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Begomoviruses are currently emerging as a major threat to vegetable production in many tropical and subtropical regions worldwide. Pepper yellow leaf curl disease (PepYLCD) has been noticed in many Capsicum annum L. producing regions from East Asia especially from Indonesia and causes devastating damage to pepper crop production since 2000. In this study we have cloned and sequenced complete nucleotide of begomoviruses from pepper exhibiting leaf curling and bright yellowing symptoms. Besides, we also determined the occurrence of disease on tomato evoking leaf curl symptoms and ageratum with yellow vein type of symptoms. On the basis of genome organization and sequence homology, these viruses were designated as Pepper yellow leaf curl Indonesia virus (PeYLCIV)- new species followed by its two new starins i.e. PeYLCIV-Tomato and PeYLCIV-Ageratum.  These viruses have   bipartite genomes. Pepper virus DNAs from Indonesia (PepYLCIV, PepYLCIV-Tomato and PepYLCIV-Ageratum DNA-As) were noticeably distinct, forming a separate branch from the other viruses infecting pepper. A considerable divergence is observed in the common region (CR) of the genomic components of PeYLCIV (77%), PeYLCIV-Tomato (82%) and PeYLCIV-Ageratum (75%). A stem-loop forming region and Rep-binding motif are identical in CRs of three viruses. CR of PepYLCIV-Ageratum DNA-A is approximately 10 nucleotides longer than those of PepYLCIV DNA-A and PepYLCIV-Tomato DNA-A. Similar insertion is also found in the common region of PepYLCIV-Ageratum DNA-B. PeYLCIV DNA-A alone is infectious in pepper and N. benthamiana plants and association with DNA-B increases symptom severity

Pepper yellow leaf curl Indonesia virus, a new bipartite begomovirus species that belongs to distinct clade of Old World geminiviruses