Molecular characterization of a new strain of tomato leaf curl Philippines virus and its associated satellite DNAβ molecule: further evidence for natural recombination amongst begomoviruses

Excerpt

The full-length genome of a begomovirus and its cognate DNAβ component associated with tomato leaf curl disease (ToLCD), from Laguna, the Philippines, were cloned. Sequence analysis revealed that the viral genome (AB307731) is 2,746 bp and the DNAβ satellite (AB307732) is 1,346 bp in length. The genome is homologous to the DNA-A of monopartite begomoviruses originating from the Old World, with six conserved ORFs. Further nucleotide (nts) sequence comparisons showed that the genome has the highest sequence identities (94%) with that of tomato leaf curl Philippines virus-Los Banos (ToLCPV-LB). The DNAβ satellite shared relatively low sequence identity (59–68%) with other DNAβ satellite molecules. Recombination analysis indicated that ToLCPV-Laguna probably originated from another begomoviruses related to ToLCPV-Los Banos:L3, as a major parent, and ageratum yellow vein Hualian virus-[Taiwan:Hsinchu:tom:2003] (AYVHV-[TW:His:tom:2003]) as minor parent. In this recombination event, our results revealed a high probability (RDP P value = 6.779 × 10⁻⁹) that ToLCPV-Laguna has a chimeric genome, with nts 2,515 to 31 originating from ToLCPV-LB:L3 and the other part from AYVHV-[TW:His:tom:2003], which includes the IR and the 5′ portion of the C1 ORF. This is the first report of a begomovirus associated with tomato leaf curl disease from the Philippines containing a DNAβ molecule along with DNA-A in its genome. …