Characterization, phylogeny and recombination of Rhynchosia yellow mosaic virus infecting Rhynchosia minima, a wild relative of pigeonpea (Cajanus cajan) from India

Rhynchosia minima grown at Indian Institute of Pulses Research, Kanpur, India, showed yellow mosaic symptoms on leaves and were suspected to be caused by begomovirus(es). Leaves from five different plants (Rhm1-Rhm5) were tested for the presence of four viruses in PCR. PCR assays revealed the presence of mungbean yellow mosaic India virus in four samples, whereas one sample (Rhm2) was negative. Processing of Rhm2 sample using rolling circle amplification and restriction digestion indicated the presence of DNA molecules of ~ 2.6-2.7 kb. These molecules were sequenced after cloning and found to be of 2741 and 2658 nucleotides in size. BLAST analysis revealed that DNA-A (OQ269467) and DNA-B (OQ269468) molecules of rhynchosia yellow mosaic virus (RhYMV) with 99.09% and 93.74% nucleotide similarity with DNA-A (KP752090) and DNA-B (KP752091) of the RhYMV isolate, respectively. These sequences had a genome organization typical of legume-infecting Old World bipartite begomoviruses. Full genome sequences obtained from Rhm2 are, therefore, considered to be an isolate of RhYMV, designated as RhYMV-IN-Knp. The phylogenetic analysis revealed that RhYMV-IN-Knp was grouped with other isolates of RhYMV followed by Cajanus scarabaeoides yellow mosaic virus. DNA-A of RhYMV-IN-Knp showed two recombination events. The Old World bipartite begomovirus squash leaf curl China virus (AM260205) was identified as the major parent, whereas New World bipartite begomovirus rhynchosia golden yellow mosaic Yucatan virus (EU021216) was identified as the minor parent. RhYMV holds the potential of infecting cultivated legume crops, therefore regular monitoring is crucial especially for pigeonpea breeding programs.