TreeBASE Search-Analyses for study 28452

@ARTICLE{TreeBASE2Ref32275, author = {Sergio Ortega-del Campo and Ioana Grigoras and Tania Timtchenko and Bruno Gronenborn and Ana Grande-P?rez and Sergio Ortega Del Campo}, title = {Twenty years of evolution and diversification of digitaria streak virus in Digitaria setigera}, year = {2021}, keywords = {geminiviruses, mastreviruses, digitaria streak virus, viral quasispecies, evolutionary rate, substitution rate, mutation frequency, substitution bias, genetic variability}, doi = {10.1093/ve/veab083}, url = {http://}, pmid = {34659796}, journal = { Virus Evolution}, volume = {7}, number = {2}, pages = {veab083}, 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 twenty years. From the consensus sequences, the nucleotide substitution rate was estimated for the peri-od 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 character-ized. 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 ssDNA. The differences in variability in each of the genomic regions reflected a dynamic and modular evo-lution 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 (MP), 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.} }