IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata

Camargo, Antonio Pedro; Call, Lee; Roux, Simon; Nayfach, Stephen; Huntemann, Marcel; Palaniappan, Krishnaveni; Ratner, Anna; Chu, Ken; Mukherjeep, Supratim; Reddy, T. B. K.; Chen, I-Min A.; Ivanova, Natalia N.; Eloe-Fadrosh, Emiley A.; Woyke, Tanja; Baltrus, David A.; Castañeda-Barba, Salvador; de la Cruz, Fernando; Funnell, Barbara E.; Hall, James P. J.; Mukhopadhyay, Aindrila; Rocha, Eduardo P. C.; Stalder, Thibault; Top, Eva; Kyrpides, Nikos C.

doi:10.1093/nar/gkad964

IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata

Journal Article · Wed Nov 01 00:00:00 EDT 2023 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkad964· OSTI ID:2368786

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USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
Univ. of Arizona, Tucson, AZ (United States)
Univ. of Idaho, Moscow, ID (United States)
Univ. of Cantabria (Spain); Consejo Superior de Investigaciones Cientificas (CSIC), Cantabria (Spain)
Univ. of Toronto, ON (Canada)
Univ. of Liverpool (United Kingdom)
Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Univ. de Paris Cité (France); Centre National de la Recherche Scientifique (CNRS) Paris (France)

Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.

View Accepted Manuscript (DOE)

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

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE National Nuclear Security Administration (NNSA)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2368786

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 52; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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