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

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

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish (US)
Pages (from-to)D164-D173
JournalNucleic acids research
Volume52
Issue numberD1
DOIs
StatePublished - Jan 5 2024

ASJC Scopus subject areas

  • Genetics

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