Coat Protein Gene Sequence Analysis of Three Begomovirus Isolates from Pakistan and their Affinities with other Begomoviruses

Three virus infected host plant species (Zinnia elegans, Solanum nigrum, and Ageratum conyzoides) with suspected Geminivirus symptoms were screened for conserved regions of the coat protein genes using two degenerate primers from published sequences of the whitefly-transmissible geminiviruses from the Old World. The coat protein gene of three isolates designated Zinnia leaf curl virus (ZLCV), Solanum yellow leaf curl virus (SYLCV) and Ageratum yellow vein virus- Pakistan (AYVV-P) were PCR amplified, cloned and sequenced. Sequences were compared with previous known sequences of the begomoviruses by multiple sequence alignment and a phylogenetic tree was obtained. The viruses from Pakistan were found to be closely related to Indian subcontinent viruses i.e., tomato leaf curl virus-India (TLCV-Ind), Indian cassava mosaic virus (ICMV) and cotton leaf curl virus (CLCuV). SYLCV was found to be a mechanically transmissible strain of TLCV-Ind and ZLCV was found to be the strain of AYVV-P.