Abstract
Within the family Geminiviridae, the emergence of new species results from their high mutation and recombination rates. In this study, we report the variability and evolution of digitaria streak virus (DSV), a mastrevirus isolated in 1986 from the grass Digitaria setigera in an island of the Vanuatu archipelago. Viral DNA of DSV samples was amplified from D. setigera specimens, derived from the naturally infected original plant, which were propagated in different laboratories in France and Italy for more than 20 years. From the consensus sequences, the nucleotide substitution rate was estimated for the period between a sample and the original sequence published in 1987, as well as for the period between samples. In addition, the intra-host genetic complexity and diversity of 8 DSV populations with a total of 165 sequenced haplotypes was characterized. The evolutionary rate of DSV was estimated to be between 1.13 × 10−4 and 9.87 × 10−4 substitutions/site/year, within the ranges observed in other single-stranded DNA viruses and RNA viruses. Bioinformatic analyses revealed high variability and heterogeneity in DSV populations, which confirmed that mutant spectra are continuously generated and are organized as quasispecies. The analysis of polymorphisms revealed nucleotide substitution biases in viral genomes towards deamination and oxidation of single-stranded DNA. The differences in variability in each of the genomic regions reflected a dynamic and modular evolution in the mutant spectra that was not reflected in the consensus sequences. Strikingly, the most variable region of the DSV genome, encoding the movement protein, showed rapid fixation of the mutations in the consensus sequence and a concomitant dN/dS ratio of 6.130, which suggests strong positive selection in this region. Phylogenetic analyses revealed a possible divergence in three genetic lineages from the original Vanuatu DSV isolate.
Highlights
The family Geminiviridae comprises one of the largest and most diverse groups of plant viruses
We addressed the evolution of the mastrevirus digitaria streak virus (DSV) infecting the grass D. setigera
We focused on the analysis of almost complete individual viral genomes to study evolutionary rates as well as the complexity and diversity of intra-host DSV populations and their phylogenetic relationship
Summary
The family Geminiviridae comprises one of the largest and most diverse groups of plant viruses. Geminiviruses are single-stranded DNA (ssDNA) viruses and display high mutation and recombination rates, which allow their populations to experience high variability and genetic heterogeneity (Duffy and Holmes 2008; Wu et al, 2015; Mabvakure et al, 2016; Sanchez-Campos et al, 2018; Juarez et al, 2019; Pinto et al, 2021). These features, similar to those of RNA viruses (Domingo, Sheldon, and Perales 2012; Elena, Fraile, and García-Arenal 2014; Lefeuvre et al, 2019), endow ssDNA viruses with great adaptive capacity.
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