IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata-Reference-Cited by-同舟云学术

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

Published:2023-11-01 Issue:D1 Volume:52 Page:D164-D173
ISSN:0305-1048
Container-title:Nucleic Acids Research
language:en
Short-container-title:

Author:

Camargo Antonio Pedro¹^ORCID,Call Lee¹^ORCID,Roux Simon¹^ORCID,Nayfach Stephen¹^ORCID,Huntemann Marcel¹^ORCID,Palaniappan Krishnaveni¹^ORCID,Ratner Anna¹^ORCID,Chu Ken¹^ORCID,Mukherjeep Supratim¹^ORCID,Reddy T B K¹^ORCID,Chen I-Min A¹^ORCID,Ivanova Natalia N¹^ORCID,Eloe-Fadrosh Emiley A¹^ORCID,Woyke Tanja¹^ORCID,Baltrus David A²³^ORCID,Castañeda-Barba Salvador⁴^ORCID,de la Cruz Fernando⁵^ORCID,Funnell Barbara E⁶^ORCID,Hall James P J⁷^ORCID,Mukhopadhyay Aindrila⁸⁹^ORCID,Rocha Eduardo P C¹⁰^ORCID,Stalder Thibault⁴^ORCID,Top Eva⁴^ORCID,Kyrpides Nikos C¹^ORCID

Affiliation:

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

2. School of Plant Sciences, University of Arizona , Tucson AZ , USA

3. School of Animal and Comparative Biomedical Sciences, University of Arizona , Tucson AZ , USA

4. Department of Biological Sciences, University of Idaho , Moscow , ID 83844 , USA

5. Instituto de Biomedicina y Biotecnología de Cantabria (Consejo Superior de Investigaciones Científicas – Universidad de Cantabria) , Cantabria , Spain

6. Department of Molecular Genetics, University of Toronto , Toronto , ON M5G 1M1 , Canada

7. Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Liverpool L69 7ZB , UK

8. Joint BioEnergy Institute , Emeryville , CA 94608 , USA

9. Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA

10. Institut Pasteur, Université de Paris Cité , CNRS UMR3525, Microbial Evolutionary Genomics, Paris , France

Abstract

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.

Funder

U.S. Department of Energy

Joint Genome Institute

DOE Office of Science User Facilities

Exascale Computing Project

U.S. Department of Energy Office of Science

National Nuclear Security Administration

MRC Career Development Award

Office of Science of the US Department of Science

Publisher

Oxford University Press (OUP)

Subject