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 comparing with external sequences, thus serving as an essential resource in the viral genomics community.
authors: Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors: David
authors: D
authors: Paez-Espino
authors: Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
authors: I-Min A
authors: IA
authors: Chen
authors: Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
authors: Krishna
authors: K
authors: Palaniappan
authors: Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
authors: Anna
authors: A
authors: Ratner
authors: Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
authors: Ken
authors: K
authors: Chu
authors: Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
authors: Ernest
authors: E
authors: Szeto
authors: Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
authors: Manoj
authors: M
authors: Pillay
authors: Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
authors: Jinghua
authors: J
authors: Huang
authors: Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
authors: Victor M
authors: VM
authors: Markowitz
authors: Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors: Torben
authors: T
authors: Nielsen
authors: Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors: Marcel
authors: M
authors: Huntemann
authors: Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors: T B
authors: TB
authors: K Reddy
authors: Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors: Georgios A
authors: GA
authors: Pavlopoulos
authors: Departments of Microbiology and Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH 43210, USA.
authors: Matthew B
authors: MB
authors: Sullivan
authors: Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA.
authors: Barbara J
authors: BJ
authors: Campbell
authors: Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA.
authors: Feng
authors: F
authors: Chen
authors: Department of Civil and Environmental Engineering, Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA.
authors: Katherine
authors: K
authors: McMahon
authors: Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.|Genome Science, Technology, and Program in Bioinformatics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.|Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, BC V6T 1Z2, Canada.|ECOSCOPE Training Program, University of British Columbia, Vancouver, BC V6T 0A1, Canada.
authors: Steve J
authors: SJ
authors: Hallam
authors: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA.
authors: Vincent
authors: V
authors: Denef
authors: School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
authors: Ricardo
authors: R
authors: Cavicchioli
authors: Department of Biological Sciences, University of Calgary, Calgary, AB T2N 4V8, Canada.
authors: Sean M
authors: SM
authors: Caffrey
authors: Biocenter Klein Flottbek, Department of Microbiology and Biotechnology, University of Hamburg, Hamburg 22609, Germany.
authors: Wolfgang R
authors: WR
authors: Streit
authors: School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
authors: John
authors: J
authors: Webster
authors: School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand.
authors: Kim M
authors: KM
authors: Handley
authors: Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj 31535-1897, Iran.
authors: Ghasem H
authors: GH
authors: Salekdeh
authors: Shell International Exploration and Production Inc., Houston, TX 77082, USA.
authors: Nicolas
authors: N
authors: Tsesmetzis
authors: Department of Biochemistry, Institute of Chemistry, Universidade de Sao Paulo, SP 05508-000, Brazil.
authors: Joao C
authors: JC
authors: Setubal
authors: Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås 1432, Norway.
authors: Phillip B
authors: PB
authors: Pope
authors: Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors: Wen-Tso
authors: WT
authors: Liu
authors: Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors: Adam R
authors: AR
authors: Rivers
authors: Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors: Natalia N
authors: NN
authors: Ivanova
authors: Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA nckyrpides@lbl.gov.
authors: Nikos C
authors: NC
authors: Kyrpides
mesh_terms: D004267:DNA Viruses / Q000235:genetics*; D030541:Databases, Genetic; D004783:Environmental Microbiology; D016679:Genome, Viral; D023281:Genomics / Q000379:methods*; D054884:Host-Pathogen Interactions; D054892:Metagenome; D056186:Metagenomics / Q000379:methods*; D012190:Retroviridae / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012984:Software