Taxonomy, molecular phylogeny and evolution of plant reverse transcribing viruses (family Caulimoviridae) inferred from full-length genome and reverse transcriptase sequences

This study constitutes the first evaluation and application of quantitative taxonomy to the family Caulimoviridae and the first in-depth phylogenetic study of the family Caulimoviridae that integrates the common origin between LTR retrotransposons and caulimoviruses. The phylogenetic trees and PASC analyses derived from the full genome and from the corresponding partial RT concurred, providing strong support for the current genus classification based mainly on genome organisation and use of partial RT sequence as a molecular marker. The PASC distributions obtained are multimodal, making it possible to distinguish between genus, species and strain. The taxonomy of badnaviruses infecting banana (Musa spp.) was clarified, and the consequence of endogenous badnaviruses on the genetic diversity and evolution of caulimoviruses is discussed. The use of LTR retrotransposons as outgroups reveals a structured bipolar topology separating the genus Badnavirus from the other genera. Badnaviruses appear to be the most recent genus, with the genus Tungrovirus in an intermediary position. This structuring intersects the one established by genomic and biological properties and allows us to make a correlation between phylogeny and biogeography. The variability shown between members of the family Caulimoviridae is in a similiar range to that reported within other DNA and RNA plant virus families.