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

Abstract

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.

Authors:
 [1];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [1];  [1];  [1];  [1];  [3];  [4];  [5];  [6];  [7];  [8];  [9] more »;  [10];  [11];  [9];  [12];  [13];  [14];  [15];  [16];  [17];  [1];  [1];  [1] « less
  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
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1379663
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 45; Journal Issue: D1; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; metadata; dna viruses; foreign medical graduates; viral genome; geographic area; retroviridae; viruses; host (organism)

Citation Formats

Paez-Espino, David, Chen, I. -Min A., Palaniappan, Krishna, Ratner, Anna, Chu, Ken, Szeto, Ernest, Pillay, Manoj, Huang, Jinghua, Markowitz, Victor M., Nielsen, Torben, Huntemann, Marcel, K. Reddy, T. B., Pavlopoulos, Georgios A., Sullivan, Matthew B., Campbell, Barbara J., Chen, Feng, McMahon, Katherine, Hallam, Steve J., Denef, Vincent, Cavicchioli, Ricardo, Caffrey, Sean M., Streit, Wolfgang R., Webster, John, Handley, Kim M., Salekdeh, Ghasem H., Tsesmetzis, Nicolas, Setubal, Joao C., Pope, Phillip B., Liu, Wen-Tso, Rivers, Adam R., Ivanova, Natalia N., and Kyrpides, Nikos C. IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. United States: N. p., 2016. Web. doi:10.1093/nar/gkw1030.
Paez-Espino, David, Chen, I. -Min A., Palaniappan, Krishna, Ratner, Anna, Chu, Ken, Szeto, Ernest, Pillay, Manoj, Huang, Jinghua, Markowitz, Victor M., Nielsen, Torben, Huntemann, Marcel, K. Reddy, T. B., Pavlopoulos, Georgios A., Sullivan, Matthew B., Campbell, Barbara J., Chen, Feng, McMahon, Katherine, Hallam, Steve J., Denef, Vincent, Cavicchioli, Ricardo, Caffrey, Sean M., Streit, Wolfgang R., Webster, John, Handley, Kim M., Salekdeh, Ghasem H., Tsesmetzis, Nicolas, Setubal, Joao C., Pope, Phillip B., Liu, Wen-Tso, Rivers, Adam R., Ivanova, Natalia N., & Kyrpides, Nikos C. IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. United States. https://doi.org/10.1093/nar/gkw1030
Paez-Espino, David, Chen, I. -Min A., Palaniappan, Krishna, Ratner, Anna, Chu, Ken, Szeto, Ernest, Pillay, Manoj, Huang, Jinghua, Markowitz, Victor M., Nielsen, Torben, Huntemann, Marcel, K. Reddy, T. B., Pavlopoulos, Georgios A., Sullivan, Matthew B., Campbell, Barbara J., Chen, Feng, McMahon, Katherine, Hallam, Steve J., Denef, Vincent, Cavicchioli, Ricardo, Caffrey, Sean M., Streit, Wolfgang R., Webster, John, Handley, Kim M., Salekdeh, Ghasem H., Tsesmetzis, Nicolas, Setubal, Joao C., Pope, Phillip B., Liu, Wen-Tso, Rivers, Adam R., Ivanova, Natalia N., and Kyrpides, Nikos C. Sun . "IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses". United States. https://doi.org/10.1093/nar/gkw1030. https://www.osti.gov/servlets/purl/1379663.
@article{osti_1379663,
title = {IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses},
author = {Paez-Espino, David and Chen, I. -Min A. and Palaniappan, Krishna and Ratner, Anna and Chu, Ken and Szeto, Ernest and Pillay, Manoj and Huang, Jinghua and Markowitz, Victor M. and Nielsen, Torben and Huntemann, Marcel and K. Reddy, T. B. and Pavlopoulos, Georgios A. and Sullivan, Matthew B. and Campbell, Barbara J. and Chen, Feng and McMahon, Katherine and Hallam, Steve J. and Denef, Vincent and Cavicchioli, Ricardo and Caffrey, Sean M. and Streit, Wolfgang R. and Webster, John and Handley, Kim M. and Salekdeh, Ghasem H. and Tsesmetzis, Nicolas and Setubal, Joao C. and Pope, Phillip B. and Liu, Wen-Tso and Rivers, Adam R. and Ivanova, Natalia N. and Kyrpides, Nikos C.},
abstractNote = {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.},
doi = {10.1093/nar/gkw1030},
journal = {Nucleic Acids Research},
number = D1,
volume = 45,
place = {United States},
year = {2016},
month = {10}
}

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Archaea dominate oxic subseafloor communities over multimillion-year time scales
journal, June 2019

  • Vuillemin, Aurèle; Wankel, Scott D.; Coskun, Ömer K.
  • Science Advances, Vol. 5, Issue 6
  • DOI: 10.1126/sciadv.aaw4108

Host-hijacking and planktonic piracy: how phages command the microbial high seas
journal, February 2019

  • Warwick-Dugdale, Joanna; Buchholz, Holger H.; Allen, Michael J.
  • Virology Journal, Vol. 16, Issue 1
  • DOI: 10.1186/s12985-019-1120-1

Minimum information about an uncultivated virus genome (MIUVIG)
text, January 2019


Uncovering a hidden diversity: optimized protocols for the extraction of dsDNA bacteriophages from soil
text, January 2020


Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber
journal, September 2020


Bioinformatic evidence of widespread priming in type I and II CRISPR-Cas systems
text, January 2020


Bioinformatic evidence of widespread priming in Type I and II CRISPR-Cas systems
text, January 2018


Bioinformatic evidence of widespread priming in type I and II CRISPR-Cas systems
journal, June 2018