Skip to main content
eScholarship
Open Access Publications from the University of California

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

  • Author(s): 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
  • et al.
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.

Main Content
Current View