mirzapur and Varanasi Districts of Eastern Uttar Pradesh, India revealed incidence of leaf curl up to 30–40% and mosaic disease up to 50–60% in both the crops. Totally, 103 leaf samples of muskmelon (58) and cucumber (45) were collected from the plants showing viral disease symptoms. These samples were tested for infection by different viruses using DAC-ELISA and PCR. A total of ten samples reacted for CGMMV, nine for PRSV-W, 25 for GBNV, 21 for CMV, 7 for ZYMV and 21 for DNA virus. Together, ELISA and PCR detected mixed infection of RNA viruses (CGMMV, CMV, PRSV-W and GBNV) and DNA virus in different combination in ten samples. The partial DNA virus genome (1.2 kb fragment) sequencing performed on samples indicated possible infection by a known bipartite begomovirus (Tomato leaf curl Palampur virus, ToLCPalV) in 21 samples. Therefore, one sample each from muskmelon (Mm-1) and cucumber (Cb-1) were used for full-length genome amplification of begomovirus genome using RCA method. Sequencing of the full-length viral genome (DNA A) and subsequent analysis using SDT program revealed that Mm-1 and Cb-1 isolates share a nucleotide (nt) identity of 90.4–92.2% and 95.9–99.1%, respectively with ToLCPalV infecting tomato and cucurbits. Similarly, analysis of full-length DNA B of Mm-1 and Cb-1 isolates indicated that they shared genome identity of 88.4–94.0% with tomato infecting ToLCPalV. Further, recombination breakpoint analysis of the viral genome indicated the recombinant nature of the virus isolates. The significance of ToLCPalV strains/variants as an emerging threat in the production of cucurbits in India is discussed. © 2021, Indian Phytopathological Society.