Genome-wide variation in recombination rate in Eucalyptus.
Identifieur interne : 001A81 ( PubMed/Curation ); précédent : 001A80; suivant : 001A82Genome-wide variation in recombination rate in Eucalyptus.
Auteurs : Jean-Marc Gion [France] ; Corey J. Hudson [Australie] ; Isabelle Lesur [France] ; René E. Vaillancourt [Australie] ; Brad M. Potts [Australie] ; Jules S. Freeman [Australie]Source :
- BMC genomics [ 1471-2164 ] ; 2016.
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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 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.
DOI: 10.1186/s12864-016-2884-y
PubMed: 27507140
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Hudson</name><affiliation wicri:level="1"><nlm:affiliation>School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001</wicri:regionArea></affiliation></author><author><name sortKey="Lesur, Isabelle" sort="Lesur, Isabelle" uniqKey="Lesur I" first="Isabelle" last="Lesur">Isabelle Lesur</name><affiliation wicri:level="1"><nlm:affiliation>HelixVenture, Merignac, F33700, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>HelixVenture, Merignac, F33700</wicri:regionArea></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 wicri:level="1"><nlm:affiliation>School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001</wicri:regionArea></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 wicri:level="1"><nlm:affiliation>School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001</wicri:regionArea></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 wicri:level="1"><nlm:affiliation>School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia. Jules.Freeman@utas.edu.au.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001</wicri:regionArea></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Composition</term><term>Chromosomes, Plant</term><term>Crosses, Genetic</term><term>Eucalyptus (genetics)</term><term>Evolution, Molecular</term><term>Genetic Variation</term><term>Genetics, Population</term><term>Genome, Plant</term><term>Genomics (methods)</term><term>Polymorphism, Single Nucleotide</term><term>Recombination, Genetic</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Chromosomes de plante</term><term>Composition en bases nucléiques</term><term>Croisements génétiques</term><term>Eucalyptus (génétique)</term><term>Génome végétal</term><term>Génomique ()</term><term>Génétique des populations</term><term>Polymorphisme de nucléotide simple</term><term>Recombinaison génétique</term><term>Variation génétique</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Eucalyptus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Eucalyptus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Composition</term><term>Chromosomes, Plant</term><term>Crosses, Genetic</term><term>Evolution, Molecular</term><term>Genetic Variation</term><term>Genetics, Population</term><term>Genome, Plant</term><term>Polymorphism, Single Nucleotide</term><term>Recombination, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Chromosomes de plante</term><term>Composition en bases nucléiques</term><term>Croisements génétiques</term><term>Génome végétal</term><term>Génomique</term><term>Génétique des populations</term><term>Polymorphisme de nucléotide simple</term><term>Recombinaison génétique</term><term>Variation génétique</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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 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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">27507140</PMID><DateCreated><Year>2016</Year><Month>08</Month><Day>10</Day></DateCreated><DateCompleted><Year>2017</Year><Month>09</Month><Day>01</Day></DateCompleted><DateRevised><Year>2017</Year><Month>11</Month><Day>18</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>17</Volume><PubDate><Year>2016</Year><Month>08</Month><Day>09</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Genome-wide variation in recombination rate in Eucalyptus.</ArticleTitle><Pagination><MedlinePgn>590</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-016-2884-y</ELocationID><Abstract><AbstractText Label="BACKGROUND">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 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.</AbstractText><AbstractText Label="RESULTS">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 (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).</AbstractText><AbstractText Label="CONCLUSIONS">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 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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Gion</LastName><ForeName>Jean-Marc</ForeName><Initials>JM</Initials><AffiliationInfo><Affiliation>CIRAD, UMR AGAP, 69 route d'Arcachon, Cestas, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hudson</LastName><ForeName>Corey J</ForeName><Initials>CJ</Initials><AffiliationInfo><Affiliation>School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Present address: Tasmanian Alkaloids, P.O. Box 130, Westbury, TAS, 7303, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lesur</LastName><ForeName>Isabelle</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>HelixVenture, Merignac, F33700, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vaillancourt</LastName><ForeName>René E</ForeName><Initials>RE</Initials><AffiliationInfo><Affiliation>School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Potts</LastName><ForeName>Brad M</ForeName><Initials>BM</Initials><AffiliationInfo><Affiliation>School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Freeman</LastName><ForeName>Jules S</ForeName><Initials>JS</Initials><AffiliationInfo><Affiliation>School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia. Jules.Freeman@utas.edu.au.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>08</Month><Day>09</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>Theor Appl Genet. 2005 Dec;112(1):30-40</RefSource><PMID Version="1">16228189</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>BMC Biol. 2013 Apr 18;11:50</RefSource><PMID Version="1">23597128</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Ann Bot. 2005 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MajorTopicYN="N">Genetics, Population</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011995" MajorTopicYN="Y">Recombination, Genetic</DescriptorName></MeshHeading></MeshHeadingList><OtherID Source="NLM">PMC4979139</OtherID><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Crossover</Keyword><Keyword MajorTopicYN="Y">Eucalyptus globulus</Keyword><Keyword MajorTopicYN="Y">Gene density</Keyword><Keyword MajorTopicYN="Y">Genetic diversity</Keyword><Keyword MajorTopicYN="Y">Genomic features</Keyword><Keyword MajorTopicYN="Y">Meiotic recombination</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>09</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>07</Month><Day>06</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>8</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>8</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>9</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27507140</ArticleId><ArticleId IdType="doi">10.1186/s12864-016-2884-y</ArticleId><ArticleId IdType="pii">10.1186/s12864-016-2884-y</ArticleId><ArticleId IdType="pmc">PMC4979139</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour 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