IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata. Issue Volume 51:Issue D1(2023) (18th November 2022)

• Record Type: Journal Article
• Authors: Camargo, Antonio Pedro; Nayfach, Stephen; Chen, I-Min A; Palaniappan, Krishnaveni; Ratner, Anna; Chu, Ken; Ritter, Stephan J; Reddy, T B K; Mukherjee, Supratim; Schulz, Frederik; Call, Lee; Neches, Russell Y; Woyke, Tanja; Ivanova, Natalia N; Eloe-Fadrosh, Emiley A; Kyrpides, Nikos C; Roux, Simon
• Is Part Of: Nucleic acids research. Volume 51:Issue D1(2023)
• Page Start: D733
• Page End: D743
• Publication Date: 2022-11-18
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkac1037
• Languages: English
• ISSNs: 0305-1048

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 .