Molecular detection and characterisation of Horsegram Yellow Mosaic Virus (HgYMV) infecting Lima bean (Phaseolus lunatus) in India

Abstract

The present study developed a PCR protocol using designed sequence virus-specific sets of primers (HYMV-A1500F & HYMV-A1500R and D-HYMV-B2200F & D-HYMV-B2200R) for the amplification of the complete DNA-A and DNA-B components of lima bean isolate of Horsegram yellow mosaic virus (HgYMV-Lb). The PCR products were cloned and sequenced. The nucleotide sequences of HgYMV-Lb was determined and compared with those of other whitefly-transmitted geminiviruses. The length of the single-stranded DNA-A and DNA-B components of HgYMV-Lb were 2735 and 2670 nucleotide, respectively. The DNA-A sequences were found most similar to the corresponding sequences of begomovirus species infecting legumes by up to 97% nucleotide identity. The DNA-B sequences were most similar to isolates of both Mungbean yellow mosaic virus and Mungbean yellow mosaic India virus at approximately 70% nucleotide identity. The genome organisation of HgYMV-Lb was also similar to that of a typical begomovirus bipartite genome. The DNA-A component has six Open Reading Frames (AV1/CP, AV2, AC1/REP, AC2/TrAP, AC3/REn, and AC4) and DNA-B has two (BC1 and BV2). The number, size and arrangement of the Open Reading Frames in the genome were similar to the Old world begomoviruses. In addition, phylogenetic analysis of DNA-A sequence clustered HgYMV-Lb into a group of legume-infecting begomoviruses from the Indian sub-continent, particularly with Mungbean yellow mosaic virus. Based on DNA-B sequences, HgYMV-Lb was clustered into the group with Mungbean yellow mosaic virus infecting soybean in Madurai (MYMV-Sb:Mad) and Mungbean yellow mosaic India virus in Bangladesh (MYMIV-BD:Yb). Thus, based on the PCR and sequence analysis, the association of a bipartite begomovirus with lima bean showing symptoms yellow mosaic disease in India was confirmed. Also, it was identified that the begomovirus was a novel isolate of previously described Horsegram yellow mosaic virus.

Keywords: Horsegram, Lima bean, Yellow mosaic virus, Begomovirus