Abstract
Although exchange of genetic information by recombination plays an important role in the evolution of viruses, it is not clear how it generates diversity. Understanding recombination events helps with the study of the evolution of new virus strains or new viruses. Geminiviruses are plant viruses which have ambisense single-stranded circular DNA genomes and are one of the most economically important plant viruses in agricultural production. Small circular single-stranded DNA satellites, termed DNA-β, have recently been found to be associated with some geminivirus infections. In this paper we analyze several DNA-β sequences of geminiviruses for recombination events using phylogenetic and statistical analysis and we find that one strain from ToLCMaB has a recombination pattern and is a recombinant molecule between two strains from two species, PaLCuB-[IN:Chi:05] (major parent) and ToLCB-[IN:CP:04] (minor parent). We propose that this recombination event contributed to the evolution of the strain of ToLCMaB in South India. The Hidden Markov Chain (HMM) method developed by Webb et al. (2009) estimating phylogenetic tree through out the whole alignment provide us a recombination history of these DNA-β strains. It is the first time that this statistic method has been used on DNA-β recombination study and give a clear recombination history of DNA-β recombination.
Highlights
Geminiviruses are emerging as one of the most economically important plant viruses in agricultural production (Abou-Jawdah et al, 2006; Briddon et al, 2008; Zhou et al, 2008)
Tomato leaf curl Maharashtra betasatellite (ToLCMaB)-[IN;Pun;04] and Papaya leaf curl betasatellite (PaLCuB)-[IN;Chi;05] are closely related in their phylogeny compared to other species (Sivalingam et al, 2010)
Our study showed that ToLCMaB-[IN;Pun;04] shares sequence identity mainly with PaLCuB-[IN;Chi;05], while a small portion of its genome is potentially migrated from another species, Tomato leaf curl betasatellite (ToLCB)[PK;RYK;97]
Summary
Geminiviruses are emerging as one of the most economically important plant viruses in agricultural production (Abou-Jawdah et al, 2006; Briddon et al, 2008; Zhou et al, 2008). DNA-β has a genome approximately 1.3–1.5 kb long, and depends on the helper virus DNA-A for its replication, movement, and transmission (Saunders et al, 2000; Briddon et al, 2001; Cui et al, 2004). It is grouped into sub-viral agents by the International Committee on Taxonomy of Viruses (ICTV). C1 gene encoded by DNA-β were found to suppress host defense systems (Cui et al, 2005) and modulate host development (Yang et al, 2008), and was believed to be one of the determining factors for geminivirus-induced disease symptom development (Briddon et al, 2008)
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