DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2016-09-07

AUTHORS

Thomas Wicker, Yeisoo Yu, Georg Haberer, Klaus F. X. Mayer, Pradeep Reddy Marri, Steve Rounsley, Mingsheng Chen, Andrea Zuccolo, Olivier Panaud, Rod A. Wing, Stefan Roffler

ABSTRACT

DNA (class 2) transposons are mobile genetic elements which move within their 'host' genome through excising and re-inserting elsewhere. Although the rice genome contains tens of thousands of such elements, their actual role in evolution is still unclear. Analysing over 650 transposon polymorphisms in the rice species Oryza sativa and Oryza glaberrima, we find that DNA repair following transposon excisions is associated with an increased number of mutations in the sequences neighbouring the transposon. Indeed, the 3,000 bp flanking the excised transposons can contain over 10 times more mutations than the genome-wide average. Since DNA transposons preferably insert near genes, this is correlated with increases in mutation rates in coding sequences and regulatory regions. Most importantly, we find this phenomenon also in maize, wheat and barley. Thus, these findings suggest that DNA transposon activity is a major evolutionary force in grasses which provide the basis of most food consumed by humankind. More... »

PAGES

12790

References to SciGraph publications

  • 2005-09. The Oryza Map Alignment Project: The Golden Path to Unlocking the Genetic Potential of Wild Rice Species in PLANT MOLECULAR BIOLOGY
  • 2007-12. A unified classification system for eukaryotic transposable elements in NATURE REVIEWS GENETICS
  • 2015-04-28. Genome-wide comparison of Asian and African rice reveals high recent activity of DNA transposons in MOBILE DNA
  • 2006-04-23. A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture in NATURE GENETICS
  • 2014-09-01. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication in NATURE GENETICS
  • 2007-08-01. Break-induced replication and telomerase-independent telomere maintenance require Pol32 in NATURE
  • 2015-12-17. The making of a genomic parasite - the Mothra family sheds light on the evolution of Helitrons in plants in MOBILE DNA
  • 2007-06-26. Dating the early evolution of plants: detection and molecular clock analyses of orthologs in MOLECULAR GENETICS AND GENOMICS
  • 1998-09. The paleontology of intergene retrotransposons of maize in NATURE GENETICS
  • 2002-05. The 3′–5′ exonucleases in NATURE REVIEWS MOLECULAR CELL BIOLOGY
  • 2014-05-07. Diversity and evolution of transposable elements in Arabidopsis in CHROMOSOME RESEARCH
  • 2004-04. The Deep Phylogeny of Land Plants Inferred from a Full Analysis of Nucleotide Base Changes in Terms of Mutation and Selection in JOURNAL OF MOLECULAR EVOLUTION
  • 2010-02. Genome sequencing and analysis of the model grass Brachypodium distachyon in NATURE
  • 2011-10-27. A transposon in tb1 drove maize domestication in NATURE GENETICS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/ncomms12790

    DOI

    http://dx.doi.org/10.1038/ncomms12790

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1047610564

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/27599761


    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": "Base Sequence", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "DNA Transposable Elements", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "DNA, Plant", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Gene Expression Regulation, Plant", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Mutation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Oryza", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Plant Proteins", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Polymorphism, Single Nucleotide", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland", 
              "id": "http://www.grid.ac/institutes/grid.7400.3", 
              "name": [
                "Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Wicker", 
            "givenName": "Thomas", 
            "id": "sg:person.01133056131.64", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01133056131.64"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA", 
              "id": "http://www.grid.ac/institutes/grid.134563.6", 
              "name": [
                "Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Yu", 
            "givenName": "Yeisoo", 
            "id": "sg:person.0635153405.31", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0635153405.31"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany", 
              "id": "http://www.grid.ac/institutes/grid.4567.0", 
              "name": [
                "Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Haberer", 
            "givenName": "Georg", 
            "id": "sg:person.0667267124.69", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0667267124.69"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany", 
              "id": "http://www.grid.ac/institutes/grid.4567.0", 
              "name": [
                "Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Mayer", 
            "givenName": "Klaus F. X.", 
            "id": "sg:person.010400475132.18", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010400475132.18"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Dow AgroSciences, Indianapolis, Indiana 46268, USA", 
              "id": "http://www.grid.ac/institutes/grid.418574.b", 
              "name": [
                "Dow AgroSciences, Indianapolis, Indiana 46268, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Marri", 
            "givenName": "Pradeep Reddy", 
            "id": "sg:person.0707244327.29", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0707244327.29"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Dow AgroSciences, Indianapolis, Indiana 46268, USA", 
              "id": "http://www.grid.ac/institutes/grid.418574.b", 
              "name": [
                "Dow AgroSciences, Indianapolis, Indiana 46268, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Rounsley", 
            "givenName": "Steve", 
            "id": "sg:person.01330205131.66", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01330205131.66"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China", 
              "id": "http://www.grid.ac/institutes/grid.418558.5", 
              "name": [
                "State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Chen", 
            "givenName": "Mingsheng", 
            "id": "sg:person.01142452247.75", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01142452247.75"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy", 
              "id": "http://www.grid.ac/institutes/grid.263145.7", 
              "name": [
                "Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Zuccolo", 
            "givenName": "Andrea", 
            "id": "sg:person.01046471727.43", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01046471727.43"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Laboratoire G\u00e9nome et D\u00e9veloppement des Plantes, UMR5096 UPVD/CNRS, Universit\u00e9 de Perpignan Via Domitia, 66860 Perpignan, France", 
              "id": "http://www.grid.ac/institutes/grid.463998.9", 
              "name": [
                "Laboratoire G\u00e9nome et D\u00e9veloppement des Plantes, UMR5096 UPVD/CNRS, Universit\u00e9 de Perpignan Via Domitia, 66860 Perpignan, France"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Panaud", 
            "givenName": "Olivier", 
            "id": "sg:person.01024353410.27", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01024353410.27"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA", 
              "id": "http://www.grid.ac/institutes/grid.134563.6", 
              "name": [
                "Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA", 
                "International Rice Research Institute, Los Ba\u00f1os, 4031 Laguna, Philippines", 
                "Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Wing", 
            "givenName": "Rod A.", 
            "id": "sg:person.01040625561.93", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01040625561.93"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland", 
              "id": "http://www.grid.ac/institutes/grid.7400.3", 
              "name": [
                "Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Roffler", 
            "givenName": "Stefan", 
            "id": "sg:person.01311147311.85", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01311147311.85"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1186/s13100-015-0054-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005478710", 
              "https://doi.org/10.1186/s13100-015-0054-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00239-003-2570-y", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002188655", 
              "https://doi.org/10.1007/s00239-003-2570-y"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg2165", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1053647019", 
              "https://doi.org/10.1038/nrg2165"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng1784", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1039398234", 
              "https://doi.org/10.1038/ng1784"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.3044", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023018294", 
              "https://doi.org/10.1038/ng.3044"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00438-007-0257-6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1036262010", 
              "https://doi.org/10.1007/s00438-007-0257-6"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11103-004-6237-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1020001962", 
              "https://doi.org/10.1007/s11103-004-6237-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13100-015-0040-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1003535473", 
              "https://doi.org/10.1186/s13100-015-0040-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrm804", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051255007", 
              "https://doi.org/10.1038/nrm804"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10577-014-9418-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1024372429", 
              "https://doi.org/10.1007/s10577-014-9418-8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature06047", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032121807", 
              "https://doi.org/10.1038/nature06047"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature08747", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027862091", 
              "https://doi.org/10.1038/nature08747"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/1695", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017391035", 
              "https://doi.org/10.1038/1695"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.986", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018680690", 
              "https://doi.org/10.1038/ng.986"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2016-09-07", 
        "datePublishedReg": "2016-09-07", 
        "description": "DNA (class 2) transposons are mobile genetic elements which move within their 'host' genome through excising and re-inserting elsewhere. Although the rice genome contains tens of thousands of such elements, their actual role in evolution is still unclear. Analysing over 650 transposon polymorphisms in the rice species Oryza sativa and Oryza glaberrima, we find that DNA repair following transposon excisions is associated with an increased number of mutations in the sequences neighbouring the transposon. Indeed, the 3,000\u2009bp flanking the excised transposons can contain over 10 times more mutations than the genome-wide average. Since DNA transposons preferably insert near genes, this is correlated with increases in mutation rates in coding sequences and regulatory regions. Most importantly, we find this phenomenon also in maize, wheat and barley. Thus, these findings suggest that DNA transposon activity is a major evolutionary force in grasses which provide the basis of most food consumed by humankind.", 
        "genre": "article", 
        "id": "sg:pub.10.1038/ncomms12790", 
        "inLanguage": "en", 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.3040231", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.2999681", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.3091191", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.2995048", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.5235583", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1043282", 
            "issn": [
              "2041-1723"
            ], 
            "name": "Nature Communications", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "7"
          }
        ], 
        "keywords": [
          "DNA transposon activity", 
          "transposon activity", 
          "DNA transposons", 
          "mutation rate", 
          "genome-wide average", 
          "major evolutionary force", 
          "genes of rice", 
          "times more mutations", 
          "mobile genetic elements", 
          "rice genome", 
          "evolutionary forces", 
          "Oryza sativa", 
          "number of mutations", 
          "regulatory region", 
          "Oryza glaberrima", 
          "DNA repair", 
          "transposon excision", 
          "genetic elements", 
          "transposon", 
          "excised transposon", 
          "genome", 
          "more mutations", 
          "genes", 
          "mutations", 
          "rice", 
          "grass", 
          "sequence", 
          "glaberrima", 
          "sativa", 
          "tens of thousands", 
          "actual role", 
          "maize", 
          "wheat", 
          "barley", 
          "BP", 
          "host", 
          "polymorphism", 
          "activity", 
          "such elements", 
          "most foods", 
          "evolution", 
          "role", 
          "repair", 
          "thousands", 
          "region", 
          "elements", 
          "food", 
          "basis", 
          "number", 
          "rate", 
          "findings", 
          "increase", 
          "humankind", 
          "tens", 
          "phenomenon", 
          "average", 
          "force", 
          "excision", 
          "transposon polymorphisms"
        ], 
        "name": "DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses", 
        "pagination": "12790", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1047610564"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1038/ncomms12790"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "27599761"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1038/ncomms12790", 
          "https://app.dimensions.ai/details/publication/pub.1047610564"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2021-11-01T18:27", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20211101/entities/gbq_results/article/article_696.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1038/ncomms12790"
      }
    ]
     

    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.10.1038/ncomms12790'

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

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/ncomms12790'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/ncomms12790'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/ncomms12790'


     

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

    309 TRIPLES      22 PREDICATES      107 URIs      85 LITERALS      15 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1038/ncomms12790 schema:about N057a6194311c496cbdcfc224b8713367
    2 N18e90cc1acb242149665a611eddac309
    3 N1e60406702264d06a7fa74fbad5d544f
    4 N374aee2f66be4d44b5c862cdd658fef3
    5 N6fec3ed6cd00443eb85c3668fa7ad9e7
    6 N83518859fdb345c387e60091db47cf8e
    7 Nc7cc8ebdfb7d4ddfa213af5b443660eb
    8 Nf96b5c7e5d1c47e8a3ab271137270a8f
    9 anzsrc-for:06
    10 anzsrc-for:0604
    11 schema:author Nbc8fea1aeaac4e119c481de938ad849c
    12 schema:citation sg:pub.10.1007/s00239-003-2570-y
    13 sg:pub.10.1007/s00438-007-0257-6
    14 sg:pub.10.1007/s10577-014-9418-8
    15 sg:pub.10.1007/s11103-004-6237-x
    16 sg:pub.10.1038/1695
    17 sg:pub.10.1038/nature06047
    18 sg:pub.10.1038/nature08747
    19 sg:pub.10.1038/ng.3044
    20 sg:pub.10.1038/ng.986
    21 sg:pub.10.1038/ng1784
    22 sg:pub.10.1038/nrg2165
    23 sg:pub.10.1038/nrm804
    24 sg:pub.10.1186/s13100-015-0040-x
    25 sg:pub.10.1186/s13100-015-0054-4
    26 schema:datePublished 2016-09-07
    27 schema:datePublishedReg 2016-09-07
    28 schema:description DNA (class 2) transposons are mobile genetic elements which move within their 'host' genome through excising and re-inserting elsewhere. Although the rice genome contains tens of thousands of such elements, their actual role in evolution is still unclear. Analysing over 650 transposon polymorphisms in the rice species Oryza sativa and Oryza glaberrima, we find that DNA repair following transposon excisions is associated with an increased number of mutations in the sequences neighbouring the transposon. Indeed, the 3,000 bp flanking the excised transposons can contain over 10 times more mutations than the genome-wide average. Since DNA transposons preferably insert near genes, this is correlated with increases in mutation rates in coding sequences and regulatory regions. Most importantly, we find this phenomenon also in maize, wheat and barley. Thus, these findings suggest that DNA transposon activity is a major evolutionary force in grasses which provide the basis of most food consumed by humankind.
    29 schema:genre article
    30 schema:inLanguage en
    31 schema:isAccessibleForFree true
    32 schema:isPartOf N7fe204ea3d10402e96d203e4f5e4fcab
    33 Nf92a02612f7d4f4eab38b2cc29a9ae9b
    34 sg:journal.1043282
    35 schema:keywords BP
    36 DNA repair
    37 DNA transposon activity
    38 DNA transposons
    39 Oryza glaberrima
    40 Oryza sativa
    41 activity
    42 actual role
    43 average
    44 barley
    45 basis
    46 elements
    47 evolution
    48 evolutionary forces
    49 excised transposon
    50 excision
    51 findings
    52 food
    53 force
    54 genes
    55 genes of rice
    56 genetic elements
    57 genome
    58 genome-wide average
    59 glaberrima
    60 grass
    61 host
    62 humankind
    63 increase
    64 maize
    65 major evolutionary force
    66 mobile genetic elements
    67 more mutations
    68 most foods
    69 mutation rate
    70 mutations
    71 number
    72 number of mutations
    73 phenomenon
    74 polymorphism
    75 rate
    76 region
    77 regulatory region
    78 repair
    79 rice
    80 rice genome
    81 role
    82 sativa
    83 sequence
    84 such elements
    85 tens
    86 tens of thousands
    87 thousands
    88 times more mutations
    89 transposon
    90 transposon activity
    91 transposon excision
    92 transposon polymorphisms
    93 wheat
    94 schema:name DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses
    95 schema:pagination 12790
    96 schema:productId N6e36e0eb910c4b25a56c8ff90071779b
    97 Na8bdfea414f64f5ebe03b5c3a29fad27
    98 Nafe47638dae44793bbeaa26ac803db28
    99 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047610564
    100 https://doi.org/10.1038/ncomms12790
    101 schema:sdDatePublished 2021-11-01T18:27
    102 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    103 schema:sdPublisher N029c3c71a1eb492cb600db227011d605
    104 schema:url https://doi.org/10.1038/ncomms12790
    105 sgo:license sg:explorer/license/
    106 sgo:sdDataset articles
    107 rdf:type schema:ScholarlyArticle
    108 N029c3c71a1eb492cb600db227011d605 schema:name Springer Nature - SN SciGraph project
    109 rdf:type schema:Organization
    110 N057a6194311c496cbdcfc224b8713367 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    111 schema:name DNA, Plant
    112 rdf:type schema:DefinedTerm
    113 N0ef18963b63248058860ab794f259389 rdf:first sg:person.01040625561.93
    114 rdf:rest N380d03cc5b7a4508bc03f2b94d7db9f6
    115 N18e90cc1acb242149665a611eddac309 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    116 schema:name DNA Transposable Elements
    117 rdf:type schema:DefinedTerm
    118 N1e60406702264d06a7fa74fbad5d544f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    119 schema:name Polymorphism, Single Nucleotide
    120 rdf:type schema:DefinedTerm
    121 N2af8a60645ac470bbfe9cb350a7f66bf rdf:first sg:person.0635153405.31
    122 rdf:rest N31ecdb0e1cd143ee98f59aa4369066f8
    123 N31ecdb0e1cd143ee98f59aa4369066f8 rdf:first sg:person.0667267124.69
    124 rdf:rest Nfc09f700f862400d9fd2c1dcb2f0a722
    125 N374aee2f66be4d44b5c862cdd658fef3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    126 schema:name Oryza
    127 rdf:type schema:DefinedTerm
    128 N380d03cc5b7a4508bc03f2b94d7db9f6 rdf:first sg:person.01311147311.85
    129 rdf:rest rdf:nil
    130 N6e36e0eb910c4b25a56c8ff90071779b schema:name pubmed_id
    131 schema:value 27599761
    132 rdf:type schema:PropertyValue
    133 N6fec3ed6cd00443eb85c3668fa7ad9e7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    134 schema:name Mutation
    135 rdf:type schema:DefinedTerm
    136 N723e5e7c84204bd2b6365fe9d7628fa2 rdf:first sg:person.01142452247.75
    137 rdf:rest N7952c561890c49039a24b844240c8853
    138 N7952c561890c49039a24b844240c8853 rdf:first sg:person.01046471727.43
    139 rdf:rest Na266380bf262457b8ee85e26b4c938df
    140 N7fe204ea3d10402e96d203e4f5e4fcab schema:issueNumber 1
    141 rdf:type schema:PublicationIssue
    142 N83518859fdb345c387e60091db47cf8e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    143 schema:name Gene Expression Regulation, Plant
    144 rdf:type schema:DefinedTerm
    145 Na266380bf262457b8ee85e26b4c938df rdf:first sg:person.01024353410.27
    146 rdf:rest N0ef18963b63248058860ab794f259389
    147 Na8bdfea414f64f5ebe03b5c3a29fad27 schema:name dimensions_id
    148 schema:value pub.1047610564
    149 rdf:type schema:PropertyValue
    150 Nafe47638dae44793bbeaa26ac803db28 schema:name doi
    151 schema:value 10.1038/ncomms12790
    152 rdf:type schema:PropertyValue
    153 Nbc8fea1aeaac4e119c481de938ad849c rdf:first sg:person.01133056131.64
    154 rdf:rest N2af8a60645ac470bbfe9cb350a7f66bf
    155 Nc7cc8ebdfb7d4ddfa213af5b443660eb schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    156 schema:name Base Sequence
    157 rdf:type schema:DefinedTerm
    158 Nddc00f74a42b4e19ba3498492a425765 rdf:first sg:person.01330205131.66
    159 rdf:rest N723e5e7c84204bd2b6365fe9d7628fa2
    160 Nf92a02612f7d4f4eab38b2cc29a9ae9b schema:volumeNumber 7
    161 rdf:type schema:PublicationVolume
    162 Nf96b5c7e5d1c47e8a3ab271137270a8f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    163 schema:name Plant Proteins
    164 rdf:type schema:DefinedTerm
    165 Nfc09f700f862400d9fd2c1dcb2f0a722 rdf:first sg:person.010400475132.18
    166 rdf:rest Nff6427ef0d4b4ea788acb2e7d68fc675
    167 Nff6427ef0d4b4ea788acb2e7d68fc675 rdf:first sg:person.0707244327.29
    168 rdf:rest Nddc00f74a42b4e19ba3498492a425765
    169 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    170 schema:name Biological Sciences
    171 rdf:type schema:DefinedTerm
    172 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    173 schema:name Genetics
    174 rdf:type schema:DefinedTerm
    175 sg:grant.2995048 http://pending.schema.org/fundedItem sg:pub.10.1038/ncomms12790
    176 rdf:type schema:MonetaryGrant
    177 sg:grant.2999681 http://pending.schema.org/fundedItem sg:pub.10.1038/ncomms12790
    178 rdf:type schema:MonetaryGrant
    179 sg:grant.3040231 http://pending.schema.org/fundedItem sg:pub.10.1038/ncomms12790
    180 rdf:type schema:MonetaryGrant
    181 sg:grant.3091191 http://pending.schema.org/fundedItem sg:pub.10.1038/ncomms12790
    182 rdf:type schema:MonetaryGrant
    183 sg:grant.5235583 http://pending.schema.org/fundedItem sg:pub.10.1038/ncomms12790
    184 rdf:type schema:MonetaryGrant
    185 sg:journal.1043282 schema:issn 2041-1723
    186 schema:name Nature Communications
    187 schema:publisher Springer Nature
    188 rdf:type schema:Periodical
    189 sg:person.01024353410.27 schema:affiliation grid-institutes:grid.463998.9
    190 schema:familyName Panaud
    191 schema:givenName Olivier
    192 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01024353410.27
    193 rdf:type schema:Person
    194 sg:person.010400475132.18 schema:affiliation grid-institutes:grid.4567.0
    195 schema:familyName Mayer
    196 schema:givenName Klaus F. X.
    197 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010400475132.18
    198 rdf:type schema:Person
    199 sg:person.01040625561.93 schema:affiliation grid-institutes:grid.134563.6
    200 schema:familyName Wing
    201 schema:givenName Rod A.
    202 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01040625561.93
    203 rdf:type schema:Person
    204 sg:person.01046471727.43 schema:affiliation grid-institutes:grid.263145.7
    205 schema:familyName Zuccolo
    206 schema:givenName Andrea
    207 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01046471727.43
    208 rdf:type schema:Person
    209 sg:person.01133056131.64 schema:affiliation grid-institutes:grid.7400.3
    210 schema:familyName Wicker
    211 schema:givenName Thomas
    212 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01133056131.64
    213 rdf:type schema:Person
    214 sg:person.01142452247.75 schema:affiliation grid-institutes:grid.418558.5
    215 schema:familyName Chen
    216 schema:givenName Mingsheng
    217 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01142452247.75
    218 rdf:type schema:Person
    219 sg:person.01311147311.85 schema:affiliation grid-institutes:grid.7400.3
    220 schema:familyName Roffler
    221 schema:givenName Stefan
    222 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01311147311.85
    223 rdf:type schema:Person
    224 sg:person.01330205131.66 schema:affiliation grid-institutes:grid.418574.b
    225 schema:familyName Rounsley
    226 schema:givenName Steve
    227 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01330205131.66
    228 rdf:type schema:Person
    229 sg:person.0635153405.31 schema:affiliation grid-institutes:grid.134563.6
    230 schema:familyName Yu
    231 schema:givenName Yeisoo
    232 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0635153405.31
    233 rdf:type schema:Person
    234 sg:person.0667267124.69 schema:affiliation grid-institutes:grid.4567.0
    235 schema:familyName Haberer
    236 schema:givenName Georg
    237 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0667267124.69
    238 rdf:type schema:Person
    239 sg:person.0707244327.29 schema:affiliation grid-institutes:grid.418574.b
    240 schema:familyName Marri
    241 schema:givenName Pradeep Reddy
    242 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0707244327.29
    243 rdf:type schema:Person
    244 sg:pub.10.1007/s00239-003-2570-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1002188655
    245 https://doi.org/10.1007/s00239-003-2570-y
    246 rdf:type schema:CreativeWork
    247 sg:pub.10.1007/s00438-007-0257-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036262010
    248 https://doi.org/10.1007/s00438-007-0257-6
    249 rdf:type schema:CreativeWork
    250 sg:pub.10.1007/s10577-014-9418-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024372429
    251 https://doi.org/10.1007/s10577-014-9418-8
    252 rdf:type schema:CreativeWork
    253 sg:pub.10.1007/s11103-004-6237-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1020001962
    254 https://doi.org/10.1007/s11103-004-6237-x
    255 rdf:type schema:CreativeWork
    256 sg:pub.10.1038/1695 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017391035
    257 https://doi.org/10.1038/1695
    258 rdf:type schema:CreativeWork
    259 sg:pub.10.1038/nature06047 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032121807
    260 https://doi.org/10.1038/nature06047
    261 rdf:type schema:CreativeWork
    262 sg:pub.10.1038/nature08747 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027862091
    263 https://doi.org/10.1038/nature08747
    264 rdf:type schema:CreativeWork
    265 sg:pub.10.1038/ng.3044 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023018294
    266 https://doi.org/10.1038/ng.3044
    267 rdf:type schema:CreativeWork
    268 sg:pub.10.1038/ng.986 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018680690
    269 https://doi.org/10.1038/ng.986
    270 rdf:type schema:CreativeWork
    271 sg:pub.10.1038/ng1784 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039398234
    272 https://doi.org/10.1038/ng1784
    273 rdf:type schema:CreativeWork
    274 sg:pub.10.1038/nrg2165 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053647019
    275 https://doi.org/10.1038/nrg2165
    276 rdf:type schema:CreativeWork
    277 sg:pub.10.1038/nrm804 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051255007
    278 https://doi.org/10.1038/nrm804
    279 rdf:type schema:CreativeWork
    280 sg:pub.10.1186/s13100-015-0040-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1003535473
    281 https://doi.org/10.1186/s13100-015-0040-x
    282 rdf:type schema:CreativeWork
    283 sg:pub.10.1186/s13100-015-0054-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005478710
    284 https://doi.org/10.1186/s13100-015-0054-4
    285 rdf:type schema:CreativeWork
    286 grid-institutes:grid.134563.6 schema:alternateName Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
    287 Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
    288 schema:name Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
    289 Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
    290 International Rice Research Institute, Los Baños, 4031 Laguna, Philippines
    291 rdf:type schema:Organization
    292 grid-institutes:grid.263145.7 schema:alternateName Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy
    293 schema:name Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy
    294 rdf:type schema:Organization
    295 grid-institutes:grid.418558.5 schema:alternateName State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
    296 schema:name State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
    297 rdf:type schema:Organization
    298 grid-institutes:grid.418574.b schema:alternateName Dow AgroSciences, Indianapolis, Indiana 46268, USA
    299 schema:name Dow AgroSciences, Indianapolis, Indiana 46268, USA
    300 rdf:type schema:Organization
    301 grid-institutes:grid.4567.0 schema:alternateName Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
    302 schema:name Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
    303 rdf:type schema:Organization
    304 grid-institutes:grid.463998.9 schema:alternateName Laboratoire Génome et Développement des Plantes, UMR5096 UPVD/CNRS, Université de Perpignan Via Domitia, 66860 Perpignan, France
    305 schema:name Laboratoire Génome et Développement des Plantes, UMR5096 UPVD/CNRS, Université de Perpignan Via Domitia, 66860 Perpignan, France
    306 rdf:type schema:Organization
    307 grid-institutes:grid.7400.3 schema:alternateName Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
    308 schema:name Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
    309 rdf:type schema:Organization
     




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


    ...