Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes

Abstract

Giant and large eukaryotic double-stranded DNA viruses from the Nucleo-Cytoplasmic Large DNA Virus (NCLDV) assemblage represent a remarkably diverse and potentially ancient component of the eukaryotic virome. However, their origin(s), evolution, and potential roles in the emergence of modern eukaryotes remain subjects of intense debate. Here we present robust phylogenetic trees of NCLDVs, based on the 8 most conserved proteins responsible for virion morphogenesis and informational processes. Our results uncover the evolutionary relationships between different NCLDV families and support the existence of 2 superclades of NCLDVs, each encompassing several families. We present evidence strongly suggesting that the NCLDV core genes, which are involved in both informational processes and virion formation, were acquired vertically from a common ancestor. Among them, the largest subunits of the DNA-dependent RNA polymerase were transferred between 2 clades of NCLDVs and proto-eukaryotes, giving rise to 2 of the 3 eukaryotic DNA-dependent RNA polymerases. Our results strongly suggest that these transfers and the diversification of NCLDVs predated the emergence of modern eukaryotes, emphasizing the major role of viruses in the evolution of cellular domains.

Keywords: NCLDV; RNA polymerase; evolution; giant viruses; proto-eukaryotes.

Fig. 1.

Phylogenetic tree of the NCLDVs. Bayesian inference (CAT-GTR model) of the concatenated 8 core proteins from the NCLDVs after removal of Poxviridae and A. anophagefferens. Genome sizes (in bp) are represented next to each virus name. The scale bar indicates the average number of substitutions per site. The values at branches represent Bayesian posterior probabilities. Nodes without maximum support are indicated in red. The tree has been rooted between the MAPI and the PAM superclades [unrooted tree in Additional data at https://zenodo.org/record/3368642 (26)].

Fig. 2.

ML phylogenetic tree of the concatenated 2 largest RNAP subunits from Archaea, Eukaryotes, and NCLDVs, with Archaea serving as the outgroup. The scale bar indicates the average number of substitutions per site. Values atop and below the branches represent support calculated by the SH-like aLRT (1,000 replicates) and UFBoot (1,000 replicates), respectively.

Fig. 3.

Schematic representation of the hypothetical scenario for the transfers of RNAP between cells and NCLDVs. An ancestral RNAP that later gave rise to the eukaryotic RNAP-III, an actual ortholog of the archaeal RNAP, was transferred from proto-eukaryotes to the ancestor of modern NCLDVs. Following the emergence of the Phycodnaviridae (with an RNAP whose origin requires further investigation), a significantly divergent RNAP was transferred from the common ancestor of the Asfarviridae and Megavirales to proto-eukaryotes. A new eukaryotic RNAP also emerged from a duplication event from RNAP-III, possibly followed by replacement of the largest subunit with that of Asfarviridae; further investigations are needed to confirm the direction of this transfer. These events occurred before the LECA that marked the emergence of modern eukaryotes.