The emergence and early evolution of eukaryotes, with many complex and unique features already present in the Last Eukaryotic Common Ancestor (LECA), are challenging biological questions. The nature of LECA’s precursors that progressively accumulated these specific traits (i.e., proto-eukaryotes), as well as the mechanisms that led to modern eukaryotes, are enigmatic, and the roles that viruses could have played understudied. Yet, the NCLDVs (Nucleocytoviricota) could have significantly influenced eukaryogenesis. This viral phylum comprises diverse large and giant DNA viruses, widespread and collectively infecting the entire eukaryotic domain, and presumably already diversified before LECA. This suggests long-lasting interactions with their hosts, including gene transfers that seem particularly important between NCLDVs and eukaryotes. Homologs of eukaryotic proteins related to critical informational processes have already been detected in NCLDVs, with phylogenies supporting ancestral transfers from virus to cell. In the VirEukaGen project, we hypothesize that NCLDVs initially infected proto-eukaryotes, substantially participating in eukaryogenesis, notably through the transfers of genes that diverged or emerged in viral genomes. The objectives are to decipher the origin and early evolution of NCLDVs and Eukaryotes, respectively, and to assess their co-evolution over time. The VirEukaGen project will benefit from two recent large resources of environmental genomes of planktonic eukaryotes and NCLDVs, including new groups, and will notably combine extensive phylogenomic, phylogenetic, and gene cluster analyses. It is organized into 3 tasks: (1) the vertical evolution of marine eukaryotes and NCLDVs, (2) the horizontal transfers between them, and (3) the production of new genomic resources for informative clades and environments. Through the exploration of the (co)evolution of NCLDVs and eukaryotes, this project will clarify the roles that viruses have played in cellular evolution.