Diverse ancestries reveal complex symbiotic interactions during eukaryogenesis

The origin of eukaryotes remains a central enigma in biology. Ongoing debates agree on the pivotal role of a symbiosis between an alpha-proteobacterium and an Asgard archaeon. However, the involvement of other bacterial partners as significant donors of genetic material, or the role of interactions with viruses remain contentious. To address these questions, we employed advanced phylogenomic approaches and comprehensive datasets spanning the known diversity of cellular life and viruses. Our analysis provided an updated reconstruction of the last eukaryotic common ancestor (LECA) proteome, in which we traced the phylogenetic origin of each protein family. We found compelling evidence for multiple waves of horizontal gene transfer from diverse bacterial and viral donors, with some likely preceding the mitochondrial endosymbiosis. We inferred the proteomes of the potential major donors and their functional contributions to LECA. Our findings underscore the contribution of horizontal gene transfers in shaping the proteomes of pre-LECA ancestors and hint to a facilitating role of Nucleocytoviricota viruses. Altogether, our results suggest ancient eukaryotes originated within complex microbial ecosystems through a succession of symbiotic interactions that left a footprint of horizontally transferred genes.