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

Camargo, Antonio Pedro; Nayfach, Stephen; Chen, I-Min A.; Palaniappan, Krishnaveni; Ratner, Anna; Chu, Ken; Ritter, Stephan J.; Reddy, T. K.; Mukherjee, Supratim; Schulz, Frederik; Call, Lee; Neches, Russell  Y.; Woyke, Tanja; Ivanova, Natalia N.; Eloe-Fadrosh, Emiley A.; Kyrpides, Nikos C.; Roux, Simon

doi:10.1093/nar/gkac1037

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

Journal Article · Fri Nov 18 00:00:00 EST 2022 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkac1037· OSTI ID:1987510

^[1]; Nayfach, Stephen ^[1]; ^[1]; Palaniappan, Krishnaveni ^[1]; Ratner, Anna ^[1]; Chu, Ken ^[1]; Ritter, Stephan J. ^[1]; ^[1]; ^[1]; Schulz, Frederik ^[1]; Call, Lee ^[1]; Neches, Russell Y. ^[1]; Woyke, Tanja ^[1]; Ivanova, Natalia N. ^[1]; ^[1]; Kyrpides, Nikos C. ^[1]; ^[1]

USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)

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, for this work, 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.

View Accepted Manuscript (DOE)

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

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1987510

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 51; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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