Molecular characterization of begomoviruses causing yellow mosaic disease in Vigna stipulacea and evidence of recombination

In April 2019 symptoms similar to yellow mosaic of many pulse crops were observed on Vigna stipulacea grown in a field near the village Vijayanagar, Karnataka, India. Samples of YMD affected leaves were collected for identification and characterization of virus/es associated with the disease. Fourteen primer pairs were used to amplify the genomic DNA of Mungbean yellow mosaic India virus (MYMIV), Mungbean yellow mosaic virus (MYMV) and Horsegram yellow mosaic virus (HgYMV). Blast analysis of the full length molecules of the viral genomes revealed association of three viruses (MYMIV, MYMV and HgYMV) with the YMD in V. stipulacea. Comparison of intergenic region of DNA-A and DNA-B of corresponding virus species revealed presence of a common region with highest level of sequence identity, confirming that the DNA-B molecules are in fact cognate of DNA-A molecule of corresponding virus species. The recombination detection analysis indicated presence of a putative event in DNA-A of HgYMV-Vs (MN698282) and MYMIV-Vs (MN698280) by seven detection methods. Mixed infection by these viruses in V. stipulacea is likely to have caused exchange of genetic material among DNA as leading to the formation of recombinant DNA-A of HgYMV-Vs isolate. Multiple infections by three begomovirus species in V. stipulacea may have a bearing not only on the epidemiology of the YMD in pulse crops but also on the emergence of the new virus species or recombinant strains.