Molecular Characterization of Yellow Mosaic Disease Causing Begomoviruses in Pigeonpea (Cajanus cajan L.) from Three Agro-ecological Zones of India.

Pigeonpea (Cajanus cajan L.) plants exhibiting symptoms of yellow mosaic disease (YMD) were collected in winter 2023 from multiple agricultural fields of Kanpur, Sehore, and Madhubani, representing three different agro-ecological zones in India. The recorded disease incidence ranged from 3 to 5%, 1 to 4%, and 12 to 20% in these zones, respectively. This study aimed to identify and characterize the causal agent, suspected to be a begomovirus, an emerging plant pathogen of pigeonpea causing YMD. Total DNA was extracted from 28 YMD-affected leaf samples and subjected to rolling circle amplification for PCR-based virus detection. Of all the tested samples, one tested positive for mungbean yellow mosaic virus (MYMV), while the remaining tested positive for mungbean yellow mosaic India virus (MYMIV). Subsequently, PCR-based amplification and sequencing of the full-length DNA-A and DNA-B components were conducted. BLASTn analysis revealed that the assembled sequences of the DNA-A and DNA-B components had the highest nucleotide identity with MYMIV (DNA-A: 97-99%, DNA-B: 95-97%) and MYMV (DNA-A: 99%, DNA-B: 98%). Phylogenetic analysis supported these findings. Additionally, the DNA-A and DNA-B components obtained from each sample were found to be cognate, with over 92% similarity in their common region. Thus, the cognate DNA components constituted the isolates of MYMIV and MYMV identified from pigeonpea. The identified isolates exhibited the typical genome organization of an Old World bipartite begomovirus, with no recombination events detected. This study reports, for the first time, the complete annotated genomes of MYMIV from Sehore and Madhubani, as well as MYMIV and MYMV from Kanpur, infecting pigeonpea.