Characterisation of full genome of Dolichos yellow mosaic virus based on sequence comparison, genetic recombination and phylogenetic relationship

Yellow mosaic disease (YMD) is one of the most important diseases affecting different leguminous crops and causes significant yield losses in Indian sub-continent. Eight different bipartite begomovirus species are known to cause YMD in more than 10 leguminous crops. These species are collectively known as legume yellow mosaic viruses (LYMVs), and their full genomes have been characterised except for Dolichos yellow mosaic virus (DoYMV). In this study, full genome of DoYMV isolate (KJ481204 and KJ481205) infecting dolichos has been characterised. The DNA-A of DoYMV consists of 2761 nucleotides and DNA-B of 2733 nucleotides with a genome organisation typical of Old World bipartite begomoviruses. Nucleotide identity of DNA-B (KJ481205) of DoYMV with DNA-B of other legumoviruses was 57.5-61.0%. Both components contain a nonanucleotide and conserved inverted repeat sequences with the potential to form a stem-loop. Nucleotide identity of common region of DoYMV was 90.3%, above the threshold nucleotide identity (>85%) for considering a DNA-B molecule as cognate of DNA-A of a begomovirus. Four recombination events in DNA-A and two in DNA-B of DoYMV isolate were detected. Mungbean yellow mosaic virus, Rhynchosia yellow mosaic virus and Horsegram yellow mosaic virus were identified as probable parents.