Statistical analysis on detecting recombination sites in DNA-beta satellites associated with the old world geminiviruses

TL;DR

This paper employs phylogenetic and statistical methods to identify recombination sites in DNA-$eta$ satellites associated with old world geminiviruses, revealing a potential recombinant strain between two virus species.

Contribution

It introduces a novel statistical analysis approach to detect recombination in DNA-$eta$ satellites of geminiviruses, enhancing understanding of viral evolution.

Findings

Identified a recombinant DNA-$eta$ satellite strain from ToLCMaB.

Detected recombination between two distinct geminivirus strains.

Provided evidence of genetic exchange contributing to virus diversity.

Abstract

Although an exchange of genetic information by recombination plays an important role in the evolution of viruses, it is not clear how it generates diversity. {\it Geminiviruses} are plant viruses which have ambisense single-stranded circular DNA genomes and one of the most economically important plant viruses in agricultural production. Small circular single-stranded DNA satellites, termed DNA-$\beta$, have recently been found associated with some geminivirus infections. In this paper we analyze a satellite molecule DNA-$\beta$ of geminiviruses for recombination events using phylogenetic and statistical analysis and we find that one strain from ToLCMaB has a recombination pattern and is possibly recombinant molecule between two strains from two species, PaLCuB-[IN:Chi:05] (major parent) and ToLCB-[IN:CP:04] (minor parent).