IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata

Author:

Camargo Antonio Pedro1ORCID,Nayfach Stephen1,Chen I-Min A1ORCID,Palaniappan Krishnaveni1,Ratner Anna1,Chu Ken1,Ritter Stephan J1,Reddy T B K1ORCID,Mukherjee Supratim1ORCID,Schulz Frederik1,Call Lee1,Neches Russell Y1,Woyke Tanja1,Ivanova Natalia N1,Eloe-Fadrosh Emiley A1ORCID,Kyrpides Nikos C1,Roux Simon1ORCID

Affiliation:

1. DOE Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA

Abstract

Abstract Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration of the global virosphere, progressively revealing the extensive genomic diversity of viruses on Earth and highlighting the myriad of ways by which viruses impact biological processes. IMG/VR provides access to the largest collection of viral sequences obtained from (meta)genomes, along with functional annotation and rich metadata. A web interface enables users to efficiently browse and search viruses based on genome features and/or sequence similarity. Here, we present the fourth version of IMG/VR, composed of >15 million virus genomes and genome fragments, a ≈6-fold increase in size compared to the previous version. These clustered into 8.7 million viral operational taxonomic units, including 231 408 with at least one high-quality representative. Viral sequences in IMG/VR are now systematically identified from genomes, metagenomes, and metatranscriptomes using a new detection approach (geNomad), and IMG standard annotation are complemented with genome quality estimation using CheckV, taxonomic classification reflecting the latest taxonomic standards, and microbial host taxonomy prediction. IMG/VR v4 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.

Funder

U.S. Department of Energy Joint Genome Institute

Office of Science of the U.S. Department of Energy

Publisher

Oxford University Press (OUP)

Subject

Genetics

Reference45 articles.

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