Giant endogenous viral elements in the genome of the model protist Euglena gracilis reveal past interactions with giant viruses

Giant viruses in the phylum Nucleocytoviricota have increasingly been found integrated into the genomes of diverse eukaryotes. Here we report 8 Giant Endogenous Viral Elements (GEVEs) in the genome of the microalgae Euglena gracilis. The GEVEs bear signatures of genomic erosion, including invasion of transposable elements and duplications, suggesting that they are incapable of reactivation and virion production. Most of the GEVEs exhibit high average amino acid identity and cluster near each other in phylogenies of viral marker genes, suggesting that they are derived from the same initial viral lineage. Phylogenetic analysis of nucleocytovirus marker proteins reveals the viruses belong to the order Asfuvirales in the same broader lineage that includes African swine fever virus (ASFV), abalone asfarvirus (AbalV), and GEVEs recently found in the fungus Rhizophagus irregularis and the marine gastropod Elysia marginata, suggesting that widespread host range transitions have occurred in this lineage. This work expands the diversity of known endogenous giant viruses and expands the host range of the Asfuvirales to include the superkingdom Discoba.