Phylogeny of the Varidnaviria Morphogenesis Module: Congruence and Incongruence With the Tree of Life and Viral Taxonomy

Abstract

Double-stranded DNA viruses of the realm Varidnaviria (formerly PRD1-adenovirus lineage) are characterized by homologous major capsid proteins (MCPs) containing one (kingdom: Helvetiavirae) or two β-barrel domains (kingdom: Bamfordvirae) known as the jelly roll folds. Most of them also share homologous packaging ATPases (pATPases). Remarkably, Varidnaviria infect hosts from the three domains of life, suggesting that these viruses could be very ancient and share a common ancestor. Here, we analyzed the evolutionary history of Varidnaviria based on single and concatenated phylogenies of their MCPs and pATPases. We excluded Adenoviridae from our analysis as their MCPs and pATPases are too divergent. Sphaerolipoviridae, the only family in the kingdom Helvetiavirae, exhibit a complex history: their MCPs are very divergent from those of other Varidnaviria, as expected, but their pATPases groups them with Bamfordvirae. In single and concatenated trees, Bamfordvirae infecting archaea were grouped with those infecting bacteria, in contradiction with the cellular tree of life, whereas those infecting eukaryotes were organized into three monophyletic groups: the Nucleocytoviricota phylum, formerly known as the Nucleo-Cytoplasmic Large DNA Viruses (NCLDVs), Lavidaviridae (virophages) and Polintoviruses. Although our analysis mostly supports the recent classification proposed by the International Committee on Taxonomy of Viruses (ICTV), it also raises questions, such as the validity of the Adenoviridae and Helvetiavirae ranking. Based on our phylogeny, we discuss current hypotheses on the origin and evolution of Varidnaviria and suggest new ones to reconcile the viral and cellular trees.

Keywords: NCLDV; dsDNA viruses; evolution; giant viruses; viral taxonomy.

FIGURE 1

Single-protein trees of the two hallmark proteins of the viruses from the Varidnaviria realm, excluding Adenoviridae, Sphaerolipoviridae. Phylogenetic trees of (A) the major capsid protein (MCP) and (B) packaging ATPase (pATPase). The root of the phylogenetic tree was between the prokaryotic and eukaryotic members. The scale-bar indicates the average number of substitutions per site. The best-fit model for the MCP tree was LG + F + R4, which was chosen according to Bayesian Information Criterion (BIC) and the alignment has 103 sequences with 237 positions. The best-fit model for the pATPase tree was LG + R6, which was chosen according to BIC and the alignment has 103 sequences with 171 positions. More detailed versions of the trees are shown in Supplementary Figures 4, 5. Branches in black indicate both classical bootstrap and transfer bootstrap expectation (TBE) support values using 1,000 replicates are above 70%. Branches in blue indicate only one of the two support values is above 70% whereas branches in red indicate both support values are below 70%.

FIGURE 2

Four scenarios for the evolution of Bamfordvirae. The diversification and evolution of viruses are depicted with pale blue thick lines or triangles. Lower panels depict groups that are monophyletic (in brackets) among Tectiliviricetes (T), Preplasmiviricota except Tectiliviricetes (P*), and Nucleocytoviricota (N) in the above scenarios. The black arrows indicate the introduction of DNA replication proteins related to those of Duplodnaviria in the ancestral lineage of Nucleocytoviricota. Dotted arrows indicate transfer of viruses between different cellular domains. In all scenarios, we assumed that Bamfordvirae were present in the last archaeal common ancestor (LACA). In panels (A,B), the origin of Bamfordvirae (blue pentagon) predated the last universal common ancestor (LUCA). In panel (A), Tectiliviricetes emerged first and different lineages were selected and co-evolved with the proto-bacterial and proto-archaeal lineages. In panel (B), the ancestral Varidnaviria thriving at the time of LUCA have now disappeared, Tectiliviricetes emerged in the bacterial branch and were later transferred to Archaea. The ancestors of eukaryotic Bamfordvirae were lost in Archaea. In panels (C,D), Bamfordvirae originated after LUCA, either in proto-bacteria (C) or proto-eukaryotes (D). They appeared later in the two other domains by virus transfer. LUCA, last universal common ancestor; LACA, last archaeal common ancestor; LBCA, last bacterial common ancestor; LECA, last eukaryal common ancestor.

FIGURE 3

Phylogenetic tree of the concatenated MCP and pATPase genes. (A) Phylogenetic tree annotated with the corresponding group. The alignment has 103 sequences with 408 positions. Phylogenetic tree was rooted between the prokaryotic and eukaryotic members. The scale-bar indicates the average number of substitutions per site. The best-fit model was LG + F + R6, which was chosen according to Bayesian Information Criterion (BIC). Branches in black indicate both classical bootstrap and transfer bootstrap expectation (TBE) support using 1,000 replicates values are above 70%. Branches in blue indicate only one of the two support values is above 70% whereas branches in red indicate both support values are below 70%. (B) Phylogenetic tree annotated with the ICTV taxonomy.

FIGURE 4

Phylogenetic tree of the concatenated major capsid protein and packaging ATPase genes, excluding the Poxviridae. The alignment has 95 sequences with 434 positions. Phylogenetic tree was rooted between the prokaryotic and eukaryotic members. The scale-bar indicates the average number of substitutions per site. The best-fit model was LG + F + R5, which was chosen according to Bayesian Information Criterion (BIC). Branches in black indicate both classical bootstrap and transfer bootstrap expectation (TBE) support values using 1,000 replicates are above 70%. Branches in blue indicate only one of the two support values is above 70% whereas branches in red indicate both support values are below 70%.

FIGURE 5

Phylogenetic tree of the packaging ATPase gene of the Varidnaviria realm, excluding Adenoviridae. The alignment has 116 sequences with 151 positions. The root of the phylogenetic tree was between the prokaryotic and eukaryotic members. The scale-bar indicates the average number of substitutions per site. The best-fit model was LG + R6, which was chosen according to Bayesian Information Criterion (BIC). Branches in black indicate both classical bootstrap and transfer bootstrap expectation (TBE) support values using 1,000 replicates are above 70%. Branches in blue indicate only one of the two support values is above 70% whereas branches in red indicate both support values are below 70%.