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Title: IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

Journal Article · · Nucleic Acids Research
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  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center
  3. The Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology and Civil Environmental and Geodetic Engineering
  4. Clemson Univ., SC (United States). Dept. of Biological Sciences
  5. Univ. of Maryland Center for Environmental Sciences, Baltimore, MD (United States). Inst. of Marine and Environmental Technology
  6. Univ. of Wisconsin, Madison, WI (United States). Dept. of Bacteriology, Dept. of Civil and Environmental Engineering
  7. Univ. of British Columbia, Vancouver, BC (Canada). Dept. of Microbiology and Immunology, Genome Science, Technology and Program in Bioinformatics, Peter Wall Inst. for Advanced Studies, ECOSCOPE Training Program
  8. Univ. of Michigan, Ann Arbor, MI (United States). Dept. of Ecology and Evolutionary Biology
  9. Univ. of New South Wales, Sydney, NSW (Australia). School of biotechnology and Biomolecular Sciences
  10. Univ. of Calgary, AB (Canada). Dept. of Biological Sciences
  11. Univ. of Hamburg (Germany). Dept. of Microbiology and Biotechnology
  12. Univ. of Auckland (New Zealand). School of Biological Sciences
  13. Agricultural Research, Education and Extension Organization, Karaj (Iran). Dept. of Systems Biology
  14. Shell International Exploration and Production Inc., Houston, TX (United States)
  15. Univ. of Sao Paulo (Brazil). Dept. of Biochemistry,
  16. Norwegian Univ. of Life Sciences, As (Norway+. Dept. of Chemistry, Biotechnology, and Food Science
  17. Univ. of Illinois, Urbana-Champaign, IL (United States). Dept. of Civil and Environmental Engineering

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from > 6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparingwith external sequences, thus serving as an essential resource in the viral genomics community.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1379663
Journal Information:
Nucleic Acids Research, Vol. 45, Issue D1; ISSN 0305-1048
Publisher:
Oxford University PressCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 128 works
Citation information provided by
Web of Science

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Minimum Information about an Uncultivated Virus Genome (MIUViG) journal December 2018
Recruitment of Reverse Transcriptase-Cas1 Fusion Proteins by Type VI-A CRISPR-Cas Systems journal September 2019
Therapeutic Potential of a New Jumbo Phage That Infects Vibrio coralliilyticus, a Widespread Coral Pathogen journal October 2018
Diversity patterns of bacteriophages infecting Aggregatibacter and Haemophilus species across clades and niches journal June 2019
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes journal October 2018
Uncovering a hidden diversity: optimized protocols for the extraction of dsDNA bacteriophages from soil text January 2020
Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes journal October 2018
Murine colitis reveals a disease-associated bacteriophage community journal July 2018
Novel haloarchaeal viruses from Lake Retba infecting Haloferax and Halorubrum species journal April 2019
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Oral bacteriophages are maintained at high levels for months in individuals but infrequently transmitted between mothers and infants posted_content May 2019
Integrated mobile genetic elements in Thaumarchaeota journal March 2019
MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins journal August 2018
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes journal October 2018
“French Phage Network”—Third Meeting Report journal March 2018
Archaea dominate oxic subseafloor communities over multimillion-year time scales journal June 2019
CRISPR Spacers Indicate Preferential Matching of Specific Virioplankton Genes journal March 2019
Clades of huge phages from across Earth’s ecosystems journal February 2020
Bioinformatic evidence of widespread priming in type I and II CRISPR-Cas systems journal June 2018
vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria journal January 2017
Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber journal September 2020
A viral reckoning: viruses emerge as essential manipulators of global ecosystems: Crystal ball journal October 2018
Correction: Zablocki, O.; et al. Diversity of dsDNA Viruses in a South African Hot Spring Assessed by Metagenomics and Microscopy. Viruses 2017, 9, 348 journal January 2018
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Halobacterium salinarum virus ChaoS9, a Novel Halovirus Related to PhiH1 and PhiCh1 journal March 2019
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Diversity, evolution, and classification of virophages uncovered through global metagenomics journal December 2019
Studying the gut virome in the metagenomic era: challenges and perspectives journal October 2019
Bioinformatic evidence of widespread priming in Type I and II CRISPR-Cas systems text January 2018
Communities of Phytoplankton Viruses across the Transition Zone of the St. Lawrence Estuary journal November 2018
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the Era of the Human Microbiome: Persistent Pathogens Drive Chronic Symptoms by Interfering With Host Metabolism, Gene Expression, and Immunity journal December 2018
Bioinformatics Identification of Anti-CRISPR Loci by Using Homology, Guilt-by-Association, and CRISPR Self-Targeting Spacer Approaches journal September 2019
Genome‐resolved viral and cellular metagenomes revealed potential key virus‐host interactions in a deep freshwater lake journal September 2019
Bioinformatic evidence of widespread priming in type I and II CRISPR-Cas systems text January 2020
Origin of viruses: primordial replicators recruiting capsids from hosts journal May 2019
Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data journal July 2017
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Halobacterium salinarum virus ChaoS9, a Novel Halovirus Related to PhiH1 and PhiCh1 journal March 2019
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Investigation of recombination-intense viral groups and their genes in the Earth’s virome journal July 2018
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