Complete Genome Analysis and Molecular Characterisation of Horsegram Yellow Mosaic Virus Infecting Pole Bean (Phaseolus vulgaris L.) in Karnataka

Abstract

The yellow mosaic disease (YMD) caused by begomoviruses is a major constraint for the production of pole bean (Phaseolus vulgaris L.) in India. A survey was carried out in the eastern dry zone of Karnataka during 2019–20 to record the incidence of yellow mosaic disease in pole bean, which revealed the ubiquitous prevalence of YMD in pole bean ranging from 6.02% to 80.74%. Leaf samples collected (symptomatic and asymptomatic) were subjected to begomovirus detection using specific primers. Twelve samples, representing all the 12 taluks in the surveyed region, were considered for full genome amplification by RCA, cloned, and sequenced. The genome length of the 12 current isolates ranged from 2718 to 2744 and 2668–2671 nucleotides for DNA-A and DNA-B, respectively. Sequence analysis using the Sequence Demarcation Tool (SDT) showed > 91% nucleotide identity of current isolates (DNA-A) with other horsegram yellow mosaic virus (HgYMV) isolates available in GenBank. As per existing ICTV criteria, all the current isolates can be considered strains of HgYMV. Further, DNA-B associated with all the 12 isolates also shared > 91% nucleotide identity with DNA-B of HgYMV isolates, indicating the absence of component re-assortment in HgYMV. Variation in the pairwise nucleotide identity and phylogenetic analysis confirmed the existence of new strains within the current HgYMV isolates. GC plot analysis reveals potential recombination in the low GC-rich regions. Further, recombination breakpoint analysis indicated intra-species recombination in both DNA-A and DNA-B, which might have driven the origin of new strains in HgYMV. This is the first comprehensive study on begomovirus isolates associated with the yellow mosaic disease of pole bean based on complete genome sequencing in the world.