Identification and estimation of sequence variation dynamics of Tomato Leaf curl Palampur virus and betasatellite complex infecting a new weed host

Abstract

Leaf samples from the symptomatic Solanum nigrum plants showing curling on leaf margins, leaf chlorosis, leaf crumpling and stunting in growth were collected during spring 2018. Subsequently, the standard procedures of total genomic DNA isolation, enrichment via rolling circle amplification, polymerase chain reaction, cloning and complete genome sequencing were performed. Pairwise nucleotide (nt) sequence comparison and phylogenetic studies of the inferred genome sequences confirmed the identity of a bipartite begomovirus Tomato leaf curl Palampur virus (ToLCPalV) in the symptomatic plant samples sharing 97.6 and 95.5% nt identity with ToLCPalV isolates identified from Pakistan and India. In the phylogenetic analysis, ToLCPalV grouped with ToLCPalV isolates previously described from Pakistan and India. Additional attempts to identify any putative DNA-satellites in S. nigrum plant samples revealed an associated betasatellite component, cotton leaf curl Multan betasatellite (CLCuMuB). This is the first identification of cotton leaf curl disease-associated betasatellite with ToLCPalV in this region. The nt diversity analysis showed that ToLCPalV populations have a high mutation rate and evolve independently under strong purifying selection, but not via recombination.