Horizontal gene transfer in Histophilus somni and its role in the evolution of pathogenic strain 2336, as determined by comparative ... View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2011-11-23

AUTHORS

Shivakumara Siddaramappa, Jean F Challacombe, Alison J Duncan, Allison F Gillaspy, Matthew Carson, Jenny Gipson, Joshua Orvis, Jeremy Zaitshik, Gentry Barnes, David Bruce, Olga Chertkov, J Chris Detter, Cliff S Han, Roxanne Tapia, Linda S Thompson, David W Dyer, Thomas J Inzana

ABSTRACT

BackgroundPneumonia and myocarditis are the most commonly reported diseases due to Histophilus somni, an opportunistic pathogen of the reproductive and respiratory tracts of cattle. Thus far only a few genes involved in metabolic and virulence functions have been identified and characterized in H. somni using traditional methods. Analyses of the genome sequences of several Pasteurellaceae species have provided insights into their biology and evolution. In view of the economic and ecological importance of H. somni, the genome sequence of pneumonia strain 2336 has been determined and compared to that of commensal strain 129Pt and other members of the Pasteurellaceae.ResultsThe chromosome of strain 2336 (2,263,857 bp) contained 1,980 protein coding genes, whereas the chromosome of strain 129Pt (2,007,700 bp) contained only 1,792 protein coding genes. Although the chromosomes of the two strains differ in size, their average GC content, gene density (total number of genes predicted on the chromosome), and percentage of sequence (number of genes) that encodes proteins were similar. The chromosomes of these strains also contained a number of discrete prophage regions and genomic islands. One of the genomic islands in strain 2336 contained genes putatively involved in copper, zinc, and tetracycline resistance. Using the genome sequence data and comparative analyses with other members of the Pasteurellaceae, several H. somni genes that may encode proteins involved in virulence (e.g., filamentous haemaggutinins, adhesins, and polysaccharide biosynthesis/modification enzymes) were identified. The two strains contained a total of 17 ORFs that encode putative glycosyltransferases and some of these ORFs had characteristic simple sequence repeats within them. Most of the genes/loci common to both the strains were located in different regions of the two chromosomes and occurred in opposite orientations, indicating genome rearrangement since their divergence from a common ancestor.ConclusionsSince the genome of strain 129Pt was ~256,000 bp smaller than that of strain 2336, these genomes provide yet another paradigm for studying evolutionary gene loss and/or gain in regard to virulence repertoire and pathogenic ability. Analyses of the complete genome sequences revealed that bacteriophage- and transposon-mediated horizontal gene transfer had occurred at several loci in the chromosomes of strains 2336 and 129Pt. It appears that these mobile genetic elements have played a major role in creating genomic diversity and phenotypic variability among the two H. somni strains. More... »

PAGES

570

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2164-12-570

DOI

http://dx.doi.org/10.1186/1471-2164-12-570

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1036904136

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/22111657


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/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Chromosomes, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Comparative Genomic Hybridization", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Evolution, Molecular", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Transfer, Horizontal", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genes, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Pasteurellaceae", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "DOE Joint Genome Institute, Los Alamos National Laboratory, 87545, Los Alamos, New Mexico, USA", 
          "id": "http://www.grid.ac/institutes/grid.148313.c", 
          "name": [
            "Center for Molecular Medicine and Infectious Diseases, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, 24061, Blacksburg, Virginia, USA", 
            "DOE Joint Genome Institute, Los Alamos National Laboratory, 87545, Los Alamos, New Mexico, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Siddaramappa", 
        "givenName": "Shivakumara", 
        "id": "sg:person.01334006324.32", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01334006324.32"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "DOE Joint Genome Institute, Los Alamos National Laboratory, 87545, Los Alamos, New Mexico, USA", 
          "id": "http://www.grid.ac/institutes/grid.148313.c", 
          "name": [
            "DOE Joint Genome Institute, Los Alamos National Laboratory, 87545, Los Alamos, New Mexico, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Challacombe", 
        "givenName": "Jean F", 
        "id": "sg:person.0610243562.97", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0610243562.97"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Center for Molecular Medicine and Infectious Diseases, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, 24061, Blacksburg, Virginia, USA", 
          "id": "http://www.grid.ac/institutes/grid.470073.7", 
          "name": [
            "Center for Molecular Medicine and Infectious Diseases, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, 24061, Blacksburg, Virginia, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Duncan", 
        "givenName": "Alison J", 
        "id": "sg:person.0656515424.39", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0656515424.39"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 731042, Oklahoma City, Oklahoma, USA", 
          "id": "http://www.grid.ac/institutes/grid.266902.9", 
          "name": [
            "Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 731042, Oklahoma City, Oklahoma, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Gillaspy", 
        "givenName": "Allison F", 
        "id": "sg:person.01236506633.84", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01236506633.84"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 731042, Oklahoma City, Oklahoma, USA", 
          "id": "http://www.grid.ac/institutes/grid.266902.9", 
          "name": [
            "Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 731042, Oklahoma City, Oklahoma, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Carson", 
        "givenName": "Matthew", 
        "id": "sg:person.07405123341.88", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.07405123341.88"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 731042, Oklahoma City, Oklahoma, USA", 
          "id": "http://www.grid.ac/institutes/grid.266902.9", 
          "name": [
            "Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 731042, Oklahoma City, Oklahoma, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Gipson", 
        "givenName": "Jenny", 
        "id": "sg:person.01041057224.34", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01041057224.34"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 731042, Oklahoma City, Oklahoma, USA", 
          "id": "http://www.grid.ac/institutes/grid.266902.9", 
          "name": [
            "Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 731042, Oklahoma City, Oklahoma, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Orvis", 
        "givenName": "Joshua", 
        "id": "sg:person.01107004353.67", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01107004353.67"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 731042, Oklahoma City, Oklahoma, USA", 
          "id": "http://www.grid.ac/institutes/grid.266902.9", 
          "name": [
            "Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 731042, Oklahoma City, Oklahoma, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Zaitshik", 
        "givenName": "Jeremy", 
        "id": "sg:person.01155305624.34", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01155305624.34"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 731042, Oklahoma City, Oklahoma, USA", 
          "id": "http://www.grid.ac/institutes/grid.266902.9", 
          "name": [
            "Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 731042, Oklahoma City, Oklahoma, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Barnes", 
        "givenName": "Gentry", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "DOE Joint Genome Institute, Los Alamos National Laboratory, 87545, Los Alamos, New Mexico, USA", 
          "id": "http://www.grid.ac/institutes/grid.148313.c", 
          "name": [
            "DOE Joint Genome Institute, Los Alamos National Laboratory, 87545, Los Alamos, New Mexico, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Bruce", 
        "givenName": "David", 
        "id": "sg:person.01047233274.63", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01047233274.63"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "DOE Joint Genome Institute, Los Alamos National Laboratory, 87545, Los Alamos, New Mexico, USA", 
          "id": "http://www.grid.ac/institutes/grid.148313.c", 
          "name": [
            "DOE Joint Genome Institute, Los Alamos National Laboratory, 87545, Los Alamos, New Mexico, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Chertkov", 
        "givenName": "Olga", 
        "id": "sg:person.01031253666.47", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01031253666.47"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "DOE Joint Genome Institute, Los Alamos National Laboratory, 87545, Los Alamos, New Mexico, USA", 
          "id": "http://www.grid.ac/institutes/grid.148313.c", 
          "name": [
            "DOE Joint Genome Institute, Los Alamos National Laboratory, 87545, Los Alamos, New Mexico, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Detter", 
        "givenName": "J Chris", 
        "id": "sg:person.01316221203.46", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01316221203.46"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "DOE Joint Genome Institute, Los Alamos National Laboratory, 87545, Los Alamos, New Mexico, USA", 
          "id": "http://www.grid.ac/institutes/grid.148313.c", 
          "name": [
            "DOE Joint Genome Institute, Los Alamos National Laboratory, 87545, Los Alamos, New Mexico, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Han", 
        "givenName": "Cliff S", 
        "id": "sg:person.0732722676.07", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0732722676.07"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "DOE Joint Genome Institute, Los Alamos National Laboratory, 87545, Los Alamos, New Mexico, USA", 
          "id": "http://www.grid.ac/institutes/grid.148313.c", 
          "name": [
            "DOE Joint Genome Institute, Los Alamos National Laboratory, 87545, Los Alamos, New Mexico, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Tapia", 
        "givenName": "Roxanne", 
        "id": "sg:person.0777735614.68", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0777735614.68"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "DOE Joint Genome Institute, Los Alamos National Laboratory, 87545, Los Alamos, New Mexico, USA", 
          "id": "http://www.grid.ac/institutes/grid.148313.c", 
          "name": [
            "DOE Joint Genome Institute, Los Alamos National Laboratory, 87545, Los Alamos, New Mexico, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Thompson", 
        "givenName": "Linda S", 
        "id": "sg:person.0776605124.47", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0776605124.47"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 731042, Oklahoma City, Oklahoma, USA", 
          "id": "http://www.grid.ac/institutes/grid.266902.9", 
          "name": [
            "Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 731042, Oklahoma City, Oklahoma, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Dyer", 
        "givenName": "David W", 
        "id": "sg:person.01232564733.37", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01232564733.37"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Center for Molecular Medicine and Infectious Diseases, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, 24061, Blacksburg, Virginia, USA", 
          "id": "http://www.grid.ac/institutes/grid.470073.7", 
          "name": [
            "Center for Molecular Medicine and Infectious Diseases, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, 24061, Blacksburg, Virginia, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Inzana", 
        "givenName": "Thomas J", 
        "id": "sg:person.0723320562.70", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0723320562.70"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1186/1471-2164-9-75", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013431920", 
          "https://doi.org/10.1186/1471-2164-9-75"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-1-4899-0978-7_6", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052408293", 
          "https://doi.org/10.1007/978-1-4899-0978-7_6"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2148-9-140", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001184789", 
          "https://doi.org/10.1186/1471-2148-9-140"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrmicro884", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006108697", 
          "https://doi.org/10.1038/nrmicro884"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1023/a:1014362705613", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020365914", 
          "https://doi.org/10.1023/a:1014362705613"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrmicro2350", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015810960", 
          "https://doi.org/10.1038/nrmicro2350"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/79918", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037992750", 
          "https://doi.org/10.1038/79918"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-1-59745-515-2_10", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050448451", 
          "https://doi.org/10.1007/978-1-59745-515-2_10"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2011-11-23", 
    "datePublishedReg": "2011-11-23", 
    "description": "BackgroundPneumonia and myocarditis are the most commonly reported diseases due to Histophilus somni, an opportunistic pathogen of the reproductive and respiratory tracts of cattle. Thus far only a few genes involved in metabolic and virulence functions have been identified and characterized in H. somni using traditional methods. Analyses of the genome sequences of several Pasteurellaceae species have provided insights into their biology and evolution. In view of the economic and ecological importance of H. somni, the genome sequence of pneumonia strain 2336 has been determined and compared to that of commensal strain 129Pt and other members of the Pasteurellaceae.ResultsThe chromosome of strain 2336 (2,263,857 bp) contained 1,980 protein coding genes, whereas the chromosome of strain 129Pt (2,007,700 bp) contained only 1,792 protein coding genes. Although the chromosomes of the two strains differ in size, their average GC content, gene density (total number of genes predicted on the chromosome), and percentage of sequence (number of genes) that encodes proteins were similar. The chromosomes of these strains also contained a number of discrete prophage regions and genomic islands. One of the genomic islands in strain 2336 contained genes putatively involved in copper, zinc, and tetracycline resistance. Using the genome sequence data and comparative analyses with other members of the Pasteurellaceae, several H. somni genes that may encode proteins involved in virulence (e.g., filamentous haemaggutinins, adhesins, and polysaccharide biosynthesis/modification enzymes) were identified. The two strains contained a total of 17 ORFs that encode putative glycosyltransferases and some of these ORFs had characteristic simple sequence repeats within them. Most of the genes/loci common to both the strains were located in different regions of the two chromosomes and occurred in opposite orientations, indicating genome rearrangement since their divergence from a common ancestor.ConclusionsSince the genome of strain 129Pt was ~256,000 bp smaller than that of strain 2336, these genomes provide yet another paradigm for studying evolutionary gene loss and/or gain in regard to virulence repertoire and pathogenic ability. Analyses of the complete genome sequences revealed that bacteriophage- and transposon-mediated horizontal gene transfer had occurred at several loci in the chromosomes of strains 2336 and 129Pt. It appears that these mobile genetic elements have played a major role in creating genomic diversity and phenotypic variability among the two H. somni strains.", 
    "genre": "article", 
    "id": "sg:pub.10.1186/1471-2164-12-570", 
    "inLanguage": "en", 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.8787617", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.8755792", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.8756898", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1023790", 
        "issn": [
          "1471-2164"
        ], 
        "name": "BMC Genomics", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "12"
      }
    ], 
    "keywords": [
      "horizontal gene transfer", 
      "strain 2336", 
      "genome sequence", 
      "strain 129Pt", 
      "genomic islands", 
      "protein coding genes", 
      "comparative genomic analysis", 
      "simple sequence repeats", 
      "gene transfer", 
      "average GC content", 
      "genome sequence data", 
      "complete genome sequence", 
      "genes/loci", 
      "mobile genetic elements", 
      "gene loss", 
      "coding genes", 
      "gene density", 
      "Pasteurellaceae species", 
      "sequence repeats", 
      "genome rearrangements", 
      "common ancestor", 
      "virulence functions", 
      "H. somni strains", 
      "ecological importance", 
      "prophage regions", 
      "putative glycosyltransferases", 
      "genomic diversity", 
      "Histophilus somni", 
      "percentage of sequences", 
      "genomic analysis", 
      "GC content", 
      "sequence data", 
      "H. somni", 
      "genetic elements", 
      "chromosomes", 
      "virulence repertoire", 
      "pathogenic ability", 
      "genes", 
      "phenotypic variability", 
      "opposite orientation", 
      "opportunistic pathogen", 
      "genome", 
      "ORF", 
      "protein", 
      "loci", 
      "Pasteurellaceae", 
      "sequence", 
      "strains", 
      "major role", 
      "islands", 
      "transposon", 
      "glycosyltransferases", 
      "ancestor", 
      "tetracycline resistance", 
      "repeats", 
      "biology", 
      "species", 
      "virulence", 
      "members", 
      "diversity", 
      "bacteriophages", 
      "divergence", 
      "evolution", 
      "comparative analysis", 
      "pathogens", 
      "role", 
      "repertoire", 
      "rearrangement", 
      "region", 
      "different regions", 
      "cattle", 
      "insights", 
      "analysis", 
      "function", 
      "resistance", 
      "ability", 
      "variability", 
      "transfer", 
      "loss", 
      "zinc", 
      "importance", 
      "disease", 
      "content", 
      "elements", 
      "number", 
      "tract", 
      "size", 
      "respiratory tract", 
      "copper", 
      "data", 
      "density", 
      "total", 
      "percentage", 
      "traditional methods", 
      "gain", 
      "paradigm", 
      "regard", 
      "view", 
      "orientation", 
      "method", 
      "myocarditis", 
      "BackgroundPneumonia"
    ], 
    "name": "Horizontal gene transfer in Histophilus somni and its role in the evolution of pathogenic strain 2336, as determined by comparative genomic analyses", 
    "pagination": "570", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1036904136"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1471-2164-12-570"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "22111657"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1471-2164-12-570", 
      "https://app.dimensions.ai/details/publication/pub.1036904136"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2022-06-01T22:08", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20220601/entities/gbq_results/article/article_547.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1186/1471-2164-12-570"
  }
]
 

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.10.1186/1471-2164-12-570'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-12-570'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-12-570'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-12-570'


 

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

347 TRIPLES      22 PREDICATES      143 URIs      127 LITERALS      14 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1471-2164-12-570 schema:about N170dc4032986470280957759688f8ab0
2 N17d24ef524844731bb99302c10294b89
3 N2f638d803694475494c3b189973ef61c
4 N6cd1fee2468c4797bd655bcdbd2b4bb3
5 Naa0961c36dbe4fabbb2756b87462b274
6 Nc1083b24e584426bb35026f916fc11ff
7 Ndc420fe10e94468893a21985f05b1737
8 anzsrc-for:06
9 anzsrc-for:0604
10 schema:author N561bd1a463d549efacd81b0fffd464cb
11 schema:citation sg:pub.10.1007/978-1-4899-0978-7_6
12 sg:pub.10.1007/978-1-59745-515-2_10
13 sg:pub.10.1023/a:1014362705613
14 sg:pub.10.1038/79918
15 sg:pub.10.1038/nrmicro2350
16 sg:pub.10.1038/nrmicro884
17 sg:pub.10.1186/1471-2148-9-140
18 sg:pub.10.1186/1471-2164-9-75
19 schema:datePublished 2011-11-23
20 schema:datePublishedReg 2011-11-23
21 schema:description BackgroundPneumonia and myocarditis are the most commonly reported diseases due to Histophilus somni, an opportunistic pathogen of the reproductive and respiratory tracts of cattle. Thus far only a few genes involved in metabolic and virulence functions have been identified and characterized in H. somni using traditional methods. Analyses of the genome sequences of several Pasteurellaceae species have provided insights into their biology and evolution. In view of the economic and ecological importance of H. somni, the genome sequence of pneumonia strain 2336 has been determined and compared to that of commensal strain 129Pt and other members of the Pasteurellaceae.ResultsThe chromosome of strain 2336 (2,263,857 bp) contained 1,980 protein coding genes, whereas the chromosome of strain 129Pt (2,007,700 bp) contained only 1,792 protein coding genes. Although the chromosomes of the two strains differ in size, their average GC content, gene density (total number of genes predicted on the chromosome), and percentage of sequence (number of genes) that encodes proteins were similar. The chromosomes of these strains also contained a number of discrete prophage regions and genomic islands. One of the genomic islands in strain 2336 contained genes putatively involved in copper, zinc, and tetracycline resistance. Using the genome sequence data and comparative analyses with other members of the Pasteurellaceae, several H. somni genes that may encode proteins involved in virulence (e.g., filamentous haemaggutinins, adhesins, and polysaccharide biosynthesis/modification enzymes) were identified. The two strains contained a total of 17 ORFs that encode putative glycosyltransferases and some of these ORFs had characteristic simple sequence repeats within them. Most of the genes/loci common to both the strains were located in different regions of the two chromosomes and occurred in opposite orientations, indicating genome rearrangement since their divergence from a common ancestor.ConclusionsSince the genome of strain 129Pt was ~256,000 bp smaller than that of strain 2336, these genomes provide yet another paradigm for studying evolutionary gene loss and/or gain in regard to virulence repertoire and pathogenic ability. Analyses of the complete genome sequences revealed that bacteriophage- and transposon-mediated horizontal gene transfer had occurred at several loci in the chromosomes of strains 2336 and 129Pt. It appears that these mobile genetic elements have played a major role in creating genomic diversity and phenotypic variability among the two H. somni strains.
22 schema:genre article
23 schema:inLanguage en
24 schema:isAccessibleForFree true
25 schema:isPartOf Nb0e7ec32474540fe82336a49cf06f951
26 Nb79ae55360ff4fe4abc3ed443aa3bf7a
27 sg:journal.1023790
28 schema:keywords BackgroundPneumonia
29 GC content
30 H. somni
31 H. somni strains
32 Histophilus somni
33 ORF
34 Pasteurellaceae
35 Pasteurellaceae species
36 ability
37 analysis
38 ancestor
39 average GC content
40 bacteriophages
41 biology
42 cattle
43 chromosomes
44 coding genes
45 common ancestor
46 comparative analysis
47 comparative genomic analysis
48 complete genome sequence
49 content
50 copper
51 data
52 density
53 different regions
54 disease
55 divergence
56 diversity
57 ecological importance
58 elements
59 evolution
60 function
61 gain
62 gene density
63 gene loss
64 gene transfer
65 genes
66 genes/loci
67 genetic elements
68 genome
69 genome rearrangements
70 genome sequence
71 genome sequence data
72 genomic analysis
73 genomic diversity
74 genomic islands
75 glycosyltransferases
76 horizontal gene transfer
77 importance
78 insights
79 islands
80 loci
81 loss
82 major role
83 members
84 method
85 mobile genetic elements
86 myocarditis
87 number
88 opportunistic pathogen
89 opposite orientation
90 orientation
91 paradigm
92 pathogenic ability
93 pathogens
94 percentage
95 percentage of sequences
96 phenotypic variability
97 prophage regions
98 protein
99 protein coding genes
100 putative glycosyltransferases
101 rearrangement
102 regard
103 region
104 repeats
105 repertoire
106 resistance
107 respiratory tract
108 role
109 sequence
110 sequence data
111 sequence repeats
112 simple sequence repeats
113 size
114 species
115 strain 129Pt
116 strain 2336
117 strains
118 tetracycline resistance
119 total
120 tract
121 traditional methods
122 transfer
123 transposon
124 variability
125 view
126 virulence
127 virulence functions
128 virulence repertoire
129 zinc
130 schema:name Horizontal gene transfer in Histophilus somni and its role in the evolution of pathogenic strain 2336, as determined by comparative genomic analyses
131 schema:pagination 570
132 schema:productId N0e145db04674482c9a2f03d2546a15f6
133 N5761c41687224350ab2ff403e78740d6
134 Nb91177f8f8734ff7889e107101f88c3d
135 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036904136
136 https://doi.org/10.1186/1471-2164-12-570
137 schema:sdDatePublished 2022-06-01T22:08
138 schema:sdLicense https://scigraph.springernature.com/explorer/license/
139 schema:sdPublisher N4af9a4c9f76844e6bbac123439a29d41
140 schema:url https://doi.org/10.1186/1471-2164-12-570
141 sgo:license sg:explorer/license/
142 sgo:sdDataset articles
143 rdf:type schema:ScholarlyArticle
144 N047996ecf3ef437095f8fac5355b90fa rdf:first sg:person.0732722676.07
145 rdf:rest N8793fd9b25d14f70b61359ca84f3ae06
146 N0e145db04674482c9a2f03d2546a15f6 schema:name dimensions_id
147 schema:value pub.1036904136
148 rdf:type schema:PropertyValue
149 N119666e41606495b9efb8c59d890376d rdf:first sg:person.0656515424.39
150 rdf:rest Nec57f05224df490485b3c945c88decbb
151 N170dc4032986470280957759688f8ab0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
152 schema:name Pasteurellaceae
153 rdf:type schema:DefinedTerm
154 N17d24ef524844731bb99302c10294b89 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
155 schema:name Chromosomes, Bacterial
156 rdf:type schema:DefinedTerm
157 N2f638d803694475494c3b189973ef61c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
158 schema:name Genes, Bacterial
159 rdf:type schema:DefinedTerm
160 N4af9a4c9f76844e6bbac123439a29d41 schema:name Springer Nature - SN SciGraph project
161 rdf:type schema:Organization
162 N51531c2a9e314f06b6d571779027d897 rdf:first sg:person.0610243562.97
163 rdf:rest N119666e41606495b9efb8c59d890376d
164 N55a281783a2f4bfe8abdd8a33f30db2e rdf:first sg:person.01155305624.34
165 rdf:rest N7a7a654412864bda9fb58b74b5633f29
166 N561bd1a463d549efacd81b0fffd464cb rdf:first sg:person.01334006324.32
167 rdf:rest N51531c2a9e314f06b6d571779027d897
168 N5761c41687224350ab2ff403e78740d6 schema:name pubmed_id
169 schema:value 22111657
170 rdf:type schema:PropertyValue
171 N5b6a8857a53a4f228a8b03ea4a512b92 rdf:first sg:person.0723320562.70
172 rdf:rest rdf:nil
173 N5eb8b5069b994d43a387589b5efd8f44 rdf:first sg:person.01107004353.67
174 rdf:rest N55a281783a2f4bfe8abdd8a33f30db2e
175 N6cd1fee2468c4797bd655bcdbd2b4bb3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
176 schema:name Evolution, Molecular
177 rdf:type schema:DefinedTerm
178 N7a7a654412864bda9fb58b74b5633f29 rdf:first Nb7e3267323e9489ea6ce8c4461a889e6
179 rdf:rest N8341f26df8fc4e8595602084763d8513
180 N8341f26df8fc4e8595602084763d8513 rdf:first sg:person.01047233274.63
181 rdf:rest Nb78a391d81624151b6bfd9c3976f2694
182 N8793fd9b25d14f70b61359ca84f3ae06 rdf:first sg:person.0777735614.68
183 rdf:rest Nad3e1e72bd65418ab31d3087f191f4e5
184 N8a6cafa688ff4865abf434163e7c9790 rdf:first sg:person.01316221203.46
185 rdf:rest N047996ecf3ef437095f8fac5355b90fa
186 Naa0961c36dbe4fabbb2756b87462b274 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
187 schema:name DNA, Bacterial
188 rdf:type schema:DefinedTerm
189 Nad3e1e72bd65418ab31d3087f191f4e5 rdf:first sg:person.0776605124.47
190 rdf:rest Nd8fbe69a6f934b3982790f8851064629
191 Nb0e7ec32474540fe82336a49cf06f951 schema:issueNumber 1
192 rdf:type schema:PublicationIssue
193 Nb78a391d81624151b6bfd9c3976f2694 rdf:first sg:person.01031253666.47
194 rdf:rest N8a6cafa688ff4865abf434163e7c9790
195 Nb79ae55360ff4fe4abc3ed443aa3bf7a schema:volumeNumber 12
196 rdf:type schema:PublicationVolume
197 Nb7e3267323e9489ea6ce8c4461a889e6 schema:affiliation grid-institutes:grid.266902.9
198 schema:familyName Barnes
199 schema:givenName Gentry
200 rdf:type schema:Person
201 Nb91177f8f8734ff7889e107101f88c3d schema:name doi
202 schema:value 10.1186/1471-2164-12-570
203 rdf:type schema:PropertyValue
204 Nc1083b24e584426bb35026f916fc11ff schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
205 schema:name Comparative Genomic Hybridization
206 rdf:type schema:DefinedTerm
207 Nd8fbe69a6f934b3982790f8851064629 rdf:first sg:person.01232564733.37
208 rdf:rest N5b6a8857a53a4f228a8b03ea4a512b92
209 Ndc420fe10e94468893a21985f05b1737 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
210 schema:name Gene Transfer, Horizontal
211 rdf:type schema:DefinedTerm
212 Ne124a90e90ae49dfb84bc04e5fa7ef30 rdf:first sg:person.01041057224.34
213 rdf:rest N5eb8b5069b994d43a387589b5efd8f44
214 Nec57f05224df490485b3c945c88decbb rdf:first sg:person.01236506633.84
215 rdf:rest Ned41174efbb349e89fd011480ad00b4b
216 Ned41174efbb349e89fd011480ad00b4b rdf:first sg:person.07405123341.88
217 rdf:rest Ne124a90e90ae49dfb84bc04e5fa7ef30
218 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
219 schema:name Biological Sciences
220 rdf:type schema:DefinedTerm
221 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
222 schema:name Genetics
223 rdf:type schema:DefinedTerm
224 sg:grant.8755792 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2164-12-570
225 rdf:type schema:MonetaryGrant
226 sg:grant.8756898 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2164-12-570
227 rdf:type schema:MonetaryGrant
228 sg:grant.8787617 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2164-12-570
229 rdf:type schema:MonetaryGrant
230 sg:journal.1023790 schema:issn 1471-2164
231 schema:name BMC Genomics
232 schema:publisher Springer Nature
233 rdf:type schema:Periodical
234 sg:person.01031253666.47 schema:affiliation grid-institutes:grid.148313.c
235 schema:familyName Chertkov
236 schema:givenName Olga
237 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01031253666.47
238 rdf:type schema:Person
239 sg:person.01041057224.34 schema:affiliation grid-institutes:grid.266902.9
240 schema:familyName Gipson
241 schema:givenName Jenny
242 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01041057224.34
243 rdf:type schema:Person
244 sg:person.01047233274.63 schema:affiliation grid-institutes:grid.148313.c
245 schema:familyName Bruce
246 schema:givenName David
247 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01047233274.63
248 rdf:type schema:Person
249 sg:person.01107004353.67 schema:affiliation grid-institutes:grid.266902.9
250 schema:familyName Orvis
251 schema:givenName Joshua
252 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01107004353.67
253 rdf:type schema:Person
254 sg:person.01155305624.34 schema:affiliation grid-institutes:grid.266902.9
255 schema:familyName Zaitshik
256 schema:givenName Jeremy
257 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01155305624.34
258 rdf:type schema:Person
259 sg:person.01232564733.37 schema:affiliation grid-institutes:grid.266902.9
260 schema:familyName Dyer
261 schema:givenName David W
262 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01232564733.37
263 rdf:type schema:Person
264 sg:person.01236506633.84 schema:affiliation grid-institutes:grid.266902.9
265 schema:familyName Gillaspy
266 schema:givenName Allison F
267 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01236506633.84
268 rdf:type schema:Person
269 sg:person.01316221203.46 schema:affiliation grid-institutes:grid.148313.c
270 schema:familyName Detter
271 schema:givenName J Chris
272 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01316221203.46
273 rdf:type schema:Person
274 sg:person.01334006324.32 schema:affiliation grid-institutes:grid.148313.c
275 schema:familyName Siddaramappa
276 schema:givenName Shivakumara
277 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01334006324.32
278 rdf:type schema:Person
279 sg:person.0610243562.97 schema:affiliation grid-institutes:grid.148313.c
280 schema:familyName Challacombe
281 schema:givenName Jean F
282 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0610243562.97
283 rdf:type schema:Person
284 sg:person.0656515424.39 schema:affiliation grid-institutes:grid.470073.7
285 schema:familyName Duncan
286 schema:givenName Alison J
287 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0656515424.39
288 rdf:type schema:Person
289 sg:person.0723320562.70 schema:affiliation grid-institutes:grid.470073.7
290 schema:familyName Inzana
291 schema:givenName Thomas J
292 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0723320562.70
293 rdf:type schema:Person
294 sg:person.0732722676.07 schema:affiliation grid-institutes:grid.148313.c
295 schema:familyName Han
296 schema:givenName Cliff S
297 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0732722676.07
298 rdf:type schema:Person
299 sg:person.07405123341.88 schema:affiliation grid-institutes:grid.266902.9
300 schema:familyName Carson
301 schema:givenName Matthew
302 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.07405123341.88
303 rdf:type schema:Person
304 sg:person.0776605124.47 schema:affiliation grid-institutes:grid.148313.c
305 schema:familyName Thompson
306 schema:givenName Linda S
307 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0776605124.47
308 rdf:type schema:Person
309 sg:person.0777735614.68 schema:affiliation grid-institutes:grid.148313.c
310 schema:familyName Tapia
311 schema:givenName Roxanne
312 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0777735614.68
313 rdf:type schema:Person
314 sg:pub.10.1007/978-1-4899-0978-7_6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052408293
315 https://doi.org/10.1007/978-1-4899-0978-7_6
316 rdf:type schema:CreativeWork
317 sg:pub.10.1007/978-1-59745-515-2_10 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050448451
318 https://doi.org/10.1007/978-1-59745-515-2_10
319 rdf:type schema:CreativeWork
320 sg:pub.10.1023/a:1014362705613 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020365914
321 https://doi.org/10.1023/a:1014362705613
322 rdf:type schema:CreativeWork
323 sg:pub.10.1038/79918 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037992750
324 https://doi.org/10.1038/79918
325 rdf:type schema:CreativeWork
326 sg:pub.10.1038/nrmicro2350 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015810960
327 https://doi.org/10.1038/nrmicro2350
328 rdf:type schema:CreativeWork
329 sg:pub.10.1038/nrmicro884 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006108697
330 https://doi.org/10.1038/nrmicro884
331 rdf:type schema:CreativeWork
332 sg:pub.10.1186/1471-2148-9-140 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001184789
333 https://doi.org/10.1186/1471-2148-9-140
334 rdf:type schema:CreativeWork
335 sg:pub.10.1186/1471-2164-9-75 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013431920
336 https://doi.org/10.1186/1471-2164-9-75
337 rdf:type schema:CreativeWork
338 grid-institutes:grid.148313.c schema:alternateName DOE Joint Genome Institute, Los Alamos National Laboratory, 87545, Los Alamos, New Mexico, USA
339 schema:name Center for Molecular Medicine and Infectious Diseases, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, 24061, Blacksburg, Virginia, USA
340 DOE Joint Genome Institute, Los Alamos National Laboratory, 87545, Los Alamos, New Mexico, USA
341 rdf:type schema:Organization
342 grid-institutes:grid.266902.9 schema:alternateName Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 731042, Oklahoma City, Oklahoma, USA
343 schema:name Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 731042, Oklahoma City, Oklahoma, USA
344 rdf:type schema:Organization
345 grid-institutes:grid.470073.7 schema:alternateName Center for Molecular Medicine and Infectious Diseases, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, 24061, Blacksburg, Virginia, USA
346 schema:name Center for Molecular Medicine and Infectious Diseases, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, 24061, Blacksburg, Virginia, USA
347 rdf:type schema:Organization
 




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


...