ORIGINAL ARTICLE Characterization of leaf curl virus in chili and overwintering role of nightshade in linkage between chili and tomato Mohammad Ansar 1 & Mohammad Akram 2 & Aniruddha Kumar Agnihotri 3 & A. Srinivasaraghavan 4 & Tamoghna Saha 5 & Naimuddin 6 # Società Italiana di Patologia Vegetale (S.I.Pa.V.) 2018 Abstract 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. 2.7 kb 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 com- plementary 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 1370 nt 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). Keywords Begomovirus . Betasatellite . Chili . Leaf curl and whitefly Introduction The genus Begomovirus of the family Geminiviridae is the largest genus of whitefly ( Bemisia tabaci Gennadius) transmitted plant viruses with more than 300 species (Zerbini et al. 2017). Some of the begomoviruses are responsible for many devastating diseases in different economically important crops throughout the world mostly in the tropical and subtrop- ical regions infecting dicot plants including tomato, chili, pep- per, cassava, beans, cotton and cucurbits (Singh et al. 2012; Kumari et al. 2010 ; Inoue-Nagata et al. 2016 ). The begomoviruses are assumed to have co-evolved with their hosts for a long period of time; however, these viruses appear to have become more interactive with economically important crops (Borah and Dasgupta 2012; George et al. 2014; Khan and Khan 2017). On the basis of genomic organization, three types of begomoviruses are recognized viz, Type I: with bipartite genome, Type II: with monopartite genome, and Type III: with monopartite genome and associated satellite DNA component (Malathi and John 2008; Fauquet et al. 2008; Pandey et al. 2010). Monopartite DNA is known to code for the replication associated protein (Rep) that is essential for viral replication, replication enhancer protein (REn), transactivator protein (TrAP) which controls the late gene expression and linked to * Mohammad Ansar ansar.pantversity@gmail.com 1 Department of Plant Pathology, Bihar Agricultural University, Sabour, Bhagalpur, Bihar 813 210, India 2 Division of Crop Protection, Indian Institute of Pulses Research, Kanpur 208024, India 3 Department of Plant Pathology, Bihar Agricultural University, Sabour, Bhagalpur, Bihar 813 210, India 4 Department of Plant Pathology, Bihar Agricultural University, Sabour, Bhagalpur, Bihar 813 210, India 5 Department of Entomology, Bihar Agricultural University, Sabour, Bhagalpur, Bihar 813 210, India 6 Division of Crop Protection, Indian Institute of Pulses Research, Kanpur 208024, India Journal of Plant Pathology https://doi.org/10.1007/s42161-018-0182-z