Genome-wide variation in recombination rate in Eucalyptus View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2016-08-09

AUTHORS

Jean-Marc Gion, Corey J. Hudson, Isabelle Lesur, René E. Vaillancourt, Brad M. Potts, Jules S. Freeman

ABSTRACT

BackgroundMeiotic recombination is a fundamental evolutionary process. It not only generates diversity, but influences the efficacy of natural selection and genome evolution. There can be significant heterogeneity in recombination rates within and between species, however this variation is not well understood outside of a few model taxa, particularly in forest trees. Eucalypts are forest trees of global economic importance, and dominate many Australian ecosystems. We studied recombination rate in Eucalyptus globulus using genetic linkage maps constructed in 10 unrelated individuals, and markers anchored to the Eucalyptus reference genome. This experimental design provided the replication to study whether recombination rate varied between individuals and chromosomes, and allowed us to study the genomic attributes and population genetic parameters correlated with this variation.ResultsRecombination rate varied significantly between individuals (range = 2.71 to 3.51 centimorgans/megabase [cM/Mb]), but was not significantly influenced by sex or cross type (F1 vs. F2). Significant differences in recombination rate between chromosomes were also evident (range = 1.98 to 3.81 cM/Mb), beyond those which were due to variation in chromosome size. Variation in chromosomal recombination rate was significantly correlated with gene density (r = 0.94), GC content (r = 0.90), and the number of tandem duplicated genes (r = −0.72) per chromosome. Notably, chromosome level recombination rate was also negatively correlated with the average genetic diversity across six species from an independent set of samples (r = −0.75).ConclusionsThe correlations with genomic attributes are consistent with findings in other taxa, however, the direction of the correlation between diversity and recombination rate is opposite to that commonly observed. We argue this is likely to reflect the interaction of selection and specific genome architecture of Eucalyptus. Interestingly, the differences amongst chromosomes in recombination rates appear stable across Eucalyptus species. Together with the strong correlations between recombination rate and features of the Eucalyptus reference genome, we maintain these findings provide further evidence for a broad conservation of genome architecture across the globally significant lineages of Eucalyptus. More... »

PAGES

590

References to SciGraph publications

  • 2006-09-22. A microsatellite-based consensus linkage map for species of Eucalyptusand a novel set of 230 microsatellite markers for the genus in BMC PLANT BIOLOGY
  • 2011-06-15. Recombination rate variation in closely related species in HEREDITY
  • 2005-12-01. RECORD: a novel method for ordering loci on a genetic linkage map in THEORETICAL AND APPLIED GENETICS
  • 2013-04-18. High-density linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and provides clues to the extent and distribution of meiotic recombination in BMC BIOLOGY
  • 2002-06-24. Reciprocal crossover asymmetry and meiotic drive in a human recombination hot spot in NATURE GENETICS
  • 2011-01-18. Forest tree genomics: growing resources and applications in NATURE REVIEWS GENETICS
  • 2010-10-27. Fine-scale recombination rate differences between sexes, populations and individuals in NATURE
  • 2002-10-30. Control of meiotic recombination initiation: a role for the environment? in CURRENT GENETICS
  • 1992-04. Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster in NATURE
  • 2010-06-30. A high-density Diversity Arrays Technology (DArT) microarray for genome-wide genotyping in Eucalyptus in PLANT METHODS
  • 2013-09-19. Intraspecific variation of recombination rate in maize in GENOME BIOLOGY
  • 2009-06. Mapping genes for complex traits in domestic animals and their use in breeding programmes in NATURE REVIEWS GENETICS
  • 2011-11-17. High synteny and colinearity among Eucalyptus genomes revealed by high-density comparative genetic mapping in TREE GENETICS & GENOMES
  • 2011-02-15. Flammable biomes dominated by eucalypts originated at the Cretaceous–Palaeogene boundary in NATURE COMMUNICATIONS
  • 2011-11-09. The recombination landscape in Arabidopsis thaliana F2 populations in HEREDITY
  • 2013-02-08. Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination in BMC GENOMICS
  • 2007-01. Recombination: an underappreciated factor in the evolution of plant genomes in NATURE REVIEWS GENETICS
  • 2013-03-12. Genomic signatures of selection at linked sites: unifying the disparity among species in NATURE REVIEWS GENETICS
  • 2011-09-06. High-density genetic linkage maps with over 2,400 sequence-anchored DArT markers for genetic dissection in an F2 pseudo-backcross of Eucalyptus grandis × E. urophylla in TREE GENETICS & GENOMES
  • 1996-11. High intrinsic rate of DNA loss in Drosophila in NATURE
  • 2012-04-15. Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus in TREE GENETICS & GENOMES
  • 2013-02-02. Dissection of complex traits in forest trees — opportunities for marker-assisted selection in TREE GENETICS & GENOMES
  • 2014-06-11. The genome of Eucalyptus grandis in NATURE
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s12864-016-2884-y

    DOI

    http://dx.doi.org/10.1186/s12864-016-2884-y

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1014910353

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/27507140


    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/2008/0602", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Ecology", 
            "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 Composition", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Chromosomes, Plant", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Crosses, Genetic", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Eucalyptus", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Evolution, Molecular", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genetic Variation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genetics, Population", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genome, Plant", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genomics", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Polymorphism, Single Nucleotide", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Recombination, Genetic", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "CIRAD, UMR AGAP, 69 route d\u2019Arcachon, Cestas, France", 
              "id": "http://www.grid.ac/institutes/None", 
              "name": [
                "CIRAD, UMR AGAP, 69 route d\u2019Arcachon, Cestas, France"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Gion", 
            "givenName": "Jean-Marc", 
            "id": "sg:person.01015124413.32", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01015124413.32"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Present address: Tasmanian Alkaloids, P.O. Box 130, 7303, Westbury, TAS, Australia", 
              "id": "http://www.grid.ac/institutes/None", 
              "name": [
                "School of Biological Sciences, University of Tasmania, Private Bag 55, 7001, Hobart, TAS, Australia", 
                "Present address: Tasmanian Alkaloids, P.O. Box 130, 7303, Westbury, TAS, Australia"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Hudson", 
            "givenName": "Corey J.", 
            "id": "sg:person.01340303237.44", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01340303237.44"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "HelixVenture, F33700, Merignac, France", 
              "id": "http://www.grid.ac/institutes/None", 
              "name": [
                "HelixVenture, F33700, Merignac, France"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Lesur", 
            "givenName": "Isabelle", 
            "id": "sg:person.01337051304.79", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01337051304.79"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "School of Biological Sciences, University of Tasmania, Private Bag 55, 7001, Hobart, TAS, Australia", 
              "id": "http://www.grid.ac/institutes/grid.1009.8", 
              "name": [
                "School of Biological Sciences, University of Tasmania, Private Bag 55, 7001, Hobart, TAS, Australia"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Vaillancourt", 
            "givenName": "Ren\u00e9 E.", 
            "id": "sg:person.01043454452.31", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01043454452.31"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "School of Biological Sciences, University of Tasmania, Private Bag 55, 7001, Hobart, TAS, Australia", 
              "id": "http://www.grid.ac/institutes/grid.1009.8", 
              "name": [
                "School of Biological Sciences, University of Tasmania, Private Bag 55, 7001, Hobart, TAS, Australia"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Potts", 
            "givenName": "Brad M.", 
            "id": "sg:person.014126024501.27", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014126024501.27"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "School of Biological Sciences, University of Tasmania, Private Bag 55, 7001, Hobart, TAS, Australia", 
              "id": "http://www.grid.ac/institutes/grid.1009.8", 
              "name": [
                "School of Biological Sciences, University of Tasmania, Private Bag 55, 7001, Hobart, TAS, Australia"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Freeman", 
            "givenName": "Jules S.", 
            "id": "sg:person.01305600750.67", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01305600750.67"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1038/ng910", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1020516195", 
              "https://doi.org/10.1038/ng910"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11295-011-0430-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1047761101", 
              "https://doi.org/10.1007/s11295-011-0430-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg2575", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051461847", 
              "https://doi.org/10.1038/nrg2575"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2164-14-86", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1014923008", 
              "https://doi.org/10.1186/1471-2164-14-86"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00294-002-0340-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1044678209", 
              "https://doi.org/10.1007/s00294-002-0340-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1741-7007-11-50", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032894745", 
              "https://doi.org/10.1186/1741-7007-11-50"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/hdy.2011.95", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030214191", 
              "https://doi.org/10.1038/hdy.2011.95"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2013-14-9-r103", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002151324", 
              "https://doi.org/10.1186/gb-2013-14-9-r103"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1746-4811-6-16", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1012996085", 
              "https://doi.org/10.1186/1746-4811-6-16"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11295-012-0491-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010153501", 
              "https://doi.org/10.1007/s11295-012-0491-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00122-005-0097-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051796889", 
              "https://doi.org/10.1007/s00122-005-0097-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/356519a0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017374821", 
              "https://doi.org/10.1038/356519a0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncomms1191", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1033397378", 
              "https://doi.org/10.1038/ncomms1191"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/384346a0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050549639", 
              "https://doi.org/10.1038/384346a0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature13308", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016502030", 
              "https://doi.org/10.1038/nature13308"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11295-011-0444-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1049284539", 
              "https://doi.org/10.1007/s11295-011-0444-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2229-6-20", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013701607", 
              "https://doi.org/10.1186/1471-2229-6-20"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11295-013-0594-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1033606942", 
              "https://doi.org/10.1007/s11295-013-0594-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature09525", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030868615", 
              "https://doi.org/10.1038/nature09525"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg3425", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1001869057", 
              "https://doi.org/10.1038/nrg3425"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg2931", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013788172", 
              "https://doi.org/10.1038/nrg2931"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/hdy.2011.44", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1043281218", 
              "https://doi.org/10.1038/hdy.2011.44"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg1970", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051478791", 
              "https://doi.org/10.1038/nrg1970"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2016-08-09", 
        "datePublishedReg": "2016-08-09", 
        "description": "BackgroundMeiotic recombination is a fundamental evolutionary process. It not only generates diversity, but influences the efficacy of natural selection and genome evolution. There can be significant heterogeneity in recombination rates within and between species, however this variation is not well understood outside of a few model taxa, particularly in forest trees. Eucalypts are forest trees of global economic importance, and dominate many Australian ecosystems. We studied recombination rate in Eucalyptus globulus using genetic linkage maps constructed in 10 unrelated individuals, and markers anchored to the Eucalyptus reference genome. This experimental design provided the replication to study whether recombination rate varied between individuals and chromosomes, and allowed us to study the genomic attributes and population genetic parameters correlated with this variation.ResultsRecombination rate varied significantly between individuals (range\u2009=\u20092.71 to 3.51 centimorgans/megabase [cM/Mb]), but was not significantly influenced by sex or cross type (F1 vs. F2). Significant differences in recombination rate between chromosomes were also evident (range\u2009=\u20091.98 to 3.81\u00a0cM/Mb), beyond those which were due to variation in chromosome size. Variation in chromosomal recombination rate was significantly correlated with gene density (r\u2009=\u20090.94), GC content (r\u2009=\u20090.90), and the number of tandem duplicated genes (r\u2009=\u2009\u22120.72) per chromosome. Notably, chromosome level recombination rate was also negatively correlated with the average genetic diversity across six species from an independent set of samples (r\u2009=\u2009\u22120.75).ConclusionsThe correlations with genomic attributes are consistent with findings in other taxa, however, the direction of the correlation between diversity and recombination rate is opposite to that commonly observed. We argue this is likely to reflect the interaction of selection and specific genome architecture of Eucalyptus. Interestingly, the differences amongst chromosomes in recombination rates appear stable across Eucalyptus species. Together with the strong correlations between recombination rate and features of the Eucalyptus reference genome, we maintain these findings provide further evidence for a broad conservation of genome architecture across the globally significant lineages of Eucalyptus.", 
        "genre": "article", 
        "id": "sg:pub.10.1186/s12864-016-2884-y", 
        "inLanguage": "en", 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.3775791", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.3569504", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.3930777", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.3569291", 
            "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": "17"
          }
        ], 
        "keywords": [
          "genome architecture", 
          "genomic attributes", 
          "reference genome", 
          "forest trees", 
          "genome-wide variation", 
          "average genetic diversity", 
          "fundamental evolutionary processes", 
          "genetic linkage map", 
          "population genetic parameters", 
          "interaction of selection", 
          "global economic importance", 
          "number of tandem", 
          "genome evolution", 
          "broad conservation", 
          "model taxa", 
          "gene density", 
          "chromosome size", 
          "linkage map", 
          "genetic diversity", 
          "natural selection", 
          "Australian ecosystems", 
          "significant lineages", 
          "GC content", 
          "Eucalyptus species", 
          "recombination rate", 
          "evolutionary processes", 
          "cross type", 
          "chromosomes", 
          "genetic parameters", 
          "economic importance", 
          "genome", 
          "species", 
          "Eucalyptus globulus", 
          "taxa", 
          "diversity", 
          "unrelated individuals", 
          "Eucalyptus", 
          "trees", 
          "lineages", 
          "eucalypts", 
          "genes", 
          "ecosystems", 
          "conservation", 
          "globulus", 
          "variation", 
          "further evidence", 
          "recombination", 
          "replication", 
          "selection", 
          "markers", 
          "evolution", 
          "individuals", 
          "independent set", 
          "experimental design", 
          "tandem", 
          "interaction", 
          "heterogeneity", 
          "strong correlation", 
          "findings", 
          "importance", 
          "evidence", 
          "differences", 
          "rate", 
          "architecture", 
          "significant heterogeneity", 
          "content", 
          "correlation", 
          "maps", 
          "attributes", 
          "types", 
          "number", 
          "size", 
          "ConclusionsThe correlation", 
          "process", 
          "significant differences", 
          "sex", 
          "density", 
          "features", 
          "set", 
          "samples", 
          "efficacy", 
          "direction", 
          "parameters", 
          "design"
        ], 
        "name": "Genome-wide variation in recombination rate in Eucalyptus", 
        "pagination": "590", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1014910353"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1186/s12864-016-2884-y"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "27507140"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1186/s12864-016-2884-y", 
          "https://app.dimensions.ai/details/publication/pub.1014910353"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-06-01T22:14", 
        "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_692.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1186/s12864-016-2884-y"
      }
    ]
     

    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/s12864-016-2884-y'

    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/s12864-016-2884-y'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s12864-016-2884-y'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s12864-016-2884-y'


     

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

    336 TRIPLES      22 PREDICATES      145 URIs      113 LITERALS      18 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1186/s12864-016-2884-y schema:about N0ae07c2437534d88a184305c4c276cf3
    2 N133e60e97c9549be9357106a5bb913b6
    3 N480efa5e9098402798f0d0a5855b64c5
    4 N4d8db3497ef9494a8244b32b88f3f8ad
    5 N51676b11764546419f5ed4b0d9b11990
    6 N7cdf092f06844c068115dc04da9e3284
    7 Nac66ed1bb73c48c5971ba31355099a12
    8 Nadccee98aa7b4f6ea5734804a9e620b3
    9 Nda02c3e030434931bf706c6cd123215c
    10 Ne0c8907c544c4ace992750d64dcc0e95
    11 Nec1e805ceb5d4a438fad1cf2014c4ab8
    12 anzsrc-for:06
    13 anzsrc-for:0602
    14 anzsrc-for:0604
    15 schema:author Na3d94ce8fcd84c019e872581f883151a
    16 schema:citation sg:pub.10.1007/s00122-005-0097-x
    17 sg:pub.10.1007/s00294-002-0340-9
    18 sg:pub.10.1007/s11295-011-0430-2
    19 sg:pub.10.1007/s11295-011-0444-9
    20 sg:pub.10.1007/s11295-012-0491-x
    21 sg:pub.10.1007/s11295-013-0594-z
    22 sg:pub.10.1038/356519a0
    23 sg:pub.10.1038/384346a0
    24 sg:pub.10.1038/hdy.2011.44
    25 sg:pub.10.1038/hdy.2011.95
    26 sg:pub.10.1038/nature09525
    27 sg:pub.10.1038/nature13308
    28 sg:pub.10.1038/ncomms1191
    29 sg:pub.10.1038/ng910
    30 sg:pub.10.1038/nrg1970
    31 sg:pub.10.1038/nrg2575
    32 sg:pub.10.1038/nrg2931
    33 sg:pub.10.1038/nrg3425
    34 sg:pub.10.1186/1471-2164-14-86
    35 sg:pub.10.1186/1471-2229-6-20
    36 sg:pub.10.1186/1741-7007-11-50
    37 sg:pub.10.1186/1746-4811-6-16
    38 sg:pub.10.1186/gb-2013-14-9-r103
    39 schema:datePublished 2016-08-09
    40 schema:datePublishedReg 2016-08-09
    41 schema:description BackgroundMeiotic recombination is a fundamental evolutionary process. It not only generates diversity, but influences the efficacy of natural selection and genome evolution. There can be significant heterogeneity in recombination rates within and between species, however this variation is not well understood outside of a few model taxa, particularly in forest trees. Eucalypts are forest trees of global economic importance, and dominate many Australian ecosystems. We studied recombination rate in Eucalyptus globulus using genetic linkage maps constructed in 10 unrelated individuals, and markers anchored to the Eucalyptus reference genome. This experimental design provided the replication to study whether recombination rate varied between individuals and chromosomes, and allowed us to study the genomic attributes and population genetic parameters correlated with this variation.ResultsRecombination rate varied significantly between individuals (range = 2.71 to 3.51 centimorgans/megabase [cM/Mb]), but was not significantly influenced by sex or cross type (F1 vs. F2). Significant differences in recombination rate between chromosomes were also evident (range = 1.98 to 3.81 cM/Mb), beyond those which were due to variation in chromosome size. Variation in chromosomal recombination rate was significantly correlated with gene density (r = 0.94), GC content (r = 0.90), and the number of tandem duplicated genes (r = −0.72) per chromosome. Notably, chromosome level recombination rate was also negatively correlated with the average genetic diversity across six species from an independent set of samples (r = −0.75).ConclusionsThe correlations with genomic attributes are consistent with findings in other taxa, however, the direction of the correlation between diversity and recombination rate is opposite to that commonly observed. We argue this is likely to reflect the interaction of selection and specific genome architecture of Eucalyptus. Interestingly, the differences amongst chromosomes in recombination rates appear stable across Eucalyptus species. Together with the strong correlations between recombination rate and features of the Eucalyptus reference genome, we maintain these findings provide further evidence for a broad conservation of genome architecture across the globally significant lineages of Eucalyptus.
    42 schema:genre article
    43 schema:inLanguage en
    44 schema:isAccessibleForFree true
    45 schema:isPartOf N245a78ef216041e8a6203728cfb40a14
    46 N989f7c5900894d4e8b7de540e93c4daf
    47 sg:journal.1023790
    48 schema:keywords Australian ecosystems
    49 ConclusionsThe correlation
    50 Eucalyptus
    51 Eucalyptus globulus
    52 Eucalyptus species
    53 GC content
    54 architecture
    55 attributes
    56 average genetic diversity
    57 broad conservation
    58 chromosome size
    59 chromosomes
    60 conservation
    61 content
    62 correlation
    63 cross type
    64 density
    65 design
    66 differences
    67 direction
    68 diversity
    69 economic importance
    70 ecosystems
    71 efficacy
    72 eucalypts
    73 evidence
    74 evolution
    75 evolutionary processes
    76 experimental design
    77 features
    78 findings
    79 forest trees
    80 fundamental evolutionary processes
    81 further evidence
    82 gene density
    83 genes
    84 genetic diversity
    85 genetic linkage map
    86 genetic parameters
    87 genome
    88 genome architecture
    89 genome evolution
    90 genome-wide variation
    91 genomic attributes
    92 global economic importance
    93 globulus
    94 heterogeneity
    95 importance
    96 independent set
    97 individuals
    98 interaction
    99 interaction of selection
    100 lineages
    101 linkage map
    102 maps
    103 markers
    104 model taxa
    105 natural selection
    106 number
    107 number of tandem
    108 parameters
    109 population genetic parameters
    110 process
    111 rate
    112 recombination
    113 recombination rate
    114 reference genome
    115 replication
    116 samples
    117 selection
    118 set
    119 sex
    120 significant differences
    121 significant heterogeneity
    122 significant lineages
    123 size
    124 species
    125 strong correlation
    126 tandem
    127 taxa
    128 trees
    129 types
    130 unrelated individuals
    131 variation
    132 schema:name Genome-wide variation in recombination rate in Eucalyptus
    133 schema:pagination 590
    134 schema:productId N13f65b0e9c5847a088b1d0ecbbaf2a10
    135 N5791522376454fbf8acaae3752898191
    136 Ne3928618a1d345418380c9ad5bf6527e
    137 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014910353
    138 https://doi.org/10.1186/s12864-016-2884-y
    139 schema:sdDatePublished 2022-06-01T22:14
    140 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    141 schema:sdPublisher N245e57b600b8435cae1b3036a967328a
    142 schema:url https://doi.org/10.1186/s12864-016-2884-y
    143 sgo:license sg:explorer/license/
    144 sgo:sdDataset articles
    145 rdf:type schema:ScholarlyArticle
    146 N0ae07c2437534d88a184305c4c276cf3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    147 schema:name Crosses, Genetic
    148 rdf:type schema:DefinedTerm
    149 N133e60e97c9549be9357106a5bb913b6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    150 schema:name Genome, Plant
    151 rdf:type schema:DefinedTerm
    152 N13f65b0e9c5847a088b1d0ecbbaf2a10 schema:name doi
    153 schema:value 10.1186/s12864-016-2884-y
    154 rdf:type schema:PropertyValue
    155 N245a78ef216041e8a6203728cfb40a14 schema:issueNumber 1
    156 rdf:type schema:PublicationIssue
    157 N245e57b600b8435cae1b3036a967328a schema:name Springer Nature - SN SciGraph project
    158 rdf:type schema:Organization
    159 N278985a219ab4697a9792bbe47a285bd rdf:first sg:person.01337051304.79
    160 rdf:rest Ncd41056b2cf14b9a9f76882225dc4a3e
    161 N480efa5e9098402798f0d0a5855b64c5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    162 schema:name Polymorphism, Single Nucleotide
    163 rdf:type schema:DefinedTerm
    164 N4d8db3497ef9494a8244b32b88f3f8ad schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    165 schema:name Evolution, Molecular
    166 rdf:type schema:DefinedTerm
    167 N51676b11764546419f5ed4b0d9b11990 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    168 schema:name Genetic Variation
    169 rdf:type schema:DefinedTerm
    170 N517ab5cad9404d55943324314f1e1a65 rdf:first sg:person.01340303237.44
    171 rdf:rest N278985a219ab4697a9792bbe47a285bd
    172 N5791522376454fbf8acaae3752898191 schema:name pubmed_id
    173 schema:value 27507140
    174 rdf:type schema:PropertyValue
    175 N6298b2a4e52f45669c034ec3396d2ad8 rdf:first sg:person.01305600750.67
    176 rdf:rest rdf:nil
    177 N7cdf092f06844c068115dc04da9e3284 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    178 schema:name Base Composition
    179 rdf:type schema:DefinedTerm
    180 N989f7c5900894d4e8b7de540e93c4daf schema:volumeNumber 17
    181 rdf:type schema:PublicationVolume
    182 Na3d94ce8fcd84c019e872581f883151a rdf:first sg:person.01015124413.32
    183 rdf:rest N517ab5cad9404d55943324314f1e1a65
    184 Nac66ed1bb73c48c5971ba31355099a12 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    185 schema:name Genetics, Population
    186 rdf:type schema:DefinedTerm
    187 Nadccee98aa7b4f6ea5734804a9e620b3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    188 schema:name Chromosomes, Plant
    189 rdf:type schema:DefinedTerm
    190 Nc133bf3947e04ee580701536c45d5b92 rdf:first sg:person.014126024501.27
    191 rdf:rest N6298b2a4e52f45669c034ec3396d2ad8
    192 Ncd41056b2cf14b9a9f76882225dc4a3e rdf:first sg:person.01043454452.31
    193 rdf:rest Nc133bf3947e04ee580701536c45d5b92
    194 Nda02c3e030434931bf706c6cd123215c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    195 schema:name Recombination, Genetic
    196 rdf:type schema:DefinedTerm
    197 Ne0c8907c544c4ace992750d64dcc0e95 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    198 schema:name Eucalyptus
    199 rdf:type schema:DefinedTerm
    200 Ne3928618a1d345418380c9ad5bf6527e schema:name dimensions_id
    201 schema:value pub.1014910353
    202 rdf:type schema:PropertyValue
    203 Nec1e805ceb5d4a438fad1cf2014c4ab8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    204 schema:name Genomics
    205 rdf:type schema:DefinedTerm
    206 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    207 schema:name Biological Sciences
    208 rdf:type schema:DefinedTerm
    209 anzsrc-for:0602 schema:inDefinedTermSet anzsrc-for:
    210 schema:name Ecology
    211 rdf:type schema:DefinedTerm
    212 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    213 schema:name Genetics
    214 rdf:type schema:DefinedTerm
    215 sg:grant.3569291 http://pending.schema.org/fundedItem sg:pub.10.1186/s12864-016-2884-y
    216 rdf:type schema:MonetaryGrant
    217 sg:grant.3569504 http://pending.schema.org/fundedItem sg:pub.10.1186/s12864-016-2884-y
    218 rdf:type schema:MonetaryGrant
    219 sg:grant.3775791 http://pending.schema.org/fundedItem sg:pub.10.1186/s12864-016-2884-y
    220 rdf:type schema:MonetaryGrant
    221 sg:grant.3930777 http://pending.schema.org/fundedItem sg:pub.10.1186/s12864-016-2884-y
    222 rdf:type schema:MonetaryGrant
    223 sg:journal.1023790 schema:issn 1471-2164
    224 schema:name BMC Genomics
    225 schema:publisher Springer Nature
    226 rdf:type schema:Periodical
    227 sg:person.01015124413.32 schema:affiliation grid-institutes:None
    228 schema:familyName Gion
    229 schema:givenName Jean-Marc
    230 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01015124413.32
    231 rdf:type schema:Person
    232 sg:person.01043454452.31 schema:affiliation grid-institutes:grid.1009.8
    233 schema:familyName Vaillancourt
    234 schema:givenName René E.
    235 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01043454452.31
    236 rdf:type schema:Person
    237 sg:person.01305600750.67 schema:affiliation grid-institutes:grid.1009.8
    238 schema:familyName Freeman
    239 schema:givenName Jules S.
    240 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01305600750.67
    241 rdf:type schema:Person
    242 sg:person.01337051304.79 schema:affiliation grid-institutes:None
    243 schema:familyName Lesur
    244 schema:givenName Isabelle
    245 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01337051304.79
    246 rdf:type schema:Person
    247 sg:person.01340303237.44 schema:affiliation grid-institutes:None
    248 schema:familyName Hudson
    249 schema:givenName Corey J.
    250 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01340303237.44
    251 rdf:type schema:Person
    252 sg:person.014126024501.27 schema:affiliation grid-institutes:grid.1009.8
    253 schema:familyName Potts
    254 schema:givenName Brad M.
    255 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014126024501.27
    256 rdf:type schema:Person
    257 sg:pub.10.1007/s00122-005-0097-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1051796889
    258 https://doi.org/10.1007/s00122-005-0097-x
    259 rdf:type schema:CreativeWork
    260 sg:pub.10.1007/s00294-002-0340-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044678209
    261 https://doi.org/10.1007/s00294-002-0340-9
    262 rdf:type schema:CreativeWork
    263 sg:pub.10.1007/s11295-011-0430-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047761101
    264 https://doi.org/10.1007/s11295-011-0430-2
    265 rdf:type schema:CreativeWork
    266 sg:pub.10.1007/s11295-011-0444-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049284539
    267 https://doi.org/10.1007/s11295-011-0444-9
    268 rdf:type schema:CreativeWork
    269 sg:pub.10.1007/s11295-012-0491-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1010153501
    270 https://doi.org/10.1007/s11295-012-0491-x
    271 rdf:type schema:CreativeWork
    272 sg:pub.10.1007/s11295-013-0594-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1033606942
    273 https://doi.org/10.1007/s11295-013-0594-z
    274 rdf:type schema:CreativeWork
    275 sg:pub.10.1038/356519a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017374821
    276 https://doi.org/10.1038/356519a0
    277 rdf:type schema:CreativeWork
    278 sg:pub.10.1038/384346a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050549639
    279 https://doi.org/10.1038/384346a0
    280 rdf:type schema:CreativeWork
    281 sg:pub.10.1038/hdy.2011.44 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043281218
    282 https://doi.org/10.1038/hdy.2011.44
    283 rdf:type schema:CreativeWork
    284 sg:pub.10.1038/hdy.2011.95 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030214191
    285 https://doi.org/10.1038/hdy.2011.95
    286 rdf:type schema:CreativeWork
    287 sg:pub.10.1038/nature09525 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030868615
    288 https://doi.org/10.1038/nature09525
    289 rdf:type schema:CreativeWork
    290 sg:pub.10.1038/nature13308 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016502030
    291 https://doi.org/10.1038/nature13308
    292 rdf:type schema:CreativeWork
    293 sg:pub.10.1038/ncomms1191 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033397378
    294 https://doi.org/10.1038/ncomms1191
    295 rdf:type schema:CreativeWork
    296 sg:pub.10.1038/ng910 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020516195
    297 https://doi.org/10.1038/ng910
    298 rdf:type schema:CreativeWork
    299 sg:pub.10.1038/nrg1970 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051478791
    300 https://doi.org/10.1038/nrg1970
    301 rdf:type schema:CreativeWork
    302 sg:pub.10.1038/nrg2575 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051461847
    303 https://doi.org/10.1038/nrg2575
    304 rdf:type schema:CreativeWork
    305 sg:pub.10.1038/nrg2931 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013788172
    306 https://doi.org/10.1038/nrg2931
    307 rdf:type schema:CreativeWork
    308 sg:pub.10.1038/nrg3425 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001869057
    309 https://doi.org/10.1038/nrg3425
    310 rdf:type schema:CreativeWork
    311 sg:pub.10.1186/1471-2164-14-86 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014923008
    312 https://doi.org/10.1186/1471-2164-14-86
    313 rdf:type schema:CreativeWork
    314 sg:pub.10.1186/1471-2229-6-20 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013701607
    315 https://doi.org/10.1186/1471-2229-6-20
    316 rdf:type schema:CreativeWork
    317 sg:pub.10.1186/1741-7007-11-50 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032894745
    318 https://doi.org/10.1186/1741-7007-11-50
    319 rdf:type schema:CreativeWork
    320 sg:pub.10.1186/1746-4811-6-16 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012996085
    321 https://doi.org/10.1186/1746-4811-6-16
    322 rdf:type schema:CreativeWork
    323 sg:pub.10.1186/gb-2013-14-9-r103 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002151324
    324 https://doi.org/10.1186/gb-2013-14-9-r103
    325 rdf:type schema:CreativeWork
    326 grid-institutes:None schema:alternateName CIRAD, UMR AGAP, 69 route d’Arcachon, Cestas, France
    327 HelixVenture, F33700, Merignac, France
    328 Present address: Tasmanian Alkaloids, P.O. Box 130, 7303, Westbury, TAS, Australia
    329 schema:name CIRAD, UMR AGAP, 69 route d’Arcachon, Cestas, France
    330 HelixVenture, F33700, Merignac, France
    331 Present address: Tasmanian Alkaloids, P.O. Box 130, 7303, Westbury, TAS, Australia
    332 School of Biological Sciences, University of Tasmania, Private Bag 55, 7001, Hobart, TAS, Australia
    333 rdf:type schema:Organization
    334 grid-institutes:grid.1009.8 schema:alternateName School of Biological Sciences, University of Tasmania, Private Bag 55, 7001, Hobart, TAS, Australia
    335 schema:name School of Biological Sciences, University of Tasmania, Private Bag 55, 7001, Hobart, TAS, Australia
    336 rdf:type schema:Organization
     




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


    ...