Ancient Gene Capture and Recent Gene Loss Shape the Evolution of Orthopoxvirus-Host Interaction Genes

Abstract

The survival of viruses depends on their ability to resist host defenses and, of all animal virus families, the poxviruses have the most antidefense genes. Orthopoxviruses (ORPV), a genus within the subfamily Chordopoxvirinae, infect diverse mammals and include one of the most devastating human pathogens, the now eradicated smallpox virus. ORPV encode ∼200 genes, of which roughly half are directly involved in virus genome replication and expression as well as virion morphogenesis. The remaining ∼100 "accessory" genes are responsible for virus-host interactions, particularly counter-defense of innate immunity. Complete sequences are currently available for several hundred ORPV genomes isolated from a variety of mammalian hosts, providing a rich resource for comparative genomics and reconstruction of ORPV evolution. To identify the provenance and evolutionary trends of the ORPV accessory genes, we constructed clusters including the orthologs of these genes from all chordopoxviruses. Most of the accessory genes were captured in three major waves early in chordopoxvirus evolution, prior to the divergence of ORPV and the sister genus Centapoxvirus from their common ancestor. The capture of these genes from the host was followed by extensive gene duplication, yielding several paralogous gene families. In addition, nine genes were gained during the evolution of ORPV themselves. In contrast, nearly every accessory gene was lost, some on multiple, independent occasions in numerous lineages of ORPV, so that no ORPV retains them all. A variety of functional interactions could be inferred from examination of pairs of ORPV accessory genes that were either often or rarely lost concurrently. IMPORTANCE Orthopoxviruses (ORPV) include smallpox (variola) virus, one of the most devastating human pathogens, and vaccinia virus, comprising the vaccine used for smallpox eradication. Among roughly 200 ORPV genes, about half are essential for genome replication and expression as well as virion morphogenesis, whereas the remaining half consists of accessory genes counteracting the host immune response. We reannotated the accessory genes of ORPV, predicting the functions of uncharacterized genes, and reconstructed the history of their gain and loss during the evolution of ORPV. Most of the accessory genes were acquired in three major waves antedating the origin of ORPV from chordopoxviruses. The evolution of ORPV themselves was dominated by gene loss, with numerous genes lost at the base of each major group of ORPV. Examination of pairs of ORPV accessory genes that were either often or rarely lost concurrently during ORPV evolution allows prediction of different types of functional interactions.

Keywords: Adaptive mutations; Gene gain; Gene loss; Host range; Innate immunity; Poxvirus; Poxvirus evolution; Virus evolution; Virus phylogeny.

FIG 1

Distribution of ORPV accessory genes among chordopoxviruses. (A) Number of ORPV accessory genes (OPG) represented in each chordopoxvirus genus. (B) Distribution of accessory genes among the major lineages of ORPV. (C) Representation of accessory genes in ORPV genomes. Each bar represents one of the 106 accessory OPGs.

FIG 2

Gain of ORPV genes at different stages of evolution of chordopoxviruses. Each circle associated with a tree branch shows the node number from which the branch emits (see Table S5A) and the number of genes inferred to have been gained at the branch. The callouts (blue boxes) indicate the inferred points of entry of the ancestors of the major families of paralogous accessory genes into the evolving poxvirus genomes. The chordopoxvirus genera are indicated to the right of the tree.

FIG 3

Phylogenetic tree of ORPV and gene loss in ORPV evolution. The large branches are collapsed and shown with triangles. Each box associated with a tree branch shows the node number from which the branch emits (see Fig. S2) and the number of genes inferred to have been lost at the branch (numbers in bold). The four colored boxes show major clades with many genes lost at the stem. For branches without associated boxes, no or one gain was inferred. The red shape shows the high-loss clade of ORPV.

FIG 4

Estimated rates of gene loss in the major clades of ORPV. The plot shows the loss rate in the stem of the respective clade and each of the branches within the clade. The gene loss rates were estimated as the number of genes lost per 1% nucleotide distance from the common ancestor of the respective group. Whiskers show the 90% confidence interval (5th and 95th percentile of the loss rates across 1000 bootstrap samples of genes).

FIG 5

Gene content evolution tree of ORPV derived from the patterns of gene presence-absence. The Unweighted Pair Group Method with Arithmetic mean (UPGMA) dendrogram was constructed from the matrix of distances between OPG presence-absence patterns, and therefore, reflects the overlap between the sets of lost genes (Table S3A).

FIG 6

Distribution of inferred gene losses along the ORPV genomes. Each bar shows the number of times a given OPG was lost during the evolution of the ORPV. OPG153 (A26L), a gene with an anomalously high loss rate for its position away from the genome end, is indicated.

FIG 7

Concurrent gene loss in ORPV. (A) Heatmap of gene losses. The all against all map of OPG is shown. The intensity of the red color is proportional to the frequency of the concurrent loss of the respective OPG. (B) Network of gene losses. Shown is a sub-network of the complete network of concurrent gene loses that includes 53 genes, with edges connecting genes with at least 3 independent concurrent losses. The color goes from blue (3 shared losses) to red (13 shared losses). The network was visualized using Cytoscape v.3.8.2.

FIG 8

Distribution of different gene disruption events along the ORPV genomes. The distributions of relative frequencies of 4 types of gene disruption events along the ORPV genomes are shown. The events are color-coded as shown beneath the plot: D, decaying (deletion); F, frameshift; N, in-frame stop nonsense mutation; X, complete absence (large deletion). Relative frequencies of disruption events in each gene were averaged in an 11-gene sliding windows.

FIG 9

Routes of gene disruption in ORPV. The gene disruption events for 6 OPGs are mapped onto the phylogenetic tree of the ORPV (Fig. S2). Magenta, decaying (within gene deletion); blue, frameshift; red, missing (large deletion).

FIG 10

Unique evolutionary scenarios for disrupted genes in ORPV. The inferred evolutionary events are shown for three OPGs with unusual histories. OPG188: fusion of Poxin with Schlafen followed by disruption of Schlafen, leaving the intact Poxin, or disruption of the entire fused gene. OPG177, Gasdermin homolog, duplication in branch leading to the common ancestor of ORPV and Centapoxviruses followed by the loss of one paralog in Old World ORPV. Poxvirus X denotes the common ancestor of Centapoxviruses and ORPV. Shapes with pale gray coloring and red cross denotes gene disruption. OPG010, OPG010a: exaptation of a disrupted remnant of an endoplsmic reticulum protein containing a lectin domain for a function as a TAP inhibitor (OPG10a); OPG10a evolved convergently in several groups of ORPV (see the text).