Genetic diversity of Croton Yellow Vein Mosaic Virus and betasatellites associated with yellow vein mosaic disease of Sida acuta in India

A bright yellow vein mosaic disease was noticed on several naturally infected Sida acuta plants growing around the farmer field at Ballia, India. The population of whiteflies was also observed under the leaves of infected and healthy plants therefore the begomovirus infection was suspected. The begomovirus infection was confirmed by using specific primers of coat protein gene as well as betasatellites molecules. The full genome and betasatellites were amplified, cloned and sequenced. The full genome sequence had total 2760 nucleotides while betasatellites had1354 nucleotides and submitted to GenBank under the accession numbers KY612431 (DNA-A); KY612432- (betasatellites). The full genome sequence analysis revealed the highest identities (99.8–94.9%) and the closest relationship with Croton yellow vein mosaic virus infecting Croton bonplandianum and Jatropha gossypifolia in India. The betasatellites sequences showed the highest identity (99.7%) with Croton yellow vein mosaic beta isolates. In the phylogenetic analysis, the closest clustering with Croton yellow vein mosaic virus and Croton yellow vein mosaic beta isolates from Croton sp was observed. In recombination analysis, total five major and minor inter-specific recombination hot spots and breakpoints were identified with selected begomovirus isolates. Based on the results the association of begomovirus with yellow vein mosaic disease of Sida acuta was identified as a variant strain of Croton yellow vein mosaic virus in India.