Genome-wide variation in recombination rate in Eucalyptus
Identifieur interne : 000900 ( Pmc/Checkpoint ); précédent : 000899; suivant : 000901Genome-wide variation in recombination rate in Eucalyptus
Auteurs : Jean-Marc Gion [France] ; Corey J. Hudson ; Isabelle Lesur ; René E. Vaillancourt ; Brad M. Potts ; Jules S. FreemanSource :
- BMC Genomics [ 1471-2164 ] ; 2016.
Abstract
Meiotic 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
Recombination 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 (
The 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
Url:
DOI: 10.1186/s12864-016-2884-y
PubMed: 27507140
PubMed Central: 4979139
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome-wide variation in recombination rate in <italic>Eucalyptus</italic></title><author><name sortKey="Gion, Jean Marc" sort="Gion, Jean Marc" uniqKey="Gion J" first="Jean-Marc" last="Gion">Jean-Marc Gion</name><affiliation wicri:level="1"><nlm:aff id="Aff1">CIRAD, UMR AGAP, 69 route d’Arcachon, Cestas, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>CIRAD, UMR AGAP, 69 route d’Arcachon, Cestas</wicri:regionArea><wicri:noRegion>Cestas</wicri:noRegion><wicri:noRegion>Cestas</wicri:noRegion></affiliation></author><author><name sortKey="Hudson, Corey J" sort="Hudson, Corey J" uniqKey="Hudson C" first="Corey J." last="Hudson">Corey J. Hudson</name><affiliation><nlm:aff id="Aff2">School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001 Australia</nlm:aff><wicri:noCountry code="subfield">TAS 7001 Australia</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff3">Present address: Tasmanian Alkaloids, P.O. Box 130, Westbury, TAS 7303 Australia</nlm:aff><wicri:noCountry code="subfield">TAS 7303 Australia</wicri:noCountry></affiliation></author><author><name sortKey="Lesur, Isabelle" sort="Lesur, Isabelle" uniqKey="Lesur I" first="Isabelle" last="Lesur">Isabelle Lesur</name><affiliation><nlm:aff id="Aff4">HelixVenture, Merignac, F33700 France</nlm:aff><wicri:noCountry code="subfield">F33700 France</wicri:noCountry></affiliation></author><author><name sortKey="Vaillancourt, Rene E" sort="Vaillancourt, Rene E" uniqKey="Vaillancourt R" first="René E." last="Vaillancourt">René E. Vaillancourt</name><affiliation><nlm:aff id="Aff2">School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001 Australia</nlm:aff><wicri:noCountry code="subfield">TAS 7001 Australia</wicri:noCountry></affiliation></author><author><name sortKey="Potts, Brad M" sort="Potts, Brad M" uniqKey="Potts B" first="Brad M." last="Potts">Brad M. Potts</name><affiliation><nlm:aff id="Aff2">School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001 Australia</nlm:aff><wicri:noCountry code="subfield">TAS 7001 Australia</wicri:noCountry></affiliation></author><author><name sortKey="Freeman, Jules S" sort="Freeman, Jules S" uniqKey="Freeman J" first="Jules S." last="Freeman">Jules S. Freeman</name><affiliation><nlm:aff id="Aff2">School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001 Australia</nlm:aff><wicri:noCountry code="subfield">TAS 7001 Australia</wicri:noCountry></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27507140</idno><idno type="pmc">4979139</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4979139</idno><idno type="RBID">PMC:4979139</idno><idno type="doi">10.1186/s12864-016-2884-y</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000A86</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000A86</idno><idno type="wicri:Area/Pmc/Curation">000A63</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000A63</idno><idno type="wicri:Area/Pmc/Checkpoint">000900</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000900</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genome-wide variation in recombination rate in <italic>Eucalyptus</italic></title><author><name sortKey="Gion, Jean Marc" sort="Gion, Jean Marc" uniqKey="Gion J" first="Jean-Marc" last="Gion">Jean-Marc Gion</name><affiliation wicri:level="1"><nlm:aff id="Aff1">CIRAD, UMR AGAP, 69 route d’Arcachon, Cestas, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>CIRAD, UMR AGAP, 69 route d’Arcachon, Cestas</wicri:regionArea><wicri:noRegion>Cestas</wicri:noRegion><wicri:noRegion>Cestas</wicri:noRegion></affiliation></author><author><name sortKey="Hudson, Corey J" sort="Hudson, Corey J" uniqKey="Hudson C" first="Corey J." last="Hudson">Corey J. Hudson</name><affiliation><nlm:aff id="Aff2">School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001 Australia</nlm:aff><wicri:noCountry code="subfield">TAS 7001 Australia</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff3">Present address: Tasmanian Alkaloids, P.O. Box 130, Westbury, TAS 7303 Australia</nlm:aff><wicri:noCountry code="subfield">TAS 7303 Australia</wicri:noCountry></affiliation></author><author><name sortKey="Lesur, Isabelle" sort="Lesur, Isabelle" uniqKey="Lesur I" first="Isabelle" last="Lesur">Isabelle Lesur</name><affiliation><nlm:aff id="Aff4">HelixVenture, Merignac, F33700 France</nlm:aff><wicri:noCountry code="subfield">F33700 France</wicri:noCountry></affiliation></author><author><name sortKey="Vaillancourt, Rene E" sort="Vaillancourt, Rene E" uniqKey="Vaillancourt R" first="René E." last="Vaillancourt">René E. Vaillancourt</name><affiliation><nlm:aff id="Aff2">School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001 Australia</nlm:aff><wicri:noCountry code="subfield">TAS 7001 Australia</wicri:noCountry></affiliation></author><author><name sortKey="Potts, Brad M" sort="Potts, Brad M" uniqKey="Potts B" first="Brad M." last="Potts">Brad M. Potts</name><affiliation><nlm:aff id="Aff2">School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001 Australia</nlm:aff><wicri:noCountry code="subfield">TAS 7001 Australia</wicri:noCountry></affiliation></author><author><name sortKey="Freeman, Jules S" sort="Freeman, Jules S" uniqKey="Freeman J" first="Jules S." last="Freeman">Jules S. Freeman</name><affiliation><nlm:aff id="Aff2">School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001 Australia</nlm:aff><wicri:noCountry code="subfield">TAS 7001 Australia</wicri:noCountry></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Meiotic 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 <italic>Eucalyptus globulus</italic> using genetic linkage maps constructed in 10 unrelated individuals, and markers anchored to the <italic>Eucalyptus</italic> 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.</p></sec><sec><title>Results</title><p>Recombination 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 (F<sub>1</sub> vs. F<sub>2</sub>). 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 (<italic>r</italic> = 0.94), GC content (<italic>r</italic> = 0.90), and the number of tandem duplicated genes (<italic>r</italic> = −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 (<italic>r</italic> = −0.75).</p></sec><sec><title>Conclusions</title><p>The 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 <italic>Eucalyptus</italic>. Interestingly, the differences amongst chromosomes in recombination rates appear stable across <italic>Eucalyptus</italic> species. Together with the strong correlations between recombination rate and features of the <italic>Eucalyptus</italic> reference genome, we maintain these findings provide further evidence for a broad conservation of genome architecture across the globally significant lineages of <italic>Eucalyptus</italic>.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Webster, Mt" uniqKey="Webster M">MT Webster</name></author><author><name sortKey="Hurst, Ld" uniqKey="Hurst L">LD Hurst</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sun, P" uniqKey="Sun P">P Sun</name></author><author><name sortKey="Zhang, R" uniqKey="Zhang R">R Zhang</name></author><author><name sortKey="Jiang, Y" uniqKey="Jiang Y">Y Jiang</name></author><author><name sortKey="Wang, X" uniqKey="Wang X">X Wang</name></author><author><name sortKey="Li, J" uniqKey="Li J">J Li</name></author><author><name sortKey="Lv, H" uniqKey="Lv H">H 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<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Genomics</journal-id><journal-id journal-id-type="iso-abbrev">BMC Genomics</journal-id><journal-title-group><journal-title>BMC Genomics</journal-title></journal-title-group><issn pub-type="epub">1471-2164</issn><publisher><publisher-name>BioMed Central</publisher-name><publisher-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27507140</article-id><article-id pub-id-type="pmc">4979139</article-id><article-id pub-id-type="publisher-id">2884</article-id><article-id pub-id-type="doi">10.1186/s12864-016-2884-y</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>Genome-wide variation in recombination rate in <italic>Eucalyptus</italic></article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Gion</surname><given-names>Jean-Marc</given-names></name><address><email>jean-marc.gion@cirad.fr</email></address><xref ref-type="aff" rid="Aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Hudson</surname><given-names>Corey J.</given-names></name><address><email>chudso18@its.jnj.com</email></address><xref ref-type="aff" rid="Aff2">2</xref><xref ref-type="aff" rid="Aff3">3</xref></contrib><contrib contrib-type="author"><name><surname>Lesur</surname><given-names>Isabelle</given-names></name><address><email>ilesur@pierroton.inra.fr</email></address><xref ref-type="aff" rid="Aff4">4</xref></contrib><contrib contrib-type="author"><name><surname>Vaillancourt</surname><given-names>René E.</given-names></name><address><email>rene.vaillancourt@utas.edu.au</email></address><xref ref-type="aff" rid="Aff2">2</xref></contrib><contrib contrib-type="author"><name><surname>Potts</surname><given-names>Brad M.</given-names></name><address><email>B.M.Potts@utas.edu.au</email></address><xref ref-type="aff" rid="Aff2">2</xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Freeman</surname><given-names>Jules S.</given-names></name><address><email>Jules.Freeman@utas.edu.au</email></address><xref ref-type="aff" rid="Aff2">2</xref></contrib><aff id="Aff1"><label>1</label>CIRAD, UMR AGAP, 69 route d’Arcachon, Cestas, France</aff><aff id="Aff2"><label>2</label>School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001 Australia</aff><aff id="Aff3"><label>3</label>Present address: Tasmanian Alkaloids, P.O. Box 130, Westbury, TAS 7303 Australia</aff><aff id="Aff4"><label>4</label>HelixVenture, Merignac, F33700 France</aff></contrib-group><pub-date pub-type="epub"><day>9</day><month>8</month><year>2016</year></pub-date><pub-date pub-type="pmc-release"><day>9</day><month>8</month><year>2016</year></pub-date><pub-date pub-type="collection"><year>2016</year></pub-date><volume>17</volume><elocation-id>590</elocation-id><history><date date-type="received"><day>19</day><month>9</month><year>2015</year></date><date date-type="accepted"><day>6</day><month>7</month><year>2016</year></date></history><permissions><copyright-statement>© The Author(s). 2016</copyright-statement><license license-type="OpenAccess"><license-p><bold>Open Access</bold>This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>) applies to the data made available in this article, unless otherwise stated.</license-p></license></permissions><abstract id="Abs1"><sec><title>Background</title><p>Meiotic 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 <italic>Eucalyptus globulus</italic> using genetic linkage maps constructed in 10 unrelated individuals, and markers anchored to the <italic>Eucalyptus</italic> 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.</p></sec><sec><title>Results</title><p>Recombination 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 (F<sub>1</sub> vs. F<sub>2</sub>). 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 (<italic>r</italic> = 0.94), GC content (<italic>r</italic> = 0.90), and the number of tandem duplicated genes (<italic>r</italic> = −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 (<italic>r</italic> = −0.75).</p></sec><sec><title>Conclusions</title><p>The 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 <italic>Eucalyptus</italic>. Interestingly, the differences amongst chromosomes in recombination rates appear stable across <italic>Eucalyptus</italic> species. Together with the strong correlations between recombination rate and features of the <italic>Eucalyptus</italic> reference genome, we maintain these findings provide further evidence for a broad conservation of genome architecture across the globally significant lineages of <italic>Eucalyptus</italic>.</p></sec></abstract><kwd-group xml:lang="en"><title>Keywords</title><kwd><italic>Eucalyptus globulus</italic></kwd><kwd>Meiotic recombination</kwd><kwd>Crossover</kwd><kwd>Genomic features</kwd><kwd>Genetic diversity</kwd><kwd>Gene density</kwd></kwd-group><funding-group><award-group><funding-source><institution>TRANZFOR</institution></funding-source><award-id>230793</award-id><principal-award-recipient><name><surname>Gion</surname><given-names>Jean-Marc</given-names></name></principal-award-recipient></award-group><award-group><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/501100000923</institution-id><institution>Australian Research Council</institution></institution-wrap></funding-source><award-id>DP140102552</award-id><principal-award-recipient><name><surname>Vaillancourt</surname><given-names>René E.</given-names></name></principal-award-recipient></award-group></funding-group><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© The Author(s) 2016</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc><affiliations><list><country><li>France</li></country></list><tree><noCountry><name sortKey="Freeman, Jules S" sort="Freeman, Jules S" uniqKey="Freeman J" first="Jules S." last="Freeman">Jules S. Freeman</name><name sortKey="Hudson, Corey J" sort="Hudson, Corey J" uniqKey="Hudson C" first="Corey J." last="Hudson">Corey J. Hudson</name><name sortKey="Lesur, Isabelle" sort="Lesur, Isabelle" uniqKey="Lesur I" first="Isabelle" last="Lesur">Isabelle Lesur</name><name sortKey="Potts, Brad M" sort="Potts, Brad M" uniqKey="Potts B" first="Brad M." last="Potts">Brad M. Potts</name><name sortKey="Vaillancourt, Rene E" sort="Vaillancourt, Rene E" uniqKey="Vaillancourt R" first="René E." last="Vaillancourt">René E. Vaillancourt</name></noCountry><country name="France"><noRegion><name sortKey="Gion, Jean Marc" sort="Gion, Jean Marc" uniqKey="Gion J" first="Jean-Marc" last="Gion">Jean-Marc Gion</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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