Quantified duplications of proteins within complexes across eukaryotes

Protein complexes are central to cell biology and typically verified via a combination of interaction data, complete genome sequencing and comprehensive protein-coding gene predictions for reference eukaryotes. However this data is lacking for non-reference eukaryotes. Protein complexes can be predicted in species for which no interaction data is available by mapping orthology of verified protein complex components from reference eukaryotes to predicted proteomes. Studies that map conservation of protein complex components by orthology are often limited to a small number of protein queries, an under-representation of non-reference, microbial eukaryotes and are scattered across the literature. Here, I integrate orthology and protein interaction data by mapping proteins of experimentally verified complexes to orthogroups of proteins spanning 31 diverse eukaryotes. Proteins within complex-harbouring orthogroups are retained and distributed more evenly across taxa than non-complex orthogroups. I identified 184 universal orthogroups that included orthologs of known protein complex components from all 31 eukaryotes, consistent with a conserved core repertoire, likely present in the last eukaryotic common ancestor (LECA). I generated the protein complex orthology cartographer (PCOC) suite to find significant duplications and reductions of proteins in universal orthogroups across and between eukaryotes. This revealed both multi-copy and notably single-copy proteins, in all queried species, from the exosome, spliceosome, proteasome, small-ribosomal processome, tRNA synthetases, MCM complexes and RNA polymerase III. Case analyses of Naegleria gruberi and Guillardia theta highlight taxon-specific expansions and show how broader protist inclusion improves domain-wide inference of eukaryotic protein-complex evolution.