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.

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

Microbiome. 2019 Dec 10;7(1):157

Authors: Paez-Espino D, Zhou J, Roux S, Nayfach S, Pavlopoulos GA, Schulz F, McMahon KD, Walsh D, Woyke T, Ivanova NN, Eloe-Fadrosh EA, Tringe SG, Kyrpides NC

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.

PMID: 31823797 [PubMed - in process]