Complete genome sequence of a novel bipartite begomovirus infecting butterfly pea (Clitoria ternatea L.) in India

Abstract

In India, plants from the non-cultivated, horticultural, and agricultural categories are commonly infected with various begomoviruses, most of which produce yellow mosaic, bright yellow mosaic, or curling symptoms on leaves. In this study, the complete genome of a new bipartite begomovirus causing yellow mosaic disease (YMD) in butterfly pea (Clitoria ternatea L.) was characterized using rolling-circle amplification followed by restriction digestion, cloning, and sequencing to obtain the full-length DNA-A (2727 nt) and DNA-B (2648 nt) sequences. The DNA-A and DNA-B components have a genome organization that is typical of the Old World bipartite begomoviruses, and the common regions (95 nt) of DNA-A and DNA-B share 91% nucleotide sequence identity, which is well above the threshold (>85%) for them to be considered cognate components. Both DNA molecules contain a begomovirus nonanucleotide motif, conserved iterons, and a putative stem-loop structure. The DNA-A of this virus was found to be most similar to that of Cajanus scarabaeoides yellow mosaic virus (CsYMV), with 82.61% nucleotide sequence identity, which is far below the species demarcation threshold (< 91%) for begomoviruses, whereas the DNA-B sequence showed the most similarity (77.16% identity) to that of Rhynchosia yellow mosaic virus (RhYMV). In phylogenetic analysis, both DNA-A and DNA-B were formed a clade with the corresponding genome segments of other YMD-causing begomoviruses. Based on these characteristics, this virus, for which the name “butterfly pea yellow mosaic virus” (BpYMV) is proposed, should be considered a member of a new species in the genus Begomovirus.