Abstract

Genomic and metagenomic sequencing has transformed our understanding of the diversity of large DNA viruses infecting eukaryotic microorganisms. This includes the newly described manesviruses that infect amoebae and the mirusviruses associated with the thraustochytrid Aurantiochytrium limacinum. Using long-read sequencing technology, we assembled the genomes of two thraustochytrids and discovered ubiquitous co-culturing viruses. Schizochytrium aggregatum ATCC 28209 was found to contain two nucleocytoviruses that are closely related to the previously described SmDNAV of Sicyoidochytrium minutum, and Schizochytrium sp. 20888 harbours two mirusviruses and one SmDNAV-like nucleocytovirus. We also found additional SmDNAV-type viruses associated with previously sequenced thraustochytrid genomes. Phylogenetic analysis reveals that the SmDNAV and SmDNAV-like genomes belong to a hitherto unrecognized family of Nucleocytoviricota, here named "Skiaviridae". All ten identified Skiaviridae genomes are 190-250 kilobase pairs (kb) in size and lack numerous viral hallmark genes including DNA polymerase family B and DNA-directed RNA polymerases. Transcriptomic and proteomic data from Schizochytrium sp. 20888 and Schizochytrium aggregatum show skiavirus expression without cytopathic effects. Viral particles consistent with the expected size and morphology of mirusviruses and skiaviruses were observed in a small fraction of Schizochytrium sp. 20888 cells, suggestive of restricted viral replication in laboratory cultures. Phylogenetic analyses reveal very recent genetic exchange between mirusviruses, skiaviruses, and their thraustochytrid hosts. These findings underscore the prevalence of stable long-term, persistent infections by diverse large DNA viruses and show that co-infection provides an opportunity for virus-virus and virus-host gene transfer.