Whole-proteome phylogeny of large dsDNA virus families by an alignment-free method

Abstract

The vast sequence divergence among different virus groups has presented a great challenge to alignment-based sequence comparison among different virus families. Using an alignment-free comparison method, we construct the whole-proteome phylogeny for a population of viruses from 11 viral families comprising 142 large dsDNA eukaryote viruses. The method is based on the feature frequency profiles (FFP), where the length of the feature (l-mer) is selected to be optimal for phylogenomic inference. We observe that (i) the FFP phylogeny segregates the population into clades, the membership of each has remarkable agreement with current classification by the International Committee on the Taxonomy of Viruses, with one exception that the mimivirus joins the phycodnavirus family; (ii) the FFP tree detects potential evolutionary relationships among some viral families; (iii) the relative position of the 3 herpesvirus subfamilies in the FFP tree differs from gene alignment-based analysis; (iv) the FFP tree suggests the taxonomic positions of certain "unclassified" viruses; and (v) the FFP method identifies candidates for horizontal gene transfer between virus families.

Fig. 1.

Optimal feature (l-mer) length. (A) Cumulative relative entropy (CRE) curves for 142 large dsDNA virus proteomes. (B) Relative sequence divergence (RSD) values for 4 representative viral proteomes, the smallest (NeleNPV), the intermediate (SHFV and CNPV), and the largest (APMV). The optimal feature length for whole-proteome comparison and phylogeny inference is 8 and approximately corresponds to when both CRE and RSD fall to <10% of their maximum values.

Fig. 2.

Common 8-mers and HGT. The number of interviral-family protein pairs vs. the number of common 8-mers in a protein pair for LDVs. (A) The ascovirus HvAV3e proteome against the baculovirus HzSNPV proteome, suggesting that there are several protein pairs due to interfamily HGT events. (B) Interviral-family protein pairs from all LDV proteomes. (C) Interviral-family DNA polymerase pairs. (D) Same as in B but with each protein sequence subject to random permutation of its amino acids. Interfamily HGT candidates are identified when a protein pair shares unusually high number of common 8-mers relative to the most conserved LDV protein of DNA polymerase, with a maximum of eight 8-mers as shown in C. Randomized protein sequences share much fewer common 8-mers with a maximum of four 8-mers as shown in D.

Fig. 3.

The LDV whole-proteome tree. The FFP tree of large dsDNA viruses at feature length 8 after deleting horizontally transferred genes between viral families and filtering out low-complexity features. Modified bootstrap percentages <80% are shown and are based on 200 replicates. The tree is drawn using iTOL (48), and is not drawn to scale. Outer circle color-codes 11 viral families as per ICTV and 2 groups of viruses not assigned to any family: nudivirus and saliva gland hypertrophy virus (SGHV) (see key in the bottom left). The middle layer color-codes viral subfamilies of the poxviridae and herpesviridae. The different viral genera are color-coded by both the inner ring and tree leaves.