@article{10902/30885,
year = {2023},
url = {https://hdl.handle.net/10902/30885},
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.},
organization = {Funding: U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337); National Energy Research Scientific Computing Center (NERSC) (https://ror.org/05v3mvq14), is supported by the DOE Office of Science User Facilities [DE-AC02-05CH11231]; Computational resources were partly provided by the Exascale Computing Project [17-SC-20-SC]; a collaborative effort of the U.S. Department of Energy Office of Science and the National Nuclear Security Administration; J.P.J.H. is supported by an MRC Career Development Award [MR/W02666X/1]. Funding for open access charge: Office of Science of the US Department of Science.},
publisher = {Oxford University Press},
publisher = {Nucleic Acids Research, 2023, 1-10},
title = {IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata},
author = {Camargo, Antonio Pedro and Call, Lee and Roux, Simon and Nayfach, Stephen and Huntemann, Marcel and Palaniappan, Krishnaveni and Ratner, Anna and Chu, Ken and Mukherjeep, Supratim and Reddy, T. B. K. and Chen, I-Min A. and Ivanova, Natalia N. and Eloe-Fadrosh, Emiley A. and Woyke, Tanja and Baltrus, David A. and Castañeda-Barba, Salvador and Cruz Calahorra, Fernando de la and Funnell, Barbara E. and Hall, James P. J. and Mukhopadhyay, Aindrila},
}