Marine fungi harbor, and are co-diversified with, remnants of giant endogenous viral elements

Nucleocytoplasmic large DNA viruses (NCLDVs) are ancient associates of eukaryotes and are increasingly recognized as drivers of genome evolution. However, their relationships with marine fungi remain largely unexplored. Here, we identify NCLDV-like endogenous viral elements (GEVEs) in 18 marine Ascomycota fungi isolates from Hawaiian coastal waters. Across viral-bearing contigs, we recovered a diverse set of canonical NCLDV hallmark genes co-localized with auxiliary metabolic and regulatory genes. The presence of glycosyltransferases, serine/threonine and F10-like kinases, and short-chain dehydrogenases suggest that the ancestral viruses encoded pathways capable of modulating carbon metabolism and redox balance within their hosts. Recovery of mRNA capping enzymes and ribonucleotide reductases suggests these viruses were once autonomous, with machinery supporting replication independent of the fungal host. Phylogenetic analyses infer these elements as a novel clade most closely related to fungal-infecting NCLDVs (Mycodnaviridae), expanding the known host range and evolutionary diversity of NCLDVs. Cophylogenetic analyses suggest mixed host-virus associations consistent with lineage-specific integration and episodic host shifts rather than strict coevolution, while intronization of viral genes within fungal scaffolds further supports long-term residence and assimilation following endogenization. Together, our findings reveal an undescribed lineage of fungal-associated viruses and a previously unrecognized contribution of viral influence to fungal genome diversification.