Positive selection, molecular recombination structure and phylogenetic reconstruction of members of the family Tombusviridae: Implication in virus taxonomy

Abstract

A detailed study of putative recombination events and their evolution frequency in the whole genome of the currently known members of the family Tombusviridae, comprising 79 accessions retrieved from the international databases, was carried out by using the RECCO and RDP version 3.31β algorithms. The first program allowed the detection of potential recombination sites in seven out of eight virus genera (Aureusvirus, Avenavirus, Carmovirus, Dianthovirus, Necrovirus, Panicovirus, and Tombusvirus), the second program provided the same results except for genus Dianthovirus. On the other hand, both methods failed to detect recombination breakpoints in the genome of members of genus Machlomovirus. Furthermore, based on Fisher's Exact Test of Neutrality, positive selection exerted on protein-coding genes was detected in 17 accession pairs involving 15 different lineages. Except genera Machlomovirus, and Panicovirus along with unclassified Tombusviridae, all the other taxonomical genera and the unassigned Tombusviridae encompassed representatives under positive selection. The evolutionary history of all members of the Tombusviridae family showed that they segregated into eight distinct groups corresponding to the eight genera which constitute this family. The inferred phylogeny reshuffled the classification currently adopted by the International Committee on Taxonomy of Viruses. A reclassification was proposed.

Keywords: Tombusviridae; bioinformatics; phylogeny; positive selection; recombination; sequence; taxonomy.

Figure 1

Dendrogram depicting phylogenetic relationships among the studied members of the family Tombusviridae, based on their complete genome sequences. Eight clusters representing the eight genera were clearly delineated. While members of genera Carmovirus, Necrovirus, and Dianthovirus fell into two tentative distinct subgroups (T.S/Gr I, T.SGr. II), those of genera Aureusvirus and Tombusvirus constituted a homogenous ensemble. The tree was produced using the ML algorithm option of MEGA5.03. The numbers above the branches indicate the bootstrap confidence value. The scale bar shows the number of substitutions per nucleotide.