Dominant contribution of Asgard archaea to eukaryogenesis

Key results

1. ShownAsgard archaea are the largest inferred source of conserved eukaryotic protein families likely present in the LECA. The result holds across clustering schemes and taxonomies.

   Across 13,500 Eukaryotic-Prokaryotic Orthologous Clusters (EPOCs) covering 3950 KEGG Orthology groups (KOGs), Asgard had the highest average expected likelihood weight (aELW). In the core set of 4290 EPOCs (2100 KOGs) left after removing EPOCs with maximum ELW below 0.4, Asgard held 50% of all likelihood weight. The Asgard lead persisted with tree-annealed clusters and under GTDB taxonomy. · Phylogenomic analysis and global evolutionary…; Cluster annealing; Taxonomy remapping and EPOC construction under…; Figure legends

2. ShownAsgard ancestry covers almost all core information processing and reaches many other systems, including N-linked glycosylation, glycosylphosphatidylinositol (GPI) anchor synthesis, nucleocytoplasmic transport, sphingolipid metabolism and the mevalonate pathway; fatty acid pathways look more mosaic.

   Strong Asgard aELW for ribosome, RNA and DNA polymerases, Ras-like GTPases, ubiquitin-proteasome degradation, DNA repair (nucleotide excision, mismatch), recombination and aminoacyl-tRNA biosynthesis; also for the oligosaccharyltransferase core, 7-subunit GPI-GnT complex and GPI transamidase. Fatty acid synthesis and decay gave widely spread aELW, with Actinomycetota and Alphaproteobacteria signals. · Phylogenomic analysis and global evolutionary…; Broad Asgard contributions to eukaryogenesis

3. ShownAlphaproteobacterial ancestry is clear but narrow, essentially limited to mitochondrial functions: oxidative phosphorylation, ubiquinone synthesis, mitochondrial translation and 4Fe-4S cluster assembly.

   Alphaproteobacteria were associated with oxidative phosphorylation complexes, ubiquinone synthesis, the 4Fe-4S assembly platforms, IBA57 and ferredoxin-1 and 2. In contrast, the 2Fe-2S scaffold ISCU was mosaic with a weaker Asgard signal, while NFS1, cysteine and methionine biosynthesis and the cytosolic CIA components CIA1 and CIA2B were Asgard-associated. · Limited and specific Alphaproteobacterial…; Phylogenomic analysis and global evolutionary…; Discussion

4. ShownAbout a third of core families point to bacteria other than Alphaproteobacteria, but these signals are scattered across functions; apart from a narrow Myxococcota nucleotide-metabolism signal, no pathway traces to one bacterial taxon.

   600 of 2,100 KOGs and 1,580 of 4,300 EPOCs had their top association with neither Asgard nor Alphaproteobacteria. Only Alphaproteobacteria (oxidative phosphorylation) and Myxococcota (nicotinate and nucleotide pathways, mostly nucleotidases) beat Asgard aELW in a KEGG pathway with over 20 EPOCs. Of 130 strictly filtered EPOCs (ELW > 0.7), 97 were Asgard and 33 diverse bacteria, with no functional trend. · Absence of functionally consistent contributions…; Figure legends

5. SuggestedNormalized stem lengths behave poorly as a clock for gene acquisition: shorter Alphaproteobacterial stems (the earlier mitochondria-late signal) appear only among long stems, and co-acquired oxidative phosphorylation genes vary widely.

   Of 5,850 stems (sharp peak near 0.05), Alphaproteobacterial stems below 0.3 (70% of all stems) were longer than Asgard stems, but those above 0.35 were shorter on average; the pattern held in 20 technical replicates of 175 sampled stems. Oxidative phosphorylation stems spanned more than two orders of magnitude, and information processing genes had shorter than average stems. · Ancestral stem lengths and the amount of…; Figure legends