Molecular characterization of begomovirus associated betasatellites from Xanthium strumarium L. in India.

Leaf curl disease symptom was observed on Xanthium strumarium L. during field survey conducted in and around tomato growing areas in August 2016 at district Ballia, India. The viral infection was confirmed by using begomovirus specific primers and identified as Tomato leaf curl Patna virus associated with a betasatellites. The full genome of begomovirus and associated betasatellites was cloned, sequenced, analyzed and submitted to GenBank under the accession numbers KY612435 (DNA-A); KY612436 (betasatellites). The full genome had total 2747 nucleotides and betasatellites had 1346 nucleotides. The full genome showed the highest nucleotide sequence identity (99.8%-98.7%) with Tomato leaf curl Patna virus infecting tomato and Cassia tora. The lowest sequence identity (37%) was observed with Chickpea chlorotic dwarf Pakistan virus infecting X. strumarium. The betasatellites sequence showed the highest identity (99.7%) with Tomato leaf curl Patna betasatellites. The lowest sequence identity (42.2%) was observed with Tomato leaf curl betasatellites from Mali. The recombination analysis result provided two major and minor inter-specific recombination hot spots and breakpoints. Based on genetic diversity, sequence identity and recombination analysis result, the begomovirus was identified as a variant strain of Tomato leaf curl Patna virus and designated as ToLPatV-Xanth. This is the first report of the natural occurrence of begomovirus associated betasatellites on X. strumarium from India.