Complete genome sequence and phylogenetic relationships of tobacco streak virus causing groundnut stem necrosis disease in India

Abstract

Tobacco streak virus (TSV, genus Ilarvirus family Bromoviridae)isknowntocausestemnecrosisdisease(SND) in groundnut (Arachis hypogaea) since 2000 in Southern India.TheTSVisolateinfectinggroundnutsofarhasnotbeen characterizedbasedonthecompletegenomesequence.Inthis study, TSV was isolated from a naturally infecting groundnut plant in Kadiri, the hot-spot of the SND in southern India. During the Kharif season of 2014, groundnut plants in an experimentalfieldwereaffectedwithchlorosisandnecrosisin leaf, stem and buds. The cent percent of the 48 samples with these symptoms collected from the field tested positive for TSV in ELISA samples in this context. One isolate, GN-Kad was established from a single lesion on cowpea cv. C-152 through successive sap inoculation. Cloning and sequencing of coat protein gene (717 nucleotides) of the isolate showed high sequence identity (98–99%) with the TSV isolates reported from different crops in India. The isolate produced local necrotic rings or veinal necrosis following sap inoculation to cowpea (cultivars C-152, Pusa Komal, Pusa Sukomal and Krishi Kanchan), French bean and sunflower; whereas, it produced systemic chlorotic mottling symptoms in Nicotiana benthamiana. The three segments of the virus genome (RNA 1, RNA 2 and RNA 3) contained 3523, 2903 and 2232 nucleotides,respectively.Theoverallgenomesequence(8639 nt) of the present isolate shared 77–99% of nucleotide sequenceidentitywiththatoftheothersevenisolatesreported from Australia, India and USA. The GN-Kad shared very close phylogenetic relationship with the okra and pumpkin isolates reported from India. The present report is the first comprehensive study of the molecular characterization of TSV associated with the stem necrosis disease of groundnut.