Abstract
Gene exchange between viruses and their hosts acts as a key facilitator of horizontal gene transfer and is thought to be a major driver of evolutionary change 1–3. Our understanding of this process comes primarily from bacteria and phage co-evolution4, but the mode and functional significance of gene transfers between eukaryotes and their viruses remains more anecdotal. Here we show that viral-eukaryotic gene exchange can define infection strategies and has recurrently influenced eukaryotic evolution. Using a systematic, phylogenetically-informed approach, we characterized viral-eukaryotic gene exchange across diverse taxa, identifying thousands of transfers, and revealing their frequency, taxonomic distribution, and projected functions, across the eukaryotic tree of life. Eukaryote-derived viral genes revealed common viral host-manipulation strategies, including the key cellular pathways and compartments targeted during infection, identifying potential targets for broad-spectrum host-targeted antiviral therapeutics. Furthermore, viral-derived eukaryotic genes exposed a recurring role for viral glycosyltransferases in the diversification of eukaryotic morphology, as viral-derived genes have impacted the evolution of structures as diverse as algal cell walls, trypanosome mitochondria, and animal tissues. These findings illuminate the nature of viral-eukaryotic gene exchange and its impact on the biology of viruses and their eukaryotic hosts, providing novel perspectives for understanding viral infection mechanisms and revealing the influence of viruses on eukaryotic evolution.