Diversification into the genus Badnavirus: phylogeny and population genetic variability

Abstract

The family Caulimoviridae comprises viruses with semicircular double-stranded DNA genomes encapsulated into isometric or bacilliform particles, being divided into eight genera. The genus Badnavirus is the most important due to its high number of species reported infecting cultivated plants worldwide. The present study aimed to evaluate the taxonomic/phylogenetic positioning and population genetic variability into the genus Badnavirus. Initially, a data set comprising badnavirus full-length genome sequences was obtained from the non-redundant GenBank database. Multiple nucleotide sequence alignments were obtained for the data sets: complete genome; ORF III; full (1020pb) and partial (579pb) RT/RNaseH. Pairwise sequence comparisons, phylogenetic and recombination analyses were performed for all data sets. A total of 127 isolates were obtained, representing 53 badnavirus species. Nucleotide pairwise comparisons for the data sets RT/RNaseH and ORF III showed that a number of distinct badnavirus species shared up to 82,5% of identity, higher than the 80% threshold currently used for species demarcation in the genus. Bayesian phylogenetic trees showed four well supported clusters, with clusters 1 and 3 being sister groups comprising predominantly isolates infecting sugarcane and banana. Non-tree-like evolution evidenced a complex pattern of recombination, and at least 23 independent events were detected with recombination breakpoints occurring predominantly in the ORF III and in the intergenic region. By the analysis of nucleotide diversity of the partial RT/RNaseH region in 12 badnavirus population, a high genetic variability was observed. These results showed that mutation and recombination are important evolutionary mechanisms acting on the diversification of badnaviruses, and that the partial RT/RNaseH sequence is sufficient to determine the taxonomic placement of most viral species described in this genus.