A Pathogenic Isolate of Monopartite PepYLCV DNA A-like Genome Differs Significantly in C1 Gene and CR Sequence, but not in their other Genes

Jamsari, JMS A Pathogenic Isolate of Monopartite PepYLCV DNA A-like Genome Differs Significantly in C1 Gene and CR Sequence, but not in their other Genes. Plant Pathology Journal. ISSN 1812-5387

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Abstract

Background and Objective: In order to elucidate pathogenic determining factor of pepper yellow leaf curl virus isolated from a lowland chili pepper cultivation field in West Sumatra, Indonesia, a whole genome analysis via primer walking strategy was conducted. Materials and Methods: The whole DNA A-like genome sequence of PepYLCIpsV was elucidated via five steps of primer walking, started with universal primers PAR1c715 and PAL1v1978 as the start point. Results: Whole genome comparison analysis identified only one single base insertion/deletion event located in the common region from a previously described isolate collected from the upland location (PepYLCItdV). The BLAST comparison on the nucleotide level showed 90.6% maximal homology with the existing DNA A-like genome from many pepper yellow leaf curl viruses deposited in public database so far. Further detail comparison each of six Open Reading Frames (ORFs) between PepYLCIpsV and PpepYLCItdV indicated that V1 and V2 displayed 94-95% homology, respectively, while C2 and C3 had homology in range of 99 and 97%, respectively. Interestingly C1 and C4 showed homology only 79 and 68%, respectively and the Common Region (CR) shared only 74% similarity. Conclusion: The C1 and CR could be the determining factors for the pathogenicity, therefore, characterizing of these two regions in the population could be used for management and controlling of the virus. The pathogenic isolate PepYLCIpsV (KT809345) appears to be derived by recombination from two isolates originating from different regions and hosts. Its existence seems to be more ancient than its currently mild dominant counterpart PepYLCItdV (KT809346).

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