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Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics

Author

Listed:
  • Simon Roux

    (The Ohio State University
    Department of Energy Joint Genome Institute)

  • Leong-Keat Chan

    (Department of Energy Joint Genome Institute)

  • Rob Egan

    (Department of Energy Joint Genome Institute)

  • Rex R. Malmstrom

    (Department of Energy Joint Genome Institute)

  • Katherine D. McMahon

    (University of Wisconsin-Madison
    University of Wisconsin-Madison)

  • Matthew B. Sullivan

    (The Ohio State University
    The Ohio State University)

Abstract

Virophages are small viruses that co-infect eukaryotic cells alongside giant viruses (Mimiviridae) and hijack their machinery to replicate. While two types of virophages have been isolated, their genomic diversity and ecology remain largely unknown. Here we use time series metagenomics to identify and study the dynamics of 25 uncultivated virophage populations, 17 of which represented by complete or near-complete genomes, in two North American freshwater lakes. Taxonomic analysis suggests that these freshwater virophages represent at least three new candidate genera. Ecologically, virophage populations are repeatedly detected over years and evolutionary stable, yet their distinct abundance profiles and gene content suggest that virophage genera occupy different ecological niches. Co-occurrence analyses reveal 11 virophages strongly associated with uncultivated Mimiviridae, and three associated with eukaryotes among the Dinophyceae, Rhizaria, Alveolata, and Cryptophyceae groups. Together, these findings significantly augment virophage databases, help refine virophage taxonomy, and establish baseline ecological hypotheses and tools to study virophages in nature.

Suggested Citation

  • Simon Roux & Leong-Keat Chan & Rob Egan & Rex R. Malmstrom & Katherine D. McMahon & Matthew B. Sullivan, 2017. "Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics," Nature Communications, Nature, vol. 8(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_s41467-017-01086-2
    DOI: 10.1038/s41467-017-01086-2
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    Cited by:

    1. Sofia Rigou & Sébastien Santini & Chantal Abergel & Jean-Michel Claverie & Matthieu Legendre, 2022. "Past and present giant viruses diversity explored through permafrost metagenomics," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    2. Alexandra Bessenay & Hugo Bisio & Lucid Belmudes & Yohann Couté & Lionel Bertaux & Jean-Michel Claverie & Chantal Abergel & Sandra Jeudy & Matthieu Legendre, 2024. "Complex transcriptional regulations of a hyperparasitic quadripartite system in giant viruses infecting protists," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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