Cross-species substitution matrix comparison of Tomato leaf curl New Delhi virus (ToLCNDV) with medicinal plant isolates

Abstract The main objective of this study was to estimate and compare substitution matrixes of nucleotide frequencies for Tomato leaf curl New Delhi virus (ToLCNDV) with recently identified begomoviral isolates from two medicinal false daisy ( Eclipta prostrata ) and tomato ( Solanum lycopersicum ) plants. The ToLCNDV has become a significant limitation to vegetables production in many countries. A polymerase chain reaction was conducted to conserve the existence of begomoviral infection. The acquired amplicon was amplified using primers appropriate to the sequence in order to retrieve the full genome. The sequence analysis has confirmed the presence of ToLCNDV in symptomatic plants. The complete genome sequence having a 2.6–2.7 kb entire genome of ToLCNDV was obtained. An investigation of the phylogenetic and evolutionary history has verified the connection between this virus and other closely related viruses. The available nucleotide frequencies of codon regions ( A , T / U , C , G ) with newly isolates revealed 20–28% substitution matrixes. There was a minimal difference of nucleotide frequencies’ with already submitted database of this virus. Substitution matrixes, which quantify the probability of nucleotide substitutions evolving over a period of time, offer valuable information about mutation patterns and the forces driving evolution. This comparative analysis enhanced the comprehension of the genetic diversity of ToLCNDV and its possible consequences on medicinal plants. It also assisted in the formulation of efficient control measures and the preservation of begomoviruses in medicinal plant biodiversity. The information presented here is highly valuable for understanding the ToLCNDV biology and epidemiology, and it would also assist in disease management in the future.