Molecular detection and characterization of begomoviruses from Burkina Faso and Nicaragua

Abstract: Agriculture plays a major role in the economy of countries in Africa and America. Viruses have emerged as major plant pathogens during the last few decades on agriculturally important field crop plants. The genus Begomovirus belongs to the family Geminiviridae, which is the largest family of plant-infecting viruses. Geminiviruses can infect both monocot and dicot plants. Begomoviruses have circular, single-stranded DNA (css-DNA) genomes with one or two equally sized genome components (~2.7 kb each). In previous studies, the begomoviruses, tomato leaf curl Mali virus (ToLCMLV), tomato yellow leaf curl Mali virus (ToYLCMV) and pepper yellow vein Mali virus (PeYVMLV) were found in tomato (Solanum lycopersicum) plants from Burkina Faso, while bean golden yellow mosaic virus (BGYMV) and calopogonium golden mosaic virus (CalGMV) had been found in common bean (Phaseolus vulgaris) plants from Nicaragua. The aim of this study was to confirm the reported infections by these viruses in tomato plants as well as common beans plants. Another aim of this study was to amplify the full-length genomes of CalGMV and BGYMV since only partial DNA sequences were determined in the previous study on bean-infecting begomoviruses from Nicaragua. Sequencing results of cloned amplification products derived from rolling circle amplification (RCA) of tomato plants from Burkina Faso showed the highest nucleotide identity to okra yellow crinkle virus (OkYCrV) and okra yellow mosaic Mexican virus (OYMMV), and contamination was probably the most likely reason for this result. Sequencing results of PCR products of the coat protein gene from two samples of common beans from Nicaragua showed highest nucleotide (nt) identity at 98% with BGYMV (sample 2a) or 86-88% with CalGMV (sample 15c). Moreover, the corresponding full-length sequences of DNA-A components showed 99% identity with BGYMV or 94% with the partial sequence of CalGMV available in GenBank (AF439402). Previously no complete sequence of CalGMV existed so the full-length sequences of 15c can be considered as the first full-length sequences of the DNA-A component of CalGMV.