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The virome of the last eukaryotic common ancestor and eukaryogenesis

Nature Microbiology volume 8, pages 1008–1017 (2023)Cite this article

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Abstract

All extant eukaryotes descend from the last eukaryotic common ancestor (LECA), which is thought to have featured complex cellular organization. To gain insight into LECA biology and eukaryogenesis—the origin of the eukaryotic cell, which remains poorly understood—we reconstructed the LECA virus repertoire. We compiled an inventory of eukaryotic hosts of all major virus taxa and reconstructed the LECA virome by inferring the origins of these groups of viruses. The origin of the LECA virome can be traced back to a small set of bacterial—not archaeal—viruses. This provenance of the LECA virome is probably due to the bacterial origin of eukaryotic membranes, which is most compatible with two endosymbiosis events in a syntrophic model of eukaryogenesis. In the first endosymbiosis, a bacterial host engulfed an Asgard archaeon, preventing archaeal viruses from entry owing to a lack of archaeal virus receptors on the external membranes.

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Fig. 1: The LECA virome.
Fig. 2: Viromes of prokaryotes and eukaryotes.
Fig. 3: Bacterial roots of the LECA virome.
Fig. 4: Eukaryogenesis and eukaryovirogenesis.

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Acknowledgements

We thank P. López-García for invaluable, inspiring discussions and critical reading of the manuscript and S. Roux for helpful advice. E.V.K. is supported by funds from the Intramural Research Program of the National Institutes of Health (National Library of Medicine). V.V.D. was partially supported by a National Institutes of Health/National Library of Medicine/National Center for Biotechnology Information Visiting Scientist Fellowship. M.K. was supported by l’Agence Nationale de la Recherche grant ANR-21-CE11-0001-01.

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Authors and Affiliations

  1. Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France

    Mart Krupovic

  2. Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA

    Valerian V. Dolja

  3. National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA

    Eugene V. Koonin

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  1. Mart Krupovic
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  2. Valerian V. Dolja
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  3. Eugene V. Koonin
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M.K., V.V.D. and E.V.K. researched and analysed the data and wrote the manuscript.

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Correspondence to Mart Krupovic or Eugene V. Koonin.

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Supplementary Table 1

The representation of virus phyla in major eukaryotic lineages.

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Krupovic, M., Dolja, V.V. & Koonin, E.V. The virome of the last eukaryotic common ancestor and eukaryogenesis. Nat Microbiol 8, 1008–1017 (2023). https://doi.org/10.1038/s41564-023-01378-y

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