Recombination In Watermelon

Watermelon is an important field crop in Rajasthan, India, and the infection of WMV on watermelon in India was not previously explained. WMV has an agronomic impact on the watermelon production in Rajasthan by inhibiting plant growth and reduced fruit quality. We sequenced two complete genomes of the WMV from different regions of Rajasthan and analyzed their sequence variability, microsatellites frequency, phylogeny and recombination breakpoints in different putative genomic regions. The pairwise alignment analysis of deduced amino acid sequences of different genomic regions of WMV revealed that, the variations were distributed throughout the genome, but P1 and CP region sequences were significantly more variable than other mature protein

Further, analysis of recombination with different algorithms implemented in RDP 4.0 (Genconv, Chimaera, Max Chi, Siscan, 3Seq and RDP) exhibit strong evidence for presence of past recombination events in WMV sequences. Desbeiz and Lecoq (2007) analyzed 13 complete genome sequences and, demonstrated that the HC-to-CI region is a hot spot for recombination in WMV isolates (Desbeiz et al, 2007), but in this study, we enlist a different dataset (35 complete genome sequences of WMV) to detect potential recombination events. Recombination is also affected by RNA secondary structures and microsatellite AU-rich regions (Xiaojun et al, 2009) because of the high affinity of recombination enzymes to these regions (Biet et al, 1999). Although, AU-rich regions were not found to be a main force driving the recombination; however, evidences of the presence of AU-rich regions near recombination breakpoints in many viruses including potyviruses has been previously reported (Xiaojun et al, 2009). Both the Indian isolates RKG1 and RKG2 also showed a high number of recombination breakpoints within HC-to-CI region from the all molecular groups of WMV isolates. RKG1 and RKG2 isolates also exhibited putative recombination breakpoints in P1, NIa-Pro and Nib regions (Table 2). The presence of different recombination breakpoints in the Indian WMV isolates revealed the presence of different selection pressures during natural selection of Indian WMV isolates. This study of Microsatellite variability and recombination in 35 complete genomes of WMV isolates supports earlier observations; recombination and SSR distribution plays an important role in the WMV evolution (Desbiez et al, 2007; Alam et al, 2013). The both Indian WMV isolates shared common ancestry, higher inter-lineage and intra-lineage