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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.
Affiliation
  • Camargo AP; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Call L; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Roux S; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Nayfach S; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Huntemann M; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Palaniappan K; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Ratner A; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Chu K; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Mukherjeep S; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Reddy TBK; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Chen IA; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Ivanova NN; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Eloe-Fadrosh EA; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Woyke T; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Baltrus DA; School of Plant Sciences, University of Arizona, Tucson AZ, USA.
  • Castañeda-Barba S; School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson AZ, USA.
  • de la Cruz F; Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA.
  • Funnell BE; Instituto de Biomedicina y Biotecnología de Cantabria (Consejo Superior de Investigaciones Científicas - Universidad de Cantabria), Cantabria, Spain.
  • Hall JPJ; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada.
  • Mukhopadhyay A; Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK.
  • Rocha EPC; Joint BioEnergy Institute, Emeryville, CA 94608, USA.
  • Stalder T; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Top E; Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France.
  • Kyrpides NC; Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA.
Nucleic Acids Res ; 52(D1): D164-D173, 2024 Jan 05.
Article in En | MEDLINE | ID: mdl-37930866
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.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Metagenome / Microbiota Limits: Humans Language: En Journal: Nucleic Acids Res Year: 2024 Type: Article Affiliation country: United States
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Metagenome / Microbiota Limits: Humans Language: En Journal: Nucleic Acids Res Year: 2024 Type: Article Affiliation country: United States