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The LUCA and its complex virome

Nature Reviews Microbiology volume 18, pages 661–670 (2020)Cite this article

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Abstract

The last universal cellular ancestor (LUCA) is the most recent population of organisms from which all cellular life on Earth descends. The reconstruction of the genome and phenotype of the LUCA is a major challenge in evolutionary biology. Given that all life forms are associated with viruses and/or other mobile genetic elements, there is no doubt that the LUCA was a host to viruses. Here, by projecting back in time using the extant distribution of viruses across the two primary domains of life, bacteria and archaea, and tracing the evolutionary histories of some key virus genes, we attempt a reconstruction of the LUCA virome. Even a conservative version of this reconstruction suggests a remarkably complex virome that already included the main groups of extant viruses of bacteria and archaea. We further present evidence of extensive virus evolution antedating the LUCA. The presence of a highly complex virome implies the substantial genomic and pan-genomic complexity of the LUCA itself.

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Fig. 1: Distribution of known viruses across the evolutionary tree of bacteria.
Fig. 2: Distribution of known viruses across the evolutionary tree of archaea.
Fig. 3: Reconstruction of the LUCA virome from the divergence of the bacterial and archaeal viromes.
Fig. 4: Evolution of double-stranded DNA viruses antedating the LUCA.

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Acknowledgements

E.V.K. is supported by the funds of the Intramural Research Program of the National Institutes of Health of the USA. M.K. was supported by l’Agence Nationale de la Recherche grant ANR-17-CE15-0005-01.

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Authors and Affiliations

  1. Archaeal Virology Unit, Institut Pasteur, 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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M.K. and E.V.K. researched data for article. M.K., V.V.D. and E.V.K. substantially contributed to discussion of content. M.K. and E.V.K. wrote the manuscript. M.K., V.V.D. and E.V.K. reviewed and edited the manuscript before submission.

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Correspondence to Mart Krupovic or Eugene V. Koonin.

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Nature Reviews Microbiology thanks J. P. Gogarten, P. López-García and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Krupovic, M., Dolja, V.V. & Koonin, E.V. The LUCA and its complex virome. Nat Rev Microbiol 18, 661–670 (2020). https://doi.org/10.1038/s41579-020-0408-x

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