Mixed infection of a new begomovirus, Jatropha leaf curl Guntur virus and recombinant/chimeric jatropha leaf curl Gujarat virus in Jatropha gossypiifolia

The Jatropha gossypiifolia plant showing the severe leaf curl symptoms grown in the borders of chilli fields in Guntur, Andhra Pradesh, India was collected. The infection of begomovirus was detected using the degenerate primers followed by rolling circle amplification (RCA). The RCA products digested with KpnI and EcoRI showing the unit length of the begomovirus genome were cloned in pUC19 and sequenced to obtain the complete begomoviral genome. The sequence information of DNA-A of the two clones GuWC10 contained 2794 nt (MZ217773) and an incomplete genome GuWC3 with 2337 nt (MZ217772). The BLAST analysis of GuWC3 and GuWC10 sequence showed 85·57% identity with jatropha leaf curl Gujarat virus (JLCGV) and 82·68% identity with croton yellow vein mosaic virus (CroYVMV), respectively. The sequence analysis also showed that the GuWC10 clone had a 177 bp recombinant/chimeric sequence of JLCGV while the other region containing 2611 bp showed 92·63% identity with papaya leaf curl virus (PaLCuV/PK). However, the global alignment of the GuWC10 sequence showed a maximum of 80·60% identity with croton yellow vein virus (CroYVV) (FN645902), CroYVMV (JN817516) and PaLCuV/PK (KY978407). The second clone GuWC3 although shorter in length had recombinant sequences of JLCGV, jatropha leaf curl virus (JLCuV/ND) and okra enation leaf curl virus (OELCuV). The nucleotide sequence identity among the GuWC10 and GuWC3 was 71·9%. The phylogenetic analysis placed both the viral strains in the same clade located between PaLCuV/PK and JLCuV clades. According to the ICTV species demarcation criteria of 91% DNA-A sequence identity, the present isolate was considered as a new species of begomovirus and the name Jatropha leaf curl Guntur virus was proposed. This is the first report of a new begomovirus species infecting J. gossypiifolia and the study also reports a mixed infection of Jatropha leaf curl Guntur virus with a recombinant/chimeric JLCGV in the host J. gossypiifolia. Present study suggests the role of weed Jatropha in harbouring begomoviruses and probable source for viral recombination.