Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-04-23

AUTHORS

Ricardo A. Chávez Montes, de Fátima Flor Rosas-Cárdenas, Emanuele De Paoli, Monica Accerbi, Linda A. Rymarquis, Gayathri Mahalingam, Nayelli Marsch-Martínez, Blake C. Meyers, Pamela J. Green, Stefan de Folter

ABSTRACT

Small RNAs are pivotal regulators of gene expression that guide transcriptional and post-transcriptional silencing mechanisms in eukaryotes, including plants. Here we report a comprehensive atlas of sRNA and miRNA from 3 species of algae and 31 representative species across vascular plants, including non-model plants. We sequence and quantify sRNAs from 99 different tissues or treatments across species, resulting in a data set of over 132 million distinct sequences. Using miRBase mature sequences as a reference, we identify the miRNA sequences present in these libraries. We apply diverse profiling methods to examine critical sRNA and miRNA features, such as size distribution, tissue-specific regulation and sequence conservation between species, as well as to predict putative new miRNA sequences. We also develop database resources, computational analysis tools and a dedicated website, http://smallrna.udel.edu/. This study provides new insights on plant sRNAs and miRNAs, and a foundation for future studies. More... »

PAGES

3722

References to SciGraph publications

  • 2011-04-28. Vive la différence: biogenesis and evolution of microRNAs in plants and animals in GENOME BIOLOGY
  • 2012-08-08. Analysis of plant-derived miRNAs in animal small RNA datasets in BMC GENOMICS
  • 2011-07-10. Genome sequence and analysis of the tuber crop potato in NATURE
  • 2009-01. The Sorghum bicolor genome and the diversification of grasses in NATURE
  • 2012-05-13. Reference genome sequence of the model plant Setaria in NATURE BIOTECHNOLOGY
  • 2009-02. Small silencing RNAs: an expanding universe in NATURE REVIEWS GENETICS
  • 2008. MicroRNA Metabolism in Plants in RNA INTERFERENCE
  • 2007-06-06. Mimulus is an emerging model system for the integration of ecological and genomic studies in HEREDITY
  • 2004-04. Ancient microRNA target sequences in plants in NATURE
  • 2011-10-14. Conservation and divergence in plant microRNAs in PLANT MOLECULAR BIOLOGY
  • 2009-09-06. Methods for Isolation of Total RNA to Recover miRNAs and Other Small RNAs from Diverse Species in PLANT MICRORNAS
  • 2007-08-26. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla in NATURE
  • 2005-05-05. Plant and animal microRNAs: similarities and differences in FUNCTIONAL & INTEGRATIVE GENOMICS
  • 2008-04. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) in NATURE
  • 2012-02-22. Identification of wounding and topping responsive small RNAs in tobacco (Nicotiana tabacum) in BMC PLANT BIOLOGY
  • 2009-09-06. Computational Methods for Comparative Analysis of Plant Small RNAs in PLANT MICRORNAS
  • 2012-10-17. A physical, genetic and functional sequence assembly of the barley genome in NATURE
  • 2009-03-04. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome in GENOME BIOLOGY
  • 2010-02. Genome sequencing and analysis of the model grass Brachypodium distachyon in NATURE
  • 2012-07-11. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants in NATURE
  • 2012-05-30. The tomato genome sequence provides insights into fleshy fruit evolution in NATURE
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/ncomms4722

    DOI

    http://dx.doi.org/10.1038/ncomms4722

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1009765698

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/24759728


    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"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0607", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Plant Biology", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "MicroRNAs", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Phylogeny", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Plants", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Laboratorio Nacional de Gen\u00f3mica para la Biodiversidad (LANGEBIO), Centro de Investigaci\u00f3n y de Estudios Avanzados del Instituto Polit\u00e9cnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-Le\u00f3n, CP 36821, Irapuato, Guanajuato, M\u00e9xico", 
              "id": "http://www.grid.ac/institutes/grid.512574.0", 
              "name": [
                "Laboratorio Nacional de Gen\u00f3mica para la Biodiversidad (LANGEBIO), Centro de Investigaci\u00f3n y de Estudios Avanzados del Instituto Polit\u00e9cnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-Le\u00f3n, CP 36821, Irapuato, Guanajuato, M\u00e9xico"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Ch\u00e1vez Montes", 
            "givenName": "Ricardo A.", 
            "id": "sg:person.0714262665.49", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0714262665.49"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Present address: Centro de Investigaci\u00f3n en Biotecnolog\u00eda Aplicada del Instituto Polit\u00e9cnico Nacional (CIBA-IPN), Exhacienda San Juan Molino, Tepetitla de Lardiz\u00e1bal, Tlaxcala, M\u00e9xico", 
              "id": "http://www.grid.ac/institutes/None", 
              "name": [
                "Laboratorio Nacional de Gen\u00f3mica para la Biodiversidad (LANGEBIO), Centro de Investigaci\u00f3n y de Estudios Avanzados del Instituto Polit\u00e9cnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-Le\u00f3n, CP 36821, Irapuato, Guanajuato, M\u00e9xico", 
                "Present address: Centro de Investigaci\u00f3n en Biotecnolog\u00eda Aplicada del Instituto Polit\u00e9cnico Nacional (CIBA-IPN), Exhacienda San Juan Molino, Tepetitla de Lardiz\u00e1bal, Tlaxcala, M\u00e9xico"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Rosas-C\u00e1rdenas", 
            "givenName": "de F\u00e1tima Flor", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Present address: Dipartimento di Scienze Agrarie e Ambientali, Universit\u00e0 degli Studi di Udine, via delle Scienze 206, 33100 Udine, Italy", 
              "id": "http://www.grid.ac/institutes/grid.5390.f", 
              "name": [
                "Department of Plant and Soil Sciences, University of Delaware, 19717, Newark, Delaware, USA", 
                "Delaware Biotechnology Institute, University of Delaware, 19711, Newark, Delaware, USA", 
                "Present address: Dipartimento di Scienze Agrarie e Ambientali, Universit\u00e0 degli Studi di Udine, via delle Scienze 206, 33100 Udine, Italy"
              ], 
              "type": "Organization"
            }, 
            "familyName": "De Paoli", 
            "givenName": "Emanuele", 
            "id": "sg:person.0657011733.34", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0657011733.34"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Delaware Biotechnology Institute, University of Delaware, 19711, Newark, Delaware, USA", 
              "id": "http://www.grid.ac/institutes/grid.33489.35", 
              "name": [
                "Department of Plant and Soil Sciences, University of Delaware, 19717, Newark, Delaware, USA", 
                "Delaware Biotechnology Institute, University of Delaware, 19711, Newark, Delaware, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Accerbi", 
            "givenName": "Monica", 
            "id": "sg:person.01351763613.66", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01351763613.66"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Present address: Monsanto Company, Chesterfield, Missouri 63017, USA", 
              "id": "http://www.grid.ac/institutes/grid.418554.9", 
              "name": [
                "Department of Plant and Soil Sciences, University of Delaware, 19717, Newark, Delaware, USA", 
                "Delaware Biotechnology Institute, University of Delaware, 19711, Newark, Delaware, USA", 
                "Present address: Monsanto Company, Chesterfield, Missouri 63017, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Rymarquis", 
            "givenName": "Linda A.", 
            "id": "sg:person.0650212025.44", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0650212025.44"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Delaware Biotechnology Institute, University of Delaware, 19711, Newark, Delaware, USA", 
              "id": "http://www.grid.ac/institutes/grid.33489.35", 
              "name": [
                "Department of Plant and Soil Sciences, University of Delaware, 19717, Newark, Delaware, USA", 
                "Delaware Biotechnology Institute, University of Delaware, 19711, Newark, Delaware, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Mahalingam", 
            "givenName": "Gayathri", 
            "id": "sg:person.012757577233.38", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012757577233.38"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Departamento de Biotecnolog\u00eda y Bioqu\u00edmica, CINVESTAV-IPN, Km. 9.6 Libramiento Norte, Carretera Irapuato-Le\u00f3n, CP 36821, Irapuato, Guanajuato, M\u00e9xico", 
              "id": "http://www.grid.ac/institutes/grid.512574.0", 
              "name": [
                "Departamento de Biotecnolog\u00eda y Bioqu\u00edmica, CINVESTAV-IPN, Km. 9.6 Libramiento Norte, Carretera Irapuato-Le\u00f3n, CP 36821, Irapuato, Guanajuato, M\u00e9xico"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Marsch-Mart\u00ednez", 
            "givenName": "Nayelli", 
            "id": "sg:person.0732361220.85", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0732361220.85"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Delaware Biotechnology Institute, University of Delaware, 19711, Newark, Delaware, USA", 
              "id": "http://www.grid.ac/institutes/grid.33489.35", 
              "name": [
                "Department of Plant and Soil Sciences, University of Delaware, 19717, Newark, Delaware, USA", 
                "Delaware Biotechnology Institute, University of Delaware, 19711, Newark, Delaware, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Meyers", 
            "givenName": "Blake C.", 
            "id": "sg:person.0772063006.02", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0772063006.02"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Delaware Biotechnology Institute, University of Delaware, 19711, Newark, Delaware, USA", 
              "id": "http://www.grid.ac/institutes/grid.33489.35", 
              "name": [
                "Department of Plant and Soil Sciences, University of Delaware, 19717, Newark, Delaware, USA", 
                "Delaware Biotechnology Institute, University of Delaware, 19711, Newark, Delaware, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Green", 
            "givenName": "Pamela J.", 
            "id": "sg:person.01024060464.92", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01024060464.92"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Laboratorio Nacional de Gen\u00f3mica para la Biodiversidad (LANGEBIO), Centro de Investigaci\u00f3n y de Estudios Avanzados del Instituto Polit\u00e9cnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-Le\u00f3n, CP 36821, Irapuato, Guanajuato, M\u00e9xico", 
              "id": "http://www.grid.ac/institutes/grid.512574.0", 
              "name": [
                "Laboratorio Nacional de Gen\u00f3mica para la Biodiversidad (LANGEBIO), Centro de Investigaci\u00f3n y de Estudios Avanzados del Instituto Polit\u00e9cnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-Le\u00f3n, CP 36821, Irapuato, Guanajuato, M\u00e9xico"
              ], 
              "type": "Organization"
            }, 
            "familyName": "de Folter", 
            "givenName": "Stefan", 
            "id": "sg:person.01161213237.00", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01161213237.00"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1007/978-1-60327-005-2_12", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050533340", 
              "https://doi.org/10.1007/978-1-60327-005-2_12"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature07723", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1020371055", 
              "https://doi.org/10.1038/nature07723"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg2504", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1021297038", 
              "https://doi.org/10.1038/nrg2504"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature10158", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002525491", 
              "https://doi.org/10.1038/nature10158"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.2196", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013548949", 
              "https://doi.org/10.1038/nbt.2196"
            ], 
            "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.10.1186/1471-2164-13-381", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028375979", 
              "https://doi.org/10.1186/1471-2164-13-381"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature11119", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1047486795", 
              "https://doi.org/10.1038/nature11119"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature11543", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017891944", 
              "https://doi.org/10.1038/nature11543"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/sj.hdy.6801018", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1046315705", 
              "https://doi.org/10.1038/sj.hdy.6801018"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature06856", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008392516", 
              "https://doi.org/10.1038/nature06856"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/428485a", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035666241", 
              "https://doi.org/10.1038/428485a"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature06148", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040664071", 
              "https://doi.org/10.1038/nature06148"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2229-12-28", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1039708679", 
              "https://doi.org/10.1186/1471-2229-12-28"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2009-10-3-r25", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1049583368", 
              "https://doi.org/10.1186/gb-2009-10-3-r25"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/978-3-540-75157-1_6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008237587", 
              "https://doi.org/10.1007/978-3-540-75157-1_6"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10142-005-0145-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015107869", 
              "https://doi.org/10.1007/s10142-005-0145-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2011-12-4-221", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050594305", 
              "https://doi.org/10.1186/gb-2011-12-4-221"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/978-1-60327-005-2_3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008303215", 
              "https://doi.org/10.1007/978-1-60327-005-2_3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature11241", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000546815", 
              "https://doi.org/10.1038/nature11241"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11103-011-9829-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030103737", 
              "https://doi.org/10.1007/s11103-011-9829-2"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2014-04-23", 
        "datePublishedReg": "2014-04-23", 
        "description": "Small RNAs are pivotal regulators of gene expression that guide transcriptional and post-transcriptional silencing mechanisms in eukaryotes, including plants. Here we report a comprehensive atlas of sRNA and miRNA from 3 species of algae and 31 representative species across vascular plants, including non-model plants. We sequence and quantify sRNAs from 99 different tissues or treatments across species, resulting in a data set of over 132 million distinct sequences. Using miRBase mature sequences as a reference, we identify the miRNA sequences present in these libraries. We apply diverse profiling methods to examine critical sRNA and miRNA features, such as size distribution, tissue-specific regulation and sequence conservation between species, as well as to predict putative new miRNA sequences. We also develop database resources, computational analysis tools and a dedicated website, http://smallrna.udel.edu/. This study provides new insights on plant sRNAs and miRNAs, and a foundation for future studies.", 
        "genre": "article", 
        "id": "sg:pub.10.1038/ncomms4722", 
        "inLanguage": "en", 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.3072857", 
            "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": "5"
          }
        ], 
        "keywords": [
          "vascular plants", 
          "miRNA sequences", 
          "post-transcriptional silencing mechanisms", 
          "non-model plants", 
          "species of algae", 
          "new miRNA sequences", 
          "tissue-specific regulation", 
          "plant sRNAs", 
          "widespread conservation", 
          "sequence conservation", 
          "small RNAs", 
          "silencing mechanism", 
          "mature sequence", 
          "representative species", 
          "miRNA features", 
          "gene expression", 
          "comprehensive atlas", 
          "pivotal regulator", 
          "sample sequencing", 
          "different tissues", 
          "database resources", 
          "sRNAs", 
          "species", 
          "plants", 
          "sRNAs", 
          "distinct sequences", 
          "profiling method", 
          "sequence", 
          "new insights", 
          "computational analysis tools", 
          "conservation", 
          "eukaryotes", 
          "algae", 
          "miRNAs", 
          "miRNA", 
          "microRNAs", 
          "RNA", 
          "regulator", 
          "sequencing", 
          "divergence", 
          "regulation", 
          "expression", 
          "future studies", 
          "atlas", 
          "tissue", 
          "library", 
          "insights", 
          "mechanism", 
          "data sets", 
          "analysis tools", 
          "study", 
          "distribution", 
          "dedicated website", 
          "resources", 
          "tool", 
          "features", 
          "set", 
          "treatment", 
          "foundation", 
          "reference", 
          "size distribution", 
          "method", 
          "websites"
        ], 
        "name": "Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs", 
        "pagination": "3722", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1009765698"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1038/ncomms4722"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "24759728"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1038/ncomms4722", 
          "https://app.dimensions.ai/details/publication/pub.1009765698"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-05-10T10:09", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20220509/entities/gbq_results/article/article_642.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1038/ncomms4722"
      }
    ]
     

    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/ncomms4722'

    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/ncomms4722'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/ncomms4722'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/ncomms4722'


     

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

    307 TRIPLES      22 PREDICATES      113 URIs      83 LITERALS      10 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1038/ncomms4722 schema:about N1530d6f9023541fcb6385e27df2f487c
    2 N19b4da8f88d74e558d22a8d880bf35c0
    3 N79a763973a4d41aeb064897b9d61b62b
    4 anzsrc-for:06
    5 anzsrc-for:0604
    6 anzsrc-for:0607
    7 schema:author Nc94803732730484abf43809aba7e2640
    8 schema:citation sg:pub.10.1007/978-1-60327-005-2_12
    9 sg:pub.10.1007/978-1-60327-005-2_3
    10 sg:pub.10.1007/978-3-540-75157-1_6
    11 sg:pub.10.1007/s10142-005-0145-2
    12 sg:pub.10.1007/s11103-011-9829-2
    13 sg:pub.10.1038/428485a
    14 sg:pub.10.1038/nature06148
    15 sg:pub.10.1038/nature06856
    16 sg:pub.10.1038/nature07723
    17 sg:pub.10.1038/nature08747
    18 sg:pub.10.1038/nature10158
    19 sg:pub.10.1038/nature11119
    20 sg:pub.10.1038/nature11241
    21 sg:pub.10.1038/nature11543
    22 sg:pub.10.1038/nbt.2196
    23 sg:pub.10.1038/nrg2504
    24 sg:pub.10.1038/sj.hdy.6801018
    25 sg:pub.10.1186/1471-2164-13-381
    26 sg:pub.10.1186/1471-2229-12-28
    27 sg:pub.10.1186/gb-2009-10-3-r25
    28 sg:pub.10.1186/gb-2011-12-4-221
    29 schema:datePublished 2014-04-23
    30 schema:datePublishedReg 2014-04-23
    31 schema:description Small RNAs are pivotal regulators of gene expression that guide transcriptional and post-transcriptional silencing mechanisms in eukaryotes, including plants. Here we report a comprehensive atlas of sRNA and miRNA from 3 species of algae and 31 representative species across vascular plants, including non-model plants. We sequence and quantify sRNAs from 99 different tissues or treatments across species, resulting in a data set of over 132 million distinct sequences. Using miRBase mature sequences as a reference, we identify the miRNA sequences present in these libraries. We apply diverse profiling methods to examine critical sRNA and miRNA features, such as size distribution, tissue-specific regulation and sequence conservation between species, as well as to predict putative new miRNA sequences. We also develop database resources, computational analysis tools and a dedicated website, http://smallrna.udel.edu/. This study provides new insights on plant sRNAs and miRNAs, and a foundation for future studies.
    32 schema:genre article
    33 schema:inLanguage en
    34 schema:isAccessibleForFree true
    35 schema:isPartOf N138d6bf1814f443cb0c7bbab413e82a8
    36 N8b74f5a00291467ba5ff2026ddc128a2
    37 sg:journal.1043282
    38 schema:keywords RNA
    39 algae
    40 analysis tools
    41 atlas
    42 comprehensive atlas
    43 computational analysis tools
    44 conservation
    45 data sets
    46 database resources
    47 dedicated website
    48 different tissues
    49 distinct sequences
    50 distribution
    51 divergence
    52 eukaryotes
    53 expression
    54 features
    55 foundation
    56 future studies
    57 gene expression
    58 insights
    59 library
    60 mature sequence
    61 mechanism
    62 method
    63 miRNA
    64 miRNA features
    65 miRNA sequences
    66 miRNAs
    67 microRNAs
    68 new insights
    69 new miRNA sequences
    70 non-model plants
    71 pivotal regulator
    72 plant sRNAs
    73 plants
    74 post-transcriptional silencing mechanisms
    75 profiling method
    76 reference
    77 regulation
    78 regulator
    79 representative species
    80 resources
    81 sRNAs
    82 sample sequencing
    83 sequence
    84 sequence conservation
    85 sequencing
    86 set
    87 silencing mechanism
    88 size distribution
    89 small RNAs
    90 species
    91 species of algae
    92 study
    93 tissue
    94 tissue-specific regulation
    95 tool
    96 treatment
    97 vascular plants
    98 websites
    99 widespread conservation
    100 schema:name Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs
    101 schema:pagination 3722
    102 schema:productId N38afcac3ddba4746a74c822373661315
    103 N3a2bf0885e4345adb15cab44c8af92c4
    104 N8b0acf2596684b31bca23c7a97f01d28
    105 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009765698
    106 https://doi.org/10.1038/ncomms4722
    107 schema:sdDatePublished 2022-05-10T10:09
    108 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    109 schema:sdPublisher N86aeedde58ae4e4d88c248b67a29aef7
    110 schema:url https://doi.org/10.1038/ncomms4722
    111 sgo:license sg:explorer/license/
    112 sgo:sdDataset articles
    113 rdf:type schema:ScholarlyArticle
    114 N04f3859c842842f9982a7faa16026cef rdf:first sg:person.0732361220.85
    115 rdf:rest N493870dfcbd34fe8a7028d229e058fb5
    116 N138d6bf1814f443cb0c7bbab413e82a8 schema:volumeNumber 5
    117 rdf:type schema:PublicationVolume
    118 N1530d6f9023541fcb6385e27df2f487c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    119 schema:name MicroRNAs
    120 rdf:type schema:DefinedTerm
    121 N19b4da8f88d74e558d22a8d880bf35c0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    122 schema:name Phylogeny
    123 rdf:type schema:DefinedTerm
    124 N25fbf0437bc249529a5bbae0e0eaa3e6 rdf:first sg:person.01024060464.92
    125 rdf:rest Nd47bca5abbc94b5592ec1462214d72c3
    126 N26bacd3439af45f9b6858a8b794ce81a rdf:first sg:person.01351763613.66
    127 rdf:rest N5fff6f78fd0a41b4aeadaa2d73263069
    128 N38afcac3ddba4746a74c822373661315 schema:name pubmed_id
    129 schema:value 24759728
    130 rdf:type schema:PropertyValue
    131 N3a2bf0885e4345adb15cab44c8af92c4 schema:name doi
    132 schema:value 10.1038/ncomms4722
    133 rdf:type schema:PropertyValue
    134 N493870dfcbd34fe8a7028d229e058fb5 rdf:first sg:person.0772063006.02
    135 rdf:rest N25fbf0437bc249529a5bbae0e0eaa3e6
    136 N596c329d52394dbe9b15f6fcaf8e08e2 schema:affiliation grid-institutes:None
    137 schema:familyName Rosas-Cárdenas
    138 schema:givenName de Fátima Flor
    139 rdf:type schema:Person
    140 N5fff6f78fd0a41b4aeadaa2d73263069 rdf:first sg:person.0650212025.44
    141 rdf:rest Nc34ac1c7e82045b79a0ee8d730be9b7c
    142 N6d307162b67c4da7925fbc03d018afb4 rdf:first sg:person.0657011733.34
    143 rdf:rest N26bacd3439af45f9b6858a8b794ce81a
    144 N79a763973a4d41aeb064897b9d61b62b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    145 schema:name Plants
    146 rdf:type schema:DefinedTerm
    147 N86aeedde58ae4e4d88c248b67a29aef7 schema:name Springer Nature - SN SciGraph project
    148 rdf:type schema:Organization
    149 N8b0acf2596684b31bca23c7a97f01d28 schema:name dimensions_id
    150 schema:value pub.1009765698
    151 rdf:type schema:PropertyValue
    152 N8b74f5a00291467ba5ff2026ddc128a2 schema:issueNumber 1
    153 rdf:type schema:PublicationIssue
    154 Na94cba4a0d5d4aa696afc98e092c2a3b rdf:first N596c329d52394dbe9b15f6fcaf8e08e2
    155 rdf:rest N6d307162b67c4da7925fbc03d018afb4
    156 Nc34ac1c7e82045b79a0ee8d730be9b7c rdf:first sg:person.012757577233.38
    157 rdf:rest N04f3859c842842f9982a7faa16026cef
    158 Nc94803732730484abf43809aba7e2640 rdf:first sg:person.0714262665.49
    159 rdf:rest Na94cba4a0d5d4aa696afc98e092c2a3b
    160 Nd47bca5abbc94b5592ec1462214d72c3 rdf:first sg:person.01161213237.00
    161 rdf:rest rdf:nil
    162 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    163 schema:name Biological Sciences
    164 rdf:type schema:DefinedTerm
    165 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    166 schema:name Genetics
    167 rdf:type schema:DefinedTerm
    168 anzsrc-for:0607 schema:inDefinedTermSet anzsrc-for:
    169 schema:name Plant Biology
    170 rdf:type schema:DefinedTerm
    171 sg:grant.3072857 http://pending.schema.org/fundedItem sg:pub.10.1038/ncomms4722
    172 rdf:type schema:MonetaryGrant
    173 sg:journal.1043282 schema:issn 2041-1723
    174 schema:name Nature Communications
    175 schema:publisher Springer Nature
    176 rdf:type schema:Periodical
    177 sg:person.01024060464.92 schema:affiliation grid-institutes:grid.33489.35
    178 schema:familyName Green
    179 schema:givenName Pamela J.
    180 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01024060464.92
    181 rdf:type schema:Person
    182 sg:person.01161213237.00 schema:affiliation grid-institutes:grid.512574.0
    183 schema:familyName de Folter
    184 schema:givenName Stefan
    185 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01161213237.00
    186 rdf:type schema:Person
    187 sg:person.012757577233.38 schema:affiliation grid-institutes:grid.33489.35
    188 schema:familyName Mahalingam
    189 schema:givenName Gayathri
    190 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012757577233.38
    191 rdf:type schema:Person
    192 sg:person.01351763613.66 schema:affiliation grid-institutes:grid.33489.35
    193 schema:familyName Accerbi
    194 schema:givenName Monica
    195 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01351763613.66
    196 rdf:type schema:Person
    197 sg:person.0650212025.44 schema:affiliation grid-institutes:grid.418554.9
    198 schema:familyName Rymarquis
    199 schema:givenName Linda A.
    200 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0650212025.44
    201 rdf:type schema:Person
    202 sg:person.0657011733.34 schema:affiliation grid-institutes:grid.5390.f
    203 schema:familyName De Paoli
    204 schema:givenName Emanuele
    205 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0657011733.34
    206 rdf:type schema:Person
    207 sg:person.0714262665.49 schema:affiliation grid-institutes:grid.512574.0
    208 schema:familyName Chávez Montes
    209 schema:givenName Ricardo A.
    210 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0714262665.49
    211 rdf:type schema:Person
    212 sg:person.0732361220.85 schema:affiliation grid-institutes:grid.512574.0
    213 schema:familyName Marsch-Martínez
    214 schema:givenName Nayelli
    215 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0732361220.85
    216 rdf:type schema:Person
    217 sg:person.0772063006.02 schema:affiliation grid-institutes:grid.33489.35
    218 schema:familyName Meyers
    219 schema:givenName Blake C.
    220 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0772063006.02
    221 rdf:type schema:Person
    222 sg:pub.10.1007/978-1-60327-005-2_12 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050533340
    223 https://doi.org/10.1007/978-1-60327-005-2_12
    224 rdf:type schema:CreativeWork
    225 sg:pub.10.1007/978-1-60327-005-2_3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008303215
    226 https://doi.org/10.1007/978-1-60327-005-2_3
    227 rdf:type schema:CreativeWork
    228 sg:pub.10.1007/978-3-540-75157-1_6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008237587
    229 https://doi.org/10.1007/978-3-540-75157-1_6
    230 rdf:type schema:CreativeWork
    231 sg:pub.10.1007/s10142-005-0145-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015107869
    232 https://doi.org/10.1007/s10142-005-0145-2
    233 rdf:type schema:CreativeWork
    234 sg:pub.10.1007/s11103-011-9829-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030103737
    235 https://doi.org/10.1007/s11103-011-9829-2
    236 rdf:type schema:CreativeWork
    237 sg:pub.10.1038/428485a schema:sameAs https://app.dimensions.ai/details/publication/pub.1035666241
    238 https://doi.org/10.1038/428485a
    239 rdf:type schema:CreativeWork
    240 sg:pub.10.1038/nature06148 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040664071
    241 https://doi.org/10.1038/nature06148
    242 rdf:type schema:CreativeWork
    243 sg:pub.10.1038/nature06856 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008392516
    244 https://doi.org/10.1038/nature06856
    245 rdf:type schema:CreativeWork
    246 sg:pub.10.1038/nature07723 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020371055
    247 https://doi.org/10.1038/nature07723
    248 rdf:type schema:CreativeWork
    249 sg:pub.10.1038/nature08747 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027862091
    250 https://doi.org/10.1038/nature08747
    251 rdf:type schema:CreativeWork
    252 sg:pub.10.1038/nature10158 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002525491
    253 https://doi.org/10.1038/nature10158
    254 rdf:type schema:CreativeWork
    255 sg:pub.10.1038/nature11119 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047486795
    256 https://doi.org/10.1038/nature11119
    257 rdf:type schema:CreativeWork
    258 sg:pub.10.1038/nature11241 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000546815
    259 https://doi.org/10.1038/nature11241
    260 rdf:type schema:CreativeWork
    261 sg:pub.10.1038/nature11543 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017891944
    262 https://doi.org/10.1038/nature11543
    263 rdf:type schema:CreativeWork
    264 sg:pub.10.1038/nbt.2196 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013548949
    265 https://doi.org/10.1038/nbt.2196
    266 rdf:type schema:CreativeWork
    267 sg:pub.10.1038/nrg2504 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021297038
    268 https://doi.org/10.1038/nrg2504
    269 rdf:type schema:CreativeWork
    270 sg:pub.10.1038/sj.hdy.6801018 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046315705
    271 https://doi.org/10.1038/sj.hdy.6801018
    272 rdf:type schema:CreativeWork
    273 sg:pub.10.1186/1471-2164-13-381 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028375979
    274 https://doi.org/10.1186/1471-2164-13-381
    275 rdf:type schema:CreativeWork
    276 sg:pub.10.1186/1471-2229-12-28 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039708679
    277 https://doi.org/10.1186/1471-2229-12-28
    278 rdf:type schema:CreativeWork
    279 sg:pub.10.1186/gb-2009-10-3-r25 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049583368
    280 https://doi.org/10.1186/gb-2009-10-3-r25
    281 rdf:type schema:CreativeWork
    282 sg:pub.10.1186/gb-2011-12-4-221 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050594305
    283 https://doi.org/10.1186/gb-2011-12-4-221
    284 rdf:type schema:CreativeWork
    285 grid-institutes:None schema:alternateName Present address: Centro de Investigación en Biotecnología Aplicada del Instituto Politécnico Nacional (CIBA-IPN), Exhacienda San Juan Molino, Tepetitla de Lardizábal, Tlaxcala, México
    286 schema:name Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36821, Irapuato, Guanajuato, México
    287 Present address: Centro de Investigación en Biotecnología Aplicada del Instituto Politécnico Nacional (CIBA-IPN), Exhacienda San Juan Molino, Tepetitla de Lardizábal, Tlaxcala, México
    288 rdf:type schema:Organization
    289 grid-institutes:grid.33489.35 schema:alternateName Delaware Biotechnology Institute, University of Delaware, 19711, Newark, Delaware, USA
    290 schema:name Delaware Biotechnology Institute, University of Delaware, 19711, Newark, Delaware, USA
    291 Department of Plant and Soil Sciences, University of Delaware, 19717, Newark, Delaware, USA
    292 rdf:type schema:Organization
    293 grid-institutes:grid.418554.9 schema:alternateName Present address: Monsanto Company, Chesterfield, Missouri 63017, USA
    294 schema:name Delaware Biotechnology Institute, University of Delaware, 19711, Newark, Delaware, USA
    295 Department of Plant and Soil Sciences, University of Delaware, 19717, Newark, Delaware, USA
    296 Present address: Monsanto Company, Chesterfield, Missouri 63017, USA
    297 rdf:type schema:Organization
    298 grid-institutes:grid.512574.0 schema:alternateName Departamento de Biotecnología y Bioquímica, CINVESTAV-IPN, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36821, Irapuato, Guanajuato, México
    299 Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36821, Irapuato, Guanajuato, México
    300 schema:name Departamento de Biotecnología y Bioquímica, CINVESTAV-IPN, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36821, Irapuato, Guanajuato, México
    301 Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36821, Irapuato, Guanajuato, México
    302 rdf:type schema:Organization
    303 grid-institutes:grid.5390.f schema:alternateName Present address: Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Udine, via delle Scienze 206, 33100 Udine, Italy
    304 schema:name Delaware Biotechnology Institute, University of Delaware, 19711, Newark, Delaware, USA
    305 Department of Plant and Soil Sciences, University of Delaware, 19717, Newark, Delaware, USA
    306 Present address: Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Udine, via delle Scienze 206, 33100 Udine, Italy
    307 rdf:type schema:Organization
     




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


    ...