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Microbiome. 2019 Dec 10;7(1):157. doi: 10.1186/s40168-019-0768-5.

Diversity, evolution, and classification of virophages uncovered through global metagenomics.

Author information

1
Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, 94598, USA. adpaezespino@lbl.gov.
2
Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, 94598, USA.
3
BSRC "Alexander Fleming", 34 Fleming Street, Vari, 16672, Athens, Greece.
4
Departments of Civil and Environmental Engineering and Bacteriology, University of Wisconsin Madison, 1550 Linden Drive, Madison, WI, 53726, USA.
5
Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, QC, H4B 1R6, Canada.
6
Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, 94598, USA. sgtringe@lbl.gov.
7
Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, 94598, USA. nckyrpides@lbl.gov.

Abstract

BACKGROUND:

Virophages are small viruses with double-stranded DNA genomes that replicate along with giant viruses and co-infect eukaryotic cells. Due to the paucity of virophage reference genomes, a collective understanding of the global virophage diversity, distribution, and evolution is lacking.

RESULTS:

Here we screened a public collection of over 14,000 metagenomes using the virophage-specific major capsid protein (MCP) as "bait." We identified 44,221 assembled virophage sequences, of which 328 represent high-quality (complete or near-complete) genomes from diverse habitats including the human gut, plant rhizosphere, and terrestrial subsurface. Comparative genomic analysis confirmed the presence of four core genes in a conserved block. We used these genes to establish a revised virophage classification including 27 clades with consistent genome length, gene content, and habitat distribution. Moreover, for eight high-quality virophage genomes, we computationally predicted putative eukaryotic virus hosts.

CONCLUSION:

Overall, our approach has increased the number of known virophage genomes by 10-fold and revealed patterns of genome evolution and global virophage distribution. We anticipate that the expanded diversity presented here will provide the backbone for further virophage studies.

KEYWORDS:

Global distribution; Major capsid protein (MCP); Metagenomics; Virophage; Virophage classification; Virophage-NCLDV interactions

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