Genome-wide patterns of differentiation and spatially varying selection between postglacial recolonization lineages of Populus alba (Salicaceae), a widespread forest tree.
Identifieur interne : 001D30 ( Main/Exploration ); précédent : 001D29; suivant : 001D31Genome-wide patterns of differentiation and spatially varying selection between postglacial recolonization lineages of Populus alba (Salicaceae), a widespread forest tree.
Auteurs : Kai N. Stölting [Suisse] ; Margot Paris [Suisse] ; Cécile Meier [Suisse] ; Berthold Heinze [Autriche] ; Stefano Castiglione [Italie] ; Denes Bartha [Hongrie] ; Christian Lexer [Suisse]Source :
- The New phytologist [ 1469-8137 ] ; 2015.
Descripteurs français
- KwdFr :
- Analyse de séquence d'ADN (MeSH), Arbres (génétique), Couche de glace (MeSH), Forêts (MeSH), Gene Ontology (MeSH), Gènes de plante (MeSH), Génome végétal (MeSH), Hongrie (MeSH), Italie (MeSH), Phylogenèse (MeSH), Polymorphisme de nucléotide simple (génétique), Populus (génétique), Reproductibilité des résultats (MeSH), Répétitions microsatellites (génétique), Sélection génétique (MeSH), Variation génétique (MeSH), Études d'associations génétiques (MeSH).
- MESH :
- génétique : Arbres, Polymorphisme de nucléotide simple, Populus, Répétitions microsatellites.
- Analyse de séquence d'ADN, Couche de glace, Forêts, Gene Ontology, Gènes de plante, Génome végétal, Hongrie, Italie, Phylogenèse, Reproductibilité des résultats, Sélection génétique, Variation génétique, Études d'associations génétiques.
- Wicri :
English descriptors
- KwdEn :
- Forests (MeSH), Gene Ontology (MeSH), Genes, Plant (MeSH), Genetic Association Studies (MeSH), Genetic Variation (MeSH), Genome, Plant (MeSH), Hungary (MeSH), Ice Cover (MeSH), Italy (MeSH), Microsatellite Repeats (genetics), Phylogeny (MeSH), Polymorphism, Single Nucleotide (genetics), Populus (genetics), Reproducibility of Results (MeSH), Selection, Genetic (MeSH), Sequence Analysis, DNA (MeSH), Trees (genetics).
- MESH :
- geographic : Hungary, Italy.
- genetics : Microsatellite Repeats, Polymorphism, Single Nucleotide, Populus, Trees.
- Forests, Gene Ontology, Genes, Plant, Genetic Association Studies, Genetic Variation, Genome, Plant, Ice Cover, Phylogeny, Reproducibility of Results, Selection, Genetic, Sequence Analysis, DNA.
Abstract
Studying the divergence continuum in plants is relevant to fundamental and applied biology because of the potential to reveal functionally important genetic variation. In this context, whole-genome sequencing (WGS) provides the necessary rigour for uncovering footprints of selection. We resequenced populations of two divergent phylogeographic lineages of Populus alba (n = 48), thoroughly characterized by microsatellites (n = 317), and scanned their genomes for regions of unusually high allelic differentiation and reduced diversity using > 1.7 million single nucleotide polymorphisms (SNPs) from WGS. Results were confirmed by Sanger sequencing. On average, 9134 high-differentiation (≥ 4 standard deviations) outlier SNPs were uncovered between populations, 848 of which were shared by ≥ three replicate comparisons. Annotation revealed that 545 of these were located in 437 predicted genes. Twelve percent of differentiation outlier genome regions exhibited significantly reduced genetic diversity. Gene ontology (GO) searches were successful for 327 high-differentiation genes, and these were enriched for 63 GO terms. Our results provide a snapshot of the roles of 'hard selective sweeps' vs divergent selection of standing genetic variation in distinct postglacial recolonization lineages of P. alba. Thus, this study adds to our understanding of the mechanisms responsible for the origin of functionally relevant variation in temperate trees.
DOI: 10.1111/nph.13392
PubMed: 25817433
Affiliations:
- Autriche, Hongrie, Italie, Suisse
- Canton de Fribourg, Vienne (Autriche)
- Fribourg, Vienne (Autriche)
- Université de Fribourg
Links toward previous steps (curation, corpus...)
Le document en format XML
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(MeSH)</term><term>Microsatellite Repeats (genetics)</term><term>Phylogeny (MeSH)</term><term>Polymorphism, Single Nucleotide (genetics)</term><term>Populus (genetics)</term><term>Reproducibility of Results (MeSH)</term><term>Selection, Genetic (MeSH)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Trees (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN (MeSH)</term><term>Arbres (génétique)</term><term>Couche de glace (MeSH)</term><term>Forêts (MeSH)</term><term>Gene Ontology (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Génome végétal (MeSH)</term><term>Hongrie (MeSH)</term><term>Italie (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Polymorphisme de nucléotide simple (génétique)</term><term>Populus (génétique)</term><term>Reproductibilité des résultats (MeSH)</term><term>Répétitions microsatellites (génétique)</term><term>Sélection génétique (MeSH)</term><term>Variation génétique (MeSH)</term><term>Études d'associations génétiques (MeSH)</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>Hungary</term><term>Italy</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Microsatellite Repeats</term><term>Polymorphism, Single Nucleotide</term><term>Populus</term><term>Trees</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arbres</term><term>Polymorphisme de nucléotide simple</term><term>Populus</term><term>Répétitions microsatellites</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Forests</term><term>Gene Ontology</term><term>Genes, Plant</term><term>Genetic Association Studies</term><term>Genetic Variation</term><term>Genome, Plant</term><term>Ice Cover</term><term>Phylogeny</term><term>Reproducibility of Results</term><term>Selection, Genetic</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Couche de glace</term><term>Forêts</term><term>Gene Ontology</term><term>Gènes de plante</term><term>Génome végétal</term><term>Hongrie</term><term>Italie</term><term>Phylogenèse</term><term>Reproductibilité des résultats</term><term>Sélection génétique</term><term>Variation génétique</term><term>Études d'associations génétiques</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>Hongrie</term><term>Italie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Studying the divergence continuum in plants is relevant to fundamental and applied biology because of the potential to reveal functionally important genetic variation. In this context, whole-genome sequencing (WGS) provides the necessary rigour for uncovering footprints of selection. We resequenced populations of two divergent phylogeographic lineages of Populus alba (n = 48), thoroughly characterized by microsatellites (n = 317), and scanned their genomes for regions of unusually high allelic differentiation and reduced diversity using > 1.7 million single nucleotide polymorphisms (SNPs) from WGS. Results were confirmed by Sanger sequencing. On average, 9134 high-differentiation (≥ 4 standard deviations) outlier SNPs were uncovered between populations, 848 of which were shared by ≥ three replicate comparisons. Annotation revealed that 545 of these were located in 437 predicted genes. Twelve percent of differentiation outlier genome regions exhibited significantly reduced genetic diversity. Gene ontology (GO) searches were successful for 327 high-differentiation genes, and these were enriched for 63 GO terms. Our results provide a snapshot of the roles of 'hard selective sweeps' vs divergent selection of standing genetic variation in distinct postglacial recolonization lineages of P. alba. Thus, this study adds to our understanding of the mechanisms responsible for the origin of functionally relevant variation in temperate trees.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25817433</PMID><DateCompleted><Year>2016</Year><Month>04</Month><Day>26</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1469-8137</ISSN><JournalIssue CitedMedium="Internet"><Volume>207</Volume><Issue>3</Issue><PubDate><Year>2015</Year><Month>Aug</Month></PubDate></JournalIssue><Title>The New phytologist</Title><ISOAbbreviation>New Phytol</ISOAbbreviation></Journal><ArticleTitle>Genome-wide patterns of differentiation and spatially varying selection between postglacial recolonization lineages of Populus alba (Salicaceae), a widespread forest tree.</ArticleTitle><Pagination><MedlinePgn>723-34</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/nph.13392</ELocationID><Abstract><AbstractText>Studying the divergence continuum in plants is relevant to fundamental and applied biology because of the potential to reveal functionally important genetic variation. In this context, whole-genome sequencing (WGS) provides the necessary rigour for uncovering footprints of selection. We resequenced populations of two divergent phylogeographic lineages of Populus alba (n = 48), thoroughly characterized by microsatellites (n = 317), and scanned their genomes for regions of unusually high allelic differentiation and reduced diversity using > 1.7 million single nucleotide polymorphisms (SNPs) from WGS. Results were confirmed by Sanger sequencing. On average, 9134 high-differentiation (≥ 4 standard deviations) outlier SNPs were uncovered between populations, 848 of which were shared by ≥ three replicate comparisons. Annotation revealed that 545 of these were located in 437 predicted genes. Twelve percent of differentiation outlier genome regions exhibited significantly reduced genetic diversity. Gene ontology (GO) searches were successful for 327 high-differentiation genes, and these were enriched for 63 GO terms. Our results provide a snapshot of the roles of 'hard selective sweeps' vs divergent selection of standing genetic variation in distinct postglacial recolonization lineages of P. alba. Thus, this study adds to our understanding of the mechanisms responsible for the origin of functionally relevant variation in temperate trees.</AbstractText><CopyrightInformation>© 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Stölting</LastName><ForeName>Kai N</ForeName><Initials>KN</Initials><AffiliationInfo><Affiliation>Unit of Ecology and Evolution, Department of Biology, University of Fribourg, Chemin du Musee 10, 1700, Fribourg, Switzerland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Paris</LastName><ForeName>Margot</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Unit of Ecology and Evolution, Department of Biology, University of Fribourg, Chemin du Musee 10, 1700, Fribourg, Switzerland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Meier</LastName><ForeName>Cécile</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Unit of Ecology and Evolution, Department of Biology, University of Fribourg, Chemin du Musee 10, 1700, Fribourg, Switzerland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Heinze</LastName><ForeName>Berthold</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Department of Forest Genetics, Austrian Research Centre for Forests (BFW), Seckendorff-Gudent Weg 8, 1130, Vienna, Austria.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Castiglione</LastName><ForeName>Stefano</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Chemistry, University of Salerno, 84084, Fisciano, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bartha</LastName><ForeName>Denes</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Botany, West-Hungarian University, 9400, Sopron, Hungary.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lexer</LastName><ForeName>Christian</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Unit of Ecology and Evolution, Department of Biology, University of Fribourg, Chemin du Musee 10, 1700, Fribourg, Switzerland.</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>2015</Year><Month>03</Month><Day>26</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>New Phytol</MedlineTA><NlmUniqueID>9882884</NlmUniqueID><ISSNLinking>0028-646X</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D065928" MajorTopicYN="Y">Forests</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D063990" MajorTopicYN="N">Gene Ontology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D056726" MajorTopicYN="N">Genetic Association Studies</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="Y">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006814" MajorTopicYN="N" Type="Geographic">Hungary</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D046448" MajorTopicYN="Y">Ice Cover</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D007558" MajorTopicYN="N" Type="Geographic">Italy</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018895" MajorTopicYN="N">Microsatellite Repeats</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="Y">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015203" MajorTopicYN="N">Reproducibility of Results</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012641" MajorTopicYN="Y">Selection, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014197" MajorTopicYN="N">Trees</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Populus</Keyword><Keyword MajorTopicYN="N">adaptation</Keyword><Keyword MajorTopicYN="N">divergence continuum</Keyword><Keyword MajorTopicYN="N">divergent selection</Keyword><Keyword MajorTopicYN="N">population genomics</Keyword><Keyword MajorTopicYN="N">postglacial recolonization</Keyword><Keyword MajorTopicYN="N">selective sweep</Keyword><Keyword MajorTopicYN="N">whole-genome sequencing</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year><Month>12</Month><Day>22</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>02</Month><Day>25</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>3</Month><Day>31</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>3</Month><Day>31</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>4</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">25817433</ArticleId><ArticleId IdType="doi">10.1111/nph.13392</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Autriche</li><li>Hongrie</li><li>Italie</li><li>Suisse</li></country><region><li>Canton de Fribourg</li><li>Vienne (Autriche)</li></region><settlement><li>Fribourg</li><li>Vienne (Autriche)</li></settlement><orgName><li>Université de Fribourg</li></orgName></list><tree><country name="Suisse"><region name="Canton de Fribourg"><name sortKey="Stolting, Kai N" sort="Stolting, Kai N" uniqKey="Stolting K" first="Kai N" last="Stölting">Kai N. Stölting</name></region><name sortKey="Lexer, Christian" sort="Lexer, Christian" uniqKey="Lexer C" first="Christian" last="Lexer">Christian Lexer</name><name sortKey="Meier, Cecile" sort="Meier, Cecile" uniqKey="Meier C" first="Cécile" last="Meier">Cécile Meier</name><name sortKey="Paris, Margot" sort="Paris, Margot" uniqKey="Paris M" first="Margot" last="Paris">Margot Paris</name></country><country name="Autriche"><region name="Vienne (Autriche)"><name sortKey="Heinze, Berthold" sort="Heinze, Berthold" uniqKey="Heinze B" first="Berthold" last="Heinze">Berthold Heinze</name></region></country><country name="Italie"><noRegion><name sortKey="Castiglione, Stefano" sort="Castiglione, Stefano" uniqKey="Castiglione S" first="Stefano" last="Castiglione">Stefano Castiglione</name></noRegion></country><country name="Hongrie"><noRegion><name sortKey="Bartha, Denes" sort="Bartha, Denes" uniqKey="Bartha D" first="Denes" last="Bartha">Denes Bartha</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|texte= Genome-wide patterns of differentiation and spatially varying selection between postglacial recolonization lineages of Populus alba (Salicaceae), a widespread forest tree.
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