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Peer-reviewedCC BYNature

Gene ancestries reveal diverse microbial associations during eukaryogenesis

  • Moisès Bernabeu1,2
  • Saioa Manzano-Morales1,2
  • Marina Marcet‐Houben1,3,2
  • Toni Gabaldón4,5,6,7
7 affiliations
  1. 1Barcelona Supercomputing Centre (BSC), Plaça Eusebi Güell, Barcelona, Spain
  2. 2Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, Barcelona, Spain
  3. 3CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
  4. 4Barcelona Supercomputing Centre (BSC), Plaça Eusebi Güell, Barcelona, Spain. [email protected]
  5. 5CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain. [email protected]
  6. 6Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain. [email protected]
  7. 7Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, Barcelona, Spain. [email protected]
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Abstract

The origin of eukaryotes remains a central enigma in biology 1 . Continuing debates agree on the pivotal role of a symbiosis between an alphaproteobacterium and an Asgard archaeon 2,3 . However, the nature, timing and contributions of other potential bacterial partners 4–6 and the role of interactions with viruses 7–9 remain contentious. To address these questions, we used advanced phylogenomic approaches and comprehensive datasets spanning the known diversity of cellular life and viruses. Our analysis provided a revised 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 donors, with some likely to have preceded mitochondrial endosymbiosis. We inferred plausible traits of the major donors and their functional contributions to the LECA. Our findings support a contribution of horizontal gene transfers to shaping the proteomes of pre-LECA ancestors and suggest a facilitating role of Nucleocytoviricota viruses. Taken together, our results suggest that ancient eukaryotes may have originated within complex microbial ecosystems through a succession of diverse associations that left a footprint of horizontally transferred genes.

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Cite

BibTeXRIS
BibTeX
@article{bernabeu2026gene,
  title = {{Gene ancestries reveal diverse microbial associations during eukaryogenesis}},
  author = {Moisès Bernabeu and Saioa Manzano-Morales and Marina Marcet‐Houben and Toni Gabaldón},
  journal = {Nature},
  year = {2026},
  month = jun,
  doi = {10.1038/s41586-026-10639-9},
  url = {https://doi.org/10.1038/s41586-026-10639-9},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Gene ancestries reveal diverse microbial associations during eukaryogenesis
AU  - Moisès Bernabeu
AU  - Saioa Manzano-Morales
AU  - Marina Marcet‐Houben
AU  - Toni Gabaldón
PY  - 2026
DA  - 2026/06/10
JO  - Nature
DO  - 10.1038/s41586-026-10639-9
UR  - https://doi.org/10.1038/s41586-026-10639-9
AB  - The origin of eukaryotes remains a central enigma in biology 1 . Continuing debates agree on the pivotal role of a symbiosis between an alphaproteobacterium and an Asgard archaeon 2,3 . However, the nature, timing and contributions of other potential bacterial partners 4–6 and the role of interactions with viruses 7–9 remain contentious. To address these questions, we used advanced phylogenomic approaches and comprehensive datasets spanning the known diversity of cellular life and viruses. Our analysis provided a revised 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 donors, with some likely to have preceded mitochondrial endosymbiosis. We inferred plausible traits of the major donors and their functional contributions to the LECA. Our findings support a contribution of horizontal gene transfers to shaping the proteomes of pre-LECA ancestors and suggest a facilitating role of Nucleocytoviricota viruses. Taken together, our results suggest that ancient eukaryotes may have originated within complex microbial ecosystems through a succession of diverse associations that left a footprint of horizontally transferred genes.
SN  - 0028-0836
SN  - 1476-4687
ER  -