In silico analysis of Tomato Leaf Curl New Delhi Virus

Abstract

Tomato leaf curl New Delhi virus (ToLCNDV) belongs to genus Begomovirus (family Geminiviridae), with bipartite genome consisting of two components i.e. DNA A and DNA B. It causes infection and almost complete yield loss in species of many plant families including Cucurbitaceae and Solanaceae and cotton crops as well. In this study, available full-length sequences of both components of ToLCNDV (DNA A: 133 and DNA B: 115) were retrieved from GenBank, NCBI (updated upto 21st June, 17) for In-silico analysis. Pairwise sequence identity of DNA A isolates was obtained by MUSCLE Alignment in SDTv1.2 software in three output forms: i). Graph plot showed that most of the isolates shared identity above 91% as being isolates of ToLCNDV, with highest peak around 94%. ii). Color-encoded matrix showed 5 isolates near the threshold value 91%. iii). Sequence identity score confirmed ToLCNDV2-[IN:IANDS1:11] JQ897969, ToLCNDV3- [IN:Bij:Chi:12] KC465466, ToLCNDV4- [IN:Jun:TC306:11] KF551592 and ToLCNDV- [BD:Cuc:06] EF450316 as outliers that shared identity below 91%, thus, confirming that they were not isolates of ToLCNDV anymore. Alignment of all isolates was done by MUSCLE and Phylogenetic tree (maximum-likelihood) was generated using MEGA6 software which prominently showed the outliers of the study. The analysis revealed massive spread of virus in Asian Continent and its recent outbreak in some European countries i.e. Spain.