Characterization of leaf curl virus in chili and overwintering role of nightshade in linkage between chili and tomato

Diseases caused by begomoviruses are an emerging threat to many crops in tropical and sub-tropical regions of the world. Leaf curl of chili is one of the most destructive disease induced by begomoviruses causing substantial losses. Leaf curling, puckering and stunted growth of the plants are typical symptoms of leaf curl disease in chili and also in many other plants like tomato and nightshade (Solanum nigrum). Rolling circle amplification (RCA) was used to characterize the genome of the virus causing leaf curl disease in chili at Sabour, in northern state of Bihar, India. RCA product digested with BamHI and HindII released ca. 2.7kb DNA fragments. The causal virus of chili leaf curl disease at Sabour was found to have a monopartite genome consisting of 2742 nucleotides (nt) with genome organization similar to begomoviruses, having two ORFs in virion-sense and six ORFs in complementary sense, separated by an intergenic region. The complete genomic sequence (GenBank accession No. KY010624) showed highest nucleotide identity of 98% with tomato leaf curl Joydebpur virus (tomato isolate). Hence the virus isolate under study has been named as tomato leaf curl Joydebpur virus-Sabour. An associated betasatellite DNA was 1370nt long with a single ORF and had 99% identity with tomato leaf curl Joydebpur betasatellite. Abutting primers successfully amplified the full genome of tomato leaf curl Joydebpur virus-Sabour confirming its presence in tomato, nightshade and whitefly. Based on the findings, it is hypothesized that nightshade acts as a reservoir of tomato leaf curl Joydebpur virus-Sabour and is involved in spreading the virus from chili to tomato through whitefly (Bemisia tabaci).