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

Paez-Espino, David; Zhou, Jinglie; Roux, Simon; Nayfach, Stephen; Pavlopoulos, Georgios A.; Schulz, Frederik; McMahon, Katherine D.; Walsh, David; Woyke, Tanja; Ivanova, Natalia N.; Eloe-Fadrosh, Emiley A.; Tringe, Susannah G.; Kyrpides, Nikos C.

doi:10.1186/s40168-019-0768-5

Title: Diversity, evolution, and classification of virophages uncovered through global metagenomics

Journal Article · 10 December 2019 · Microbiome

DOI: https://doi.org/10.1186/s40168-019-0768-5 · OSTI ID:1591848

^[1]; Zhou, Jinglie ^[1]; Roux, Simon ^[1]; Nayfach, Stephen ^[1]; Pavlopoulos, Georgios A. ^[2]; Schulz, Frederik ^[1]; McMahon, Katherine D. ^[3]; Walsh, David ^[4]; Woyke, Tanja ^[1]; Ivanova, Natalia N. ^[1]; Eloe-Fadrosh, Emiley A. ^[1]; Tringe, Susannah G. ^[1]; Kyrpides, Nikos C. ^[1]

USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); BSRC Alexander Fleming", Athens (Greece)
Univ. of Wisconsin, Madison, WI (United States)
Concordia Univ., Montreal, QC (Canada)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1591848

Journal Information:: Microbiome, Journal Name: Microbiome Journal Issue: 1 Vol. 7; ISSN 2049-2618

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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MOESM1 of Diversity, evolution, and classification of virophages uncovered through global metagenomics Paez-Espino, David; Zhou, Jinglie; Roux, Simon https://doi.org/10.6084/m9.figshare.11352815 The current record is supplemented by this dataset	dataset	January 2019
MOESM1 of Diversity, evolution, and classification of virophages uncovered through global metagenomics Paez-Espino, David; Zhou, Jinglie; Roux, Simon https://doi.org/10.6084/m9.figshare.11352815.v1 The current record is supplemented by this dataset	dataset	January 2019
MOESM2 of Diversity, evolution, and classification of virophages uncovered through global metagenomics Paez-Espino, David; Zhou, Jinglie; Roux, Simon https://doi.org/10.6084/m9.figshare.11352824 The current record is supplemented by this dataset	dataset	January 2019
MOESM2 of Diversity, evolution, and classification of virophages uncovered through global metagenomics Paez-Espino, David; Zhou, Jinglie; Roux, Simon https://doi.org/10.6084/m9.figshare.11352824.v1 The current record is supplemented by this dataset	dataset	January 2019
Diversity, evolution, and classification of virophages uncovered through global metagenomics Paez-Espino, David; Zhou, Jinglie; Roux, Simon https://doi.org/10.6084/m9.figshare.c.4777415 The current record is supplemented by this collection	collection	January 2019
Diversity, evolution, and classification of virophages uncovered through global metagenomics Paez-Espino, David; Zhou, Jinglie; Roux, Simon https://doi.org/10.6084/m9.figshare.c.4777415.v1 The current record is supplemented by this collection	collection	January 2019

Title: Diversity, evolution, and classification of virophages uncovered through global metagenomics

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