Systematic survey of non-retroviral virus-like elements in eukaryotic genomes

Virus Res. 2019 Mar;262:30-36. doi: 10.1016/j.virusres.2018.02.002. Epub 2018 Feb 6.

Abstract

Endogenous viral elements (EVEs) are viral sequences that are endogenized in the host cell. Recently, several eukaryotic genomes have been shown to contain EVEs. To improve the understanding of EVEs in eukaryotes, we have developed a system for detecting EVE-like sequences in eukaryotes and conducted a large-scale nucleotide sequence similarity search using all available eukaryotic and viral genome assembly sequences (excluding those from retroviruses) stored in the National Center for Biotechnology Information genome database (as of August 14, 2017). We found that 3856 of 7007 viral genomes were similar to 4098 of 4102 eukaryotic genomes. For those EVE-like sequences, we constructed a database, Predicted Endogenous Viral Elements (pEVE, http://peve.med.u-tokai.ac.jp) which provides comprehensive search results summarized from an evolutionary viewpoint. A comparison of EVE-like sequences among closely related species may be useful to avoid false-positive hits. We believe that our search system and database will facilitate studies on EVEs.

Keywords: Comparative genomics; Database; Endogenous viral elements; Evolution.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Viruses / genetics*
  • DNA, Viral
  • Databases, Nucleic Acid*
  • Endogenous Retroviruses / genetics*
  • Eukaryota / genetics*
  • Eukaryota / virology
  • Evolution, Molecular
  • Genome*
  • Genome, Viral
  • Genomics / methods
  • Internet
  • Phylogeny

Substances

  • DNA, Viral