Diversity, evolution, and classification of virophages uncovered through global metagenomics View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2019-12-10

AUTHORS

David Paez-Espino, Jinglie Zhou, Simon Roux, Stephen Nayfach, Georgios A. Pavlopoulos, Frederik Schulz, Katherine D. McMahon, David Walsh, Tanja Woyke, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Susannah G. Tringe, Nikos C. Kyrpides

ABSTRACT

BackgroundVirophages are small viruses with double-stranded DNA genomes that replicate along with giant viruses and co-infect eukaryotic cells. Due to the paucity of virophage reference genomes, a collective understanding of the global virophage diversity, distribution, and evolution is lacking.ResultsHere we screened a public collection of over 14,000 metagenomes using the virophage-specific major capsid protein (MCP) as “bait.” We identified 44,221 assembled virophage sequences, of which 328 represent high-quality (complete or near-complete) genomes from diverse habitats including the human gut, plant rhizosphere, and terrestrial subsurface. Comparative genomic analysis confirmed the presence of four core genes in a conserved block. We used these genes to establish a revised virophage classification including 27 clades with consistent genome length, gene content, and habitat distribution. Moreover, for eight high-quality virophage genomes, we computationally predicted putative eukaryotic virus hosts.ConclusionOverall, our approach has increased the number of known virophage genomes by 10-fold and revealed patterns of genome evolution and global virophage distribution. We anticipate that the expanded diversity presented here will provide the backbone for further virophage studies. More... »

PAGES

157

References to SciGraph publications

  • 2009-12-17. Eukaryotic large nucleo-cytoplasmic DNA viruses: Clusters of orthologous genes and reconstruction of viral genome evolution in VIROLOGY JOURNAL
  • 2013-05-23. Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies in VIROLOGY JOURNAL
  • 2016-06-13. CRISPR-Cas-like system in giant viruses: why MIMIVIRE is not likely to be an adaptive immune system in VIROLOGICA SINICA
  • <error retrieving object. in <ERROR RETRIEVING OBJECT
  • 2015-08-06. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy in GENOME BIOLOGY
  • 2018-11-30. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries in NATURE COMMUNICATIONS
  • 2015-10-07. A classification system for virophages and satellite viruses in ARCHIVES OF VIROLOGY
  • 2010-03-08. Prodigal: prokaryotic gene recognition and translation initiation site identification in BMC BIOINFORMATICS
  • 2014-12-22. Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution in NATURE REVIEWS MICROBIOLOGY
  • 2012-08-14. Hidden evolutionary complexity of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes in VIROLOGY JOURNAL
  • 2019-03-13. New insights from uncultivated genomes of the global human gut microbiome in NATURE
  • 2016-11-21. Probing the evolution, ecology and physiology of marine protists using transcriptomics in NATURE REVIEWS MICROBIOLOGY
  • 2015-04-25. A new family of hybrid virophages from an animal gut metagenome in BIOLOGY DIRECT
  • 2015-11-11. A novel group of diverse Polinton-like viruses discovered by metagenome analysis in BMC BIOLOGY
  • 2014-04-29. Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses in BIOLOGY DIRECT
  • 2008-08-06. The virophage as a unique parasite of the giant mimivirus in NATURE
  • 2016-08-17. Uncovering Earth’s virome in NATURE
  • 2009-12-15. BLAST+: architecture and applications in BMC BIOINFORMATICS
  • 2017-10-11. Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics in NATURE COMMUNICATIONS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s40168-019-0768-5

    DOI

    http://dx.doi.org/10.1186/s40168-019-0768-5

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1123265077

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/31823797


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0603", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Evolutionary Biology", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0605", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Microbiology", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "DNA, Viral", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Databases, Genetic", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genome, Viral", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Metagenome", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Metagenomics", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Phylogeny", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Virophages", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA", 
              "id": "http://www.grid.ac/institutes/grid.451309.a", 
              "name": [
                "Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Paez-Espino", 
            "givenName": "David", 
            "id": "sg:person.01154536554.21", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01154536554.21"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA", 
              "id": "http://www.grid.ac/institutes/grid.451309.a", 
              "name": [
                "Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Zhou", 
            "givenName": "Jinglie", 
            "id": "sg:person.014365643725.56", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014365643725.56"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA", 
              "id": "http://www.grid.ac/institutes/grid.451309.a", 
              "name": [
                "Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Roux", 
            "givenName": "Simon", 
            "id": "sg:person.01326704035.18", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01326704035.18"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA", 
              "id": "http://www.grid.ac/institutes/grid.451309.a", 
              "name": [
                "Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Nayfach", 
            "givenName": "Stephen", 
            "id": "sg:person.0656131776.20", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0656131776.20"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "BSRC \u201cAlexander Fleming\u201d, 34 Fleming Street, Vari, 16672, Athens, Greece", 
              "id": "http://www.grid.ac/institutes/grid.424165.0", 
              "name": [
                "Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA", 
                "BSRC \u201cAlexander Fleming\u201d, 34 Fleming Street, Vari, 16672, Athens, Greece"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Pavlopoulos", 
            "givenName": "Georgios A.", 
            "id": "sg:person.0764710024.67", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0764710024.67"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA", 
              "id": "http://www.grid.ac/institutes/grid.451309.a", 
              "name": [
                "Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Schulz", 
            "givenName": "Frederik", 
            "id": "sg:person.01044110420.28", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01044110420.28"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Departments of Civil and Environmental Engineering and Bacteriology, University of Wisconsin Madison, 1550 Linden Drive, 53726, Madison, WI, USA", 
              "id": "http://www.grid.ac/institutes/grid.14003.36", 
              "name": [
                "Departments of Civil and Environmental Engineering and Bacteriology, University of Wisconsin Madison, 1550 Linden Drive, 53726, Madison, WI, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "McMahon", 
            "givenName": "Katherine D.", 
            "id": "sg:person.01007375500.45", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01007375500.45"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, H4B 1R6, QC, Canada", 
              "id": "http://www.grid.ac/institutes/grid.410319.e", 
              "name": [
                "Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, H4B 1R6, QC, Canada"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Walsh", 
            "givenName": "David", 
            "id": "sg:person.0616627526.18", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0616627526.18"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA", 
              "id": "http://www.grid.ac/institutes/grid.451309.a", 
              "name": [
                "Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Woyke", 
            "givenName": "Tanja", 
            "id": "sg:person.01366555074.19", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01366555074.19"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA", 
              "id": "http://www.grid.ac/institutes/grid.451309.a", 
              "name": [
                "Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Ivanova", 
            "givenName": "Natalia N.", 
            "id": "sg:person.01263456163.47", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01263456163.47"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA", 
              "id": "http://www.grid.ac/institutes/grid.451309.a", 
              "name": [
                "Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Eloe-Fadrosh", 
            "givenName": "Emiley A.", 
            "id": "sg:person.0647037714.11", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0647037714.11"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA", 
              "id": "http://www.grid.ac/institutes/grid.451309.a", 
              "name": [
                "Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Tringe", 
            "givenName": "Susannah G.", 
            "id": "sg:person.01340300137.52", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01340300137.52"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA", 
              "id": "http://www.grid.ac/institutes/grid.451309.a", 
              "name": [
                "Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Kyrpides", 
            "givenName": "Nikos C.", 
            "id": "sg:person.01230412614.56", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01230412614.56"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1038/s41467-018-07641-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1110204842", 
              "https://doi.org/10.1038/s41467-018-07641-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s12250-016-3801-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1046785737", 
              "https://doi.org/10.1007/s12250-016-3801-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13062-015-0054-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011670754", 
              "https://doi.org/10.1186/s13062-015-0054-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41467-017-01086-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1092102050", 
              "https://doi.org/10.1038/s41467-017-01086-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13059-015-0721-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026229827", 
              "https://doi.org/10.1186/s13059-015-0721-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s12915-015-0207-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1021268326", 
              "https://doi.org/10.1186/s12915-015-0207-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1743-422x-10-158", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1045078320", 
              "https://doi.org/10.1186/1743-422x-10-158"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature07218", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1033417916", 
              "https://doi.org/10.1038/nature07218"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41586-019-1058-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1112734629", 
              "https://doi.org/10.1038/s41586-019-1058-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2105-11-119", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026423599", 
              "https://doi.org/10.1186/1471-2105-11-119"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrmicro3389", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007677483", 
              "https://doi.org/10.1038/nrmicro3389"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00705-015-2622-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1009286657", 
              "https://doi.org/10.1007/s00705-015-2622-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2105-10-421", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050579230", 
              "https://doi.org/10.1186/1471-2105-10-421"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrmicro.2016.160", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1009181718", 
              "https://doi.org/10.1038/nrmicro.2016.160"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1743-422x-6-223", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1025555386", 
              "https://doi.org/10.1186/1743-422x-6-223"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1743-422x-9-161", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1012749009", 
              "https://doi.org/10.1186/1743-422x-9-161"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature17146", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1033392531", 
              "https://doi.org/10.1038/nature17146"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1745-6150-9-6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015316770", 
              "https://doi.org/10.1186/1745-6150-9-6"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature19094", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1042916120", 
              "https://doi.org/10.1038/nature19094"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2019-12-10", 
        "datePublishedReg": "2019-12-10", 
        "description": "BackgroundVirophages are small viruses with double-stranded DNA genomes that replicate along with giant viruses and co-infect eukaryotic cells. Due to the paucity of virophage reference genomes, a collective understanding of the global virophage diversity, distribution, and evolution is lacking.ResultsHere we screened a public collection of over 14,000 metagenomes using the virophage-specific major capsid protein (MCP) as \u201cbait.\u201d We identified 44,221 assembled virophage sequences, of which 328 represent high-quality (complete or near-complete) genomes from diverse habitats including the human gut, plant rhizosphere, and terrestrial subsurface. Comparative genomic analysis confirmed the presence of four core genes in a conserved block. We used these genes to establish a revised virophage classification including 27 clades with consistent genome length, gene content, and habitat distribution. Moreover, for eight high-quality virophage genomes, we computationally predicted putative eukaryotic virus hosts.ConclusionOverall, our approach has increased the number of known virophage genomes by 10-fold and revealed patterns of genome evolution and global virophage distribution. We anticipate that the expanded diversity presented here will provide the backbone for further virophage studies.", 
        "genre": "article", 
        "id": "sg:pub.10.1186/s40168-019-0768-5", 
        "inLanguage": "en", 
        "isAccessibleForFree": true, 
        "isPartOf": [
          {
            "id": "sg:journal.1048878", 
            "issn": [
              "2049-2618"
            ], 
            "name": "Microbiome", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "7"
          }
        ], 
        "keywords": [
          "major capsid protein", 
          "virophage genomes", 
          "comparative genomic analysis", 
          "genome evolution", 
          "conserved block", 
          "diverse habitats", 
          "gene content", 
          "eukaryotic cells", 
          "plant rhizosphere", 
          "giant viruses", 
          "reference genome", 
          "habitat distribution", 
          "genomic analysis", 
          "genome length", 
          "DNA genome", 
          "core genes", 
          "terrestrial subsurface", 
          "virus hosts", 
          "genome", 
          "capsid protein", 
          "human gut", 
          "diversity", 
          "small virus", 
          "genes", 
          "virophages", 
          "clade", 
          "metagenomes", 
          "metagenomics", 
          "habitats", 
          "rhizosphere", 
          "evolution", 
          "bait", 
          "protein", 
          "public collections", 
          "virus", 
          "host", 
          "sequence", 
          "cells", 
          "ResultsHere", 
          "gut", 
          "distribution", 
          "patterns", 
          "understanding", 
          "collective understanding", 
          "backbone", 
          "presence", 
          "content", 
          "length", 
          "analysis", 
          "collection", 
          "number", 
          "paucity", 
          "study", 
          "classification", 
          "approach", 
          "block", 
          "ConclusionOverall", 
          "subsurface"
        ], 
        "name": "Diversity, evolution, and classification of virophages uncovered through global metagenomics", 
        "pagination": "157", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1123265077"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1186/s40168-019-0768-5"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "31823797"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1186/s40168-019-0768-5", 
          "https://app.dimensions.ai/details/publication/pub.1123265077"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-05-20T07:35", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20220519/entities/gbq_results/article/article_815.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1186/s40168-019-0768-5"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/s40168-019-0768-5'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s40168-019-0768-5'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s40168-019-0768-5'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s40168-019-0768-5'


     

    This table displays all metadata directly associated to this object as RDF triples.

    325 TRIPLES      22 PREDICATES      112 URIs      83 LITERALS      14 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1186/s40168-019-0768-5 schema:about N03b01b3d65dd40edae9bf3b7574ab983
    2 N20b6634b2e7246a8bb4c1be30827ef7d
    3 N3dad6cb5d9ee490598732b6fca369073
    4 N4b74e057ee764cb8bd96837d56bd10b7
    5 N9d894ca6d27842a99a25c24082dbf154
    6 Na9717e2231634215bf0ddf7b8e0f3f42
    7 Neb0f0f1581d044d3afe7b34a1e139e86
    8 anzsrc-for:06
    9 anzsrc-for:0603
    10 anzsrc-for:0604
    11 anzsrc-for:0605
    12 schema:author N724038f309374e89a8f3240e80d968d9
    13 schema:citation sg:pub.10.1007/s00705-015-2622-9
    14 sg:pub.10.1007/s12250-016-3801-x
    15 sg:pub.10.1038/nature07218
    16 sg:pub.10.1038/nature17146
    17 sg:pub.10.1038/nature19094
    18 sg:pub.10.1038/nrmicro.2016.160
    19 sg:pub.10.1038/nrmicro3389
    20 sg:pub.10.1038/s41467-017-01086-2
    21 sg:pub.10.1038/s41467-018-07641-9
    22 sg:pub.10.1038/s41586-019-1058-x
    23 sg:pub.10.1186/1471-2105-10-421
    24 sg:pub.10.1186/1471-2105-11-119
    25 sg:pub.10.1186/1743-422x-10-158
    26 sg:pub.10.1186/1743-422x-6-223
    27 sg:pub.10.1186/1743-422x-9-161
    28 sg:pub.10.1186/1745-6150-9-6
    29 sg:pub.10.1186/s12915-015-0207-4
    30 sg:pub.10.1186/s13059-015-0721-2
    31 sg:pub.10.1186/s13062-015-0054-9
    32 schema:datePublished 2019-12-10
    33 schema:datePublishedReg 2019-12-10
    34 schema:description BackgroundVirophages are small viruses with double-stranded DNA genomes that replicate along with giant viruses and co-infect eukaryotic cells. Due to the paucity of virophage reference genomes, a collective understanding of the global virophage diversity, distribution, and evolution is lacking.ResultsHere we screened a public collection of over 14,000 metagenomes using the virophage-specific major capsid protein (MCP) as “bait.” We identified 44,221 assembled virophage sequences, of which 328 represent high-quality (complete or near-complete) genomes from diverse habitats including the human gut, plant rhizosphere, and terrestrial subsurface. Comparative genomic analysis confirmed the presence of four core genes in a conserved block. We used these genes to establish a revised virophage classification including 27 clades with consistent genome length, gene content, and habitat distribution. Moreover, for eight high-quality virophage genomes, we computationally predicted putative eukaryotic virus hosts.ConclusionOverall, our approach has increased the number of known virophage genomes by 10-fold and revealed patterns of genome evolution and global virophage distribution. We anticipate that the expanded diversity presented here will provide the backbone for further virophage studies.
    35 schema:genre article
    36 schema:inLanguage en
    37 schema:isAccessibleForFree true
    38 schema:isPartOf N461c268aacad49769e04923f364a04b8
    39 Ndc8ab57002874c5bb8b00791cc272009
    40 sg:journal.1048878
    41 schema:keywords ConclusionOverall
    42 DNA genome
    43 ResultsHere
    44 analysis
    45 approach
    46 backbone
    47 bait
    48 block
    49 capsid protein
    50 cells
    51 clade
    52 classification
    53 collection
    54 collective understanding
    55 comparative genomic analysis
    56 conserved block
    57 content
    58 core genes
    59 distribution
    60 diverse habitats
    61 diversity
    62 eukaryotic cells
    63 evolution
    64 gene content
    65 genes
    66 genome
    67 genome evolution
    68 genome length
    69 genomic analysis
    70 giant viruses
    71 gut
    72 habitat distribution
    73 habitats
    74 host
    75 human gut
    76 length
    77 major capsid protein
    78 metagenomes
    79 metagenomics
    80 number
    81 patterns
    82 paucity
    83 plant rhizosphere
    84 presence
    85 protein
    86 public collections
    87 reference genome
    88 rhizosphere
    89 sequence
    90 small virus
    91 study
    92 subsurface
    93 terrestrial subsurface
    94 understanding
    95 virophage genomes
    96 virophages
    97 virus
    98 virus hosts
    99 schema:name Diversity, evolution, and classification of virophages uncovered through global metagenomics
    100 schema:pagination 157
    101 schema:productId N4fee3920211c49a89c39eb4ee256d0ff
    102 N67b34071886b492d89960d00c3bad0ef
    103 N8e3bb54bad20473f8e06efc3a10d6ca4
    104 schema:sameAs https://app.dimensions.ai/details/publication/pub.1123265077
    105 https://doi.org/10.1186/s40168-019-0768-5
    106 schema:sdDatePublished 2022-05-20T07:35
    107 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    108 schema:sdPublisher N3c4fd033be2e46bbb2619442931db0ad
    109 schema:url https://doi.org/10.1186/s40168-019-0768-5
    110 sgo:license sg:explorer/license/
    111 sgo:sdDataset articles
    112 rdf:type schema:ScholarlyArticle
    113 N03b01b3d65dd40edae9bf3b7574ab983 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    114 schema:name Genome, Viral
    115 rdf:type schema:DefinedTerm
    116 N09e76cc5015d4dcf8bbb21fc0b92d92d rdf:first sg:person.01326704035.18
    117 rdf:rest N6f9c29af2040480b83a484d03fbf68f5
    118 N14834831252d452990241d7091d65cd2 rdf:first sg:person.01230412614.56
    119 rdf:rest rdf:nil
    120 N20b6634b2e7246a8bb4c1be30827ef7d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    121 schema:name DNA, Viral
    122 rdf:type schema:DefinedTerm
    123 N25f1c57a955e425bbf10863dbdf00649 rdf:first sg:person.01366555074.19
    124 rdf:rest N7b4def9c3ea245c289e0916b21999d06
    125 N3c4fd033be2e46bbb2619442931db0ad schema:name Springer Nature - SN SciGraph project
    126 rdf:type schema:Organization
    127 N3dad6cb5d9ee490598732b6fca369073 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    128 schema:name Virophages
    129 rdf:type schema:DefinedTerm
    130 N427028f1d510453c9ed8a13543e364ff rdf:first sg:person.0764710024.67
    131 rdf:rest Ndabb5dd38c0c4ee5b5934bfae5fe9549
    132 N461c268aacad49769e04923f364a04b8 schema:volumeNumber 7
    133 rdf:type schema:PublicationVolume
    134 N4b74e057ee764cb8bd96837d56bd10b7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    135 schema:name Metagenomics
    136 rdf:type schema:DefinedTerm
    137 N4fee3920211c49a89c39eb4ee256d0ff schema:name dimensions_id
    138 schema:value pub.1123265077
    139 rdf:type schema:PropertyValue
    140 N5abcff21160b4d4ca535b9fbebb5cfd6 rdf:first sg:person.0647037714.11
    141 rdf:rest Nd30d035cda4047589d0276b83874e894
    142 N67b34071886b492d89960d00c3bad0ef schema:name pubmed_id
    143 schema:value 31823797
    144 rdf:type schema:PropertyValue
    145 N6f9c29af2040480b83a484d03fbf68f5 rdf:first sg:person.0656131776.20
    146 rdf:rest N427028f1d510453c9ed8a13543e364ff
    147 N724038f309374e89a8f3240e80d968d9 rdf:first sg:person.01154536554.21
    148 rdf:rest Nf01090da7cf84bd584ea05571771051d
    149 N7b4def9c3ea245c289e0916b21999d06 rdf:first sg:person.01263456163.47
    150 rdf:rest N5abcff21160b4d4ca535b9fbebb5cfd6
    151 N8e3bb54bad20473f8e06efc3a10d6ca4 schema:name doi
    152 schema:value 10.1186/s40168-019-0768-5
    153 rdf:type schema:PropertyValue
    154 N9d894ca6d27842a99a25c24082dbf154 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    155 schema:name Phylogeny
    156 rdf:type schema:DefinedTerm
    157 Na9717e2231634215bf0ddf7b8e0f3f42 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    158 schema:name Metagenome
    159 rdf:type schema:DefinedTerm
    160 Naba6e70d4f124b509cb865661cf703d9 rdf:first sg:person.0616627526.18
    161 rdf:rest N25f1c57a955e425bbf10863dbdf00649
    162 Nbffeb4f6251e432ebdcc85d4d72f2944 rdf:first sg:person.01007375500.45
    163 rdf:rest Naba6e70d4f124b509cb865661cf703d9
    164 Nd30d035cda4047589d0276b83874e894 rdf:first sg:person.01340300137.52
    165 rdf:rest N14834831252d452990241d7091d65cd2
    166 Ndabb5dd38c0c4ee5b5934bfae5fe9549 rdf:first sg:person.01044110420.28
    167 rdf:rest Nbffeb4f6251e432ebdcc85d4d72f2944
    168 Ndc8ab57002874c5bb8b00791cc272009 schema:issueNumber 1
    169 rdf:type schema:PublicationIssue
    170 Neb0f0f1581d044d3afe7b34a1e139e86 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    171 schema:name Databases, Genetic
    172 rdf:type schema:DefinedTerm
    173 Nf01090da7cf84bd584ea05571771051d rdf:first sg:person.014365643725.56
    174 rdf:rest N09e76cc5015d4dcf8bbb21fc0b92d92d
    175 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    176 schema:name Biological Sciences
    177 rdf:type schema:DefinedTerm
    178 anzsrc-for:0603 schema:inDefinedTermSet anzsrc-for:
    179 schema:name Evolutionary Biology
    180 rdf:type schema:DefinedTerm
    181 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    182 schema:name Genetics
    183 rdf:type schema:DefinedTerm
    184 anzsrc-for:0605 schema:inDefinedTermSet anzsrc-for:
    185 schema:name Microbiology
    186 rdf:type schema:DefinedTerm
    187 sg:journal.1048878 schema:issn 2049-2618
    188 schema:name Microbiome
    189 schema:publisher Springer Nature
    190 rdf:type schema:Periodical
    191 sg:person.01007375500.45 schema:affiliation grid-institutes:grid.14003.36
    192 schema:familyName McMahon
    193 schema:givenName Katherine D.
    194 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01007375500.45
    195 rdf:type schema:Person
    196 sg:person.01044110420.28 schema:affiliation grid-institutes:grid.451309.a
    197 schema:familyName Schulz
    198 schema:givenName Frederik
    199 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01044110420.28
    200 rdf:type schema:Person
    201 sg:person.01154536554.21 schema:affiliation grid-institutes:grid.451309.a
    202 schema:familyName Paez-Espino
    203 schema:givenName David
    204 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01154536554.21
    205 rdf:type schema:Person
    206 sg:person.01230412614.56 schema:affiliation grid-institutes:grid.451309.a
    207 schema:familyName Kyrpides
    208 schema:givenName Nikos C.
    209 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01230412614.56
    210 rdf:type schema:Person
    211 sg:person.01263456163.47 schema:affiliation grid-institutes:grid.451309.a
    212 schema:familyName Ivanova
    213 schema:givenName Natalia N.
    214 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01263456163.47
    215 rdf:type schema:Person
    216 sg:person.01326704035.18 schema:affiliation grid-institutes:grid.451309.a
    217 schema:familyName Roux
    218 schema:givenName Simon
    219 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01326704035.18
    220 rdf:type schema:Person
    221 sg:person.01340300137.52 schema:affiliation grid-institutes:grid.451309.a
    222 schema:familyName Tringe
    223 schema:givenName Susannah G.
    224 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01340300137.52
    225 rdf:type schema:Person
    226 sg:person.01366555074.19 schema:affiliation grid-institutes:grid.451309.a
    227 schema:familyName Woyke
    228 schema:givenName Tanja
    229 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01366555074.19
    230 rdf:type schema:Person
    231 sg:person.014365643725.56 schema:affiliation grid-institutes:grid.451309.a
    232 schema:familyName Zhou
    233 schema:givenName Jinglie
    234 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014365643725.56
    235 rdf:type schema:Person
    236 sg:person.0616627526.18 schema:affiliation grid-institutes:grid.410319.e
    237 schema:familyName Walsh
    238 schema:givenName David
    239 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0616627526.18
    240 rdf:type schema:Person
    241 sg:person.0647037714.11 schema:affiliation grid-institutes:grid.451309.a
    242 schema:familyName Eloe-Fadrosh
    243 schema:givenName Emiley A.
    244 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0647037714.11
    245 rdf:type schema:Person
    246 sg:person.0656131776.20 schema:affiliation grid-institutes:grid.451309.a
    247 schema:familyName Nayfach
    248 schema:givenName Stephen
    249 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0656131776.20
    250 rdf:type schema:Person
    251 sg:person.0764710024.67 schema:affiliation grid-institutes:grid.424165.0
    252 schema:familyName Pavlopoulos
    253 schema:givenName Georgios A.
    254 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0764710024.67
    255 rdf:type schema:Person
    256 sg:pub.10.1007/s00705-015-2622-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009286657
    257 https://doi.org/10.1007/s00705-015-2622-9
    258 rdf:type schema:CreativeWork
    259 sg:pub.10.1007/s12250-016-3801-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1046785737
    260 https://doi.org/10.1007/s12250-016-3801-x
    261 rdf:type schema:CreativeWork
    262 sg:pub.10.1038/nature07218 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033417916
    263 https://doi.org/10.1038/nature07218
    264 rdf:type schema:CreativeWork
    265 sg:pub.10.1038/nature17146 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033392531
    266 https://doi.org/10.1038/nature17146
    267 rdf:type schema:CreativeWork
    268 sg:pub.10.1038/nature19094 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042916120
    269 https://doi.org/10.1038/nature19094
    270 rdf:type schema:CreativeWork
    271 sg:pub.10.1038/nrmicro.2016.160 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009181718
    272 https://doi.org/10.1038/nrmicro.2016.160
    273 rdf:type schema:CreativeWork
    274 sg:pub.10.1038/nrmicro3389 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007677483
    275 https://doi.org/10.1038/nrmicro3389
    276 rdf:type schema:CreativeWork
    277 sg:pub.10.1038/s41467-017-01086-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1092102050
    278 https://doi.org/10.1038/s41467-017-01086-2
    279 rdf:type schema:CreativeWork
    280 sg:pub.10.1038/s41467-018-07641-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1110204842
    281 https://doi.org/10.1038/s41467-018-07641-9
    282 rdf:type schema:CreativeWork
    283 sg:pub.10.1038/s41586-019-1058-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1112734629
    284 https://doi.org/10.1038/s41586-019-1058-x
    285 rdf:type schema:CreativeWork
    286 sg:pub.10.1186/1471-2105-10-421 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050579230
    287 https://doi.org/10.1186/1471-2105-10-421
    288 rdf:type schema:CreativeWork
    289 sg:pub.10.1186/1471-2105-11-119 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026423599
    290 https://doi.org/10.1186/1471-2105-11-119
    291 rdf:type schema:CreativeWork
    292 sg:pub.10.1186/1743-422x-10-158 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045078320
    293 https://doi.org/10.1186/1743-422x-10-158
    294 rdf:type schema:CreativeWork
    295 sg:pub.10.1186/1743-422x-6-223 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025555386
    296 https://doi.org/10.1186/1743-422x-6-223
    297 rdf:type schema:CreativeWork
    298 sg:pub.10.1186/1743-422x-9-161 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012749009
    299 https://doi.org/10.1186/1743-422x-9-161
    300 rdf:type schema:CreativeWork
    301 sg:pub.10.1186/1745-6150-9-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015316770
    302 https://doi.org/10.1186/1745-6150-9-6
    303 rdf:type schema:CreativeWork
    304 sg:pub.10.1186/s12915-015-0207-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021268326
    305 https://doi.org/10.1186/s12915-015-0207-4
    306 rdf:type schema:CreativeWork
    307 sg:pub.10.1186/s13059-015-0721-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026229827
    308 https://doi.org/10.1186/s13059-015-0721-2
    309 rdf:type schema:CreativeWork
    310 sg:pub.10.1186/s13062-015-0054-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011670754
    311 https://doi.org/10.1186/s13062-015-0054-9
    312 rdf:type schema:CreativeWork
    313 grid-institutes:grid.14003.36 schema:alternateName Departments of Civil and Environmental Engineering and Bacteriology, University of Wisconsin Madison, 1550 Linden Drive, 53726, Madison, WI, USA
    314 schema:name Departments of Civil and Environmental Engineering and Bacteriology, University of Wisconsin Madison, 1550 Linden Drive, 53726, Madison, WI, USA
    315 rdf:type schema:Organization
    316 grid-institutes:grid.410319.e schema:alternateName Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, H4B 1R6, QC, Canada
    317 schema:name Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, H4B 1R6, QC, Canada
    318 rdf:type schema:Organization
    319 grid-institutes:grid.424165.0 schema:alternateName BSRC “Alexander Fleming”, 34 Fleming Street, Vari, 16672, Athens, Greece
    320 schema:name BSRC “Alexander Fleming”, 34 Fleming Street, Vari, 16672, Athens, Greece
    321 Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA
    322 rdf:type schema:Organization
    323 grid-institutes:grid.451309.a schema:alternateName Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA
    324 schema:name Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., 94598, Walnut Creek, USA
    325 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...