Molecular characterization of a new begomovirus infecting tobacco in Kagoshima, Japan: An evidence for interspecific recombination

A virus infected tobacco sample (KG5Tob) showing leaf curl symptoms was collected in Kagoshima, Japan. The complete DNA-A like molecule of KG5Tob was determined and found to comprise 2762 nucleotides with a typical begomovirus genome organization. A comparison of the DNA-A sequences revealed that KG5Tob shared 87% with its closest relatives, Honeysuckle yellow vein mosaic virus (HYVMV) and Tobacco leaf curl Yamaguchi virus (TbLCYV), however, on comparison of the intergenic region (IR) nt sequences, the isolate shared only 66 and 64% of the IR sequences with the former and the latter, respectively. Phylogenetic analysis of full length DNA-A component clustered KG5Tob in a lone cluster but close to HYVMV and TbLCYV. When the CPs were aligned, similar results were observed and KG5Tob was placed in a lone cluster. A comparison of the Other ORFs showed that different parts of the genome had different affinities, suggesting that recombination could have played a major role in the evolution of this isolate. Molecular data show that KG5Tob isolate is an isolate of HYVMV, although the isolate was obtained from tobacco.