Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation.
Identifieur interne : 001675 ( Main/Curation ); précédent : 001674; suivant : 001676Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation.
Auteurs : Sara Pinosio [Italie] ; Stefania Giacomello [Italie] ; Patricia Faivre-Rampant [France] ; Gail Taylor [Royaume-Uni] ; Veronique Jorge [France] ; Marie Christine Le Paslier [France] ; Giusi Zaina [Italie] ; Catherine Bastien [France] ; Federica Cattonaro [Italie] ; Fabio Marroni [Italie] ; Michele Morgante [Italie]Source :
- Molecular biology and evolution [ 1537-1719 ] ; 2016.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
Abstract
Many recent studies have emphasized the important role of structural variation (SV) in determining human genetic and phenotypic variation. In plants, studies aimed at elucidating the extent of SV are still in their infancy. Evidence has indicated a high presence and an active role of SV in driving plant genome evolution in different plant species.With the aim of characterizing the size and the composition of the poplar pan-genome, we performed a genome-wide analysis of structural variation in three intercrossable poplar species: Populus nigra, Populus deltoides, and Populus trichocarpa We detected a total of 7,889 deletions and 10,586 insertions relative to the P. trichocarpa reference genome, covering respectively 33.2 Mb and 62.9 Mb of genomic sequence, and 3,230 genes affected by copy number variation (CNV). The majority of the detected variants are inter-specific in agreement with a recent origin following separation of species.Insertions and deletions (INDELs) were preferentially located in low-gene density regions of the poplar genome and were, for the majority, associated with the activity of transposable elements. Genes affected by SV showed lower-than-average expression levels and higher levels of dN/dS, suggesting that they are subject to relaxed selective pressure or correspond to pseudogenes.Functional annotation of genes affected by INDELs showed over-representation of categories associated with transposable elements activity, while genes affected by genic CNVs showed enrichment in categories related to resistance to stress and pathogens. This study provides a genome-wide catalogue of SV and the first insight on functional and structural properties of the poplar pan-genome.
DOI: 10.1093/molbev/msw161
PubMed: 27499133
PubMed Central: PMC5026262
Links toward previous steps (curation, corpus...)
- to stream Main, to step Corpus: Pour aller vers cette notice dans l'étape Curation :001675
Links to Exploration step
pubmed:27499133Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation.</title><author><name sortKey="Pinosio, Sara" sort="Pinosio, Sara" uniqKey="Pinosio S" first="Sara" last="Pinosio">Sara Pinosio</name><affiliation wicri:level="1"><nlm:affiliation>Istituto di Bioscienze e Biorisorse, Consiglio Nazionale delle Ricerche, Sesto Fiorentino, Firenze, Italy Istituto di Genomica Applicata (IGA), Udine, Italy pinosio@appliedgenomics.org michele.morgante@uniud.it.</nlm:affiliation><country wicri:rule="url">Italie</country></affiliation></author><author><name sortKey="Giacomello, Stefania" sort="Giacomello, Stefania" uniqKey="Giacomello S" first="Stefania" last="Giacomello">Stefania Giacomello</name><affiliation wicri:level="1"><nlm:affiliation>Istituto di Genomica Applicata (IGA), Udine, Italy Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Istituto di Genomica Applicata (IGA), Udine, Italy Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine</wicri:regionArea></affiliation></author><author><name sortKey="Faivre Rampant, Patricia" sort="Faivre Rampant, Patricia" uniqKey="Faivre Rampant P" first="Patricia" last="Faivre-Rampant">Patricia Faivre-Rampant</name><affiliation wicri:level="1"><nlm:affiliation>INRA US 1279 EPGV/CEA/CNG, Evry, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA US 1279 EPGV/CEA/CNG, Evry</wicri:regionArea></affiliation></author><author><name sortKey="Taylor, Gail" sort="Taylor, Gail" uniqKey="Taylor G" first="Gail" last="Taylor">Gail Taylor</name><affiliation wicri:level="1"><nlm:affiliation>School of Biological Sciences, University of Southampton, Southampton, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>School of Biological Sciences, University of Southampton, Southampton</wicri:regionArea></affiliation></author><author><name sortKey="Jorge, Veronique" sort="Jorge, Veronique" uniqKey="Jorge V" first="Veronique" last="Jorge">Veronique Jorge</name><affiliation wicri:level="1"><nlm:affiliation>INRA, UR 0588 AGPF, Centre INRA Val de Loire, Orléans, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR 0588 AGPF, Centre INRA Val de Loire, Orléans</wicri:regionArea></affiliation></author><author><name sortKey="Le Paslier, Marie Christine" sort="Le Paslier, Marie Christine" uniqKey="Le Paslier M" first="Marie Christine" last="Le Paslier">Marie Christine Le Paslier</name><affiliation wicri:level="1"><nlm:affiliation>INRA US 1279 EPGV/CEA/CNG, Evry, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA US 1279 EPGV/CEA/CNG, Evry</wicri:regionArea></affiliation></author><author><name sortKey="Zaina, Giusi" sort="Zaina, Giusi" uniqKey="Zaina G" first="Giusi" last="Zaina">Giusi Zaina</name><affiliation wicri:level="1"><nlm:affiliation>Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine</wicri:regionArea></affiliation></author><author><name sortKey="Bastien, Catherine" sort="Bastien, Catherine" uniqKey="Bastien C" first="Catherine" last="Bastien">Catherine Bastien</name><affiliation wicri:level="1"><nlm:affiliation>INRA, UR 0588 AGPF, Centre INRA Val de Loire, Orléans, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR 0588 AGPF, Centre INRA Val de Loire, Orléans</wicri:regionArea></affiliation></author><author><name sortKey="Cattonaro, Federica" sort="Cattonaro, Federica" uniqKey="Cattonaro F" first="Federica" last="Cattonaro">Federica Cattonaro</name><affiliation wicri:level="1"><nlm:affiliation>IGA Technology Services (IGATS), Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>IGA Technology Services (IGATS), Udine</wicri:regionArea></affiliation></author><author><name sortKey="Marroni, Fabio" sort="Marroni, Fabio" uniqKey="Marroni F" first="Fabio" last="Marroni">Fabio Marroni</name><affiliation wicri:level="1"><nlm:affiliation>Istituto di Genomica Applicata (IGA), Udine, Italy Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Istituto di Genomica Applicata (IGA), Udine, Italy Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine</wicri:regionArea></affiliation></author><author><name sortKey="Morgante, Michele" sort="Morgante, Michele" uniqKey="Morgante M" first="Michele" last="Morgante">Michele Morgante</name><affiliation wicri:level="1"><nlm:affiliation>Istituto di Genomica Applicata (IGA), Udine, Italy Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy pinosio@appliedgenomics.org michele.morgante@uniud.it.</nlm:affiliation><country wicri:rule="url">Italie</country></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2016">2016</date><idno type="RBID">pubmed:27499133</idno><idno type="pmid">27499133</idno><idno type="doi">10.1093/molbev/msw161</idno><idno type="pmc">PMC5026262</idno><idno type="wicri:Area/Main/Corpus">001675</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">001675</idno><idno type="wicri:Area/Main/Curation">001675</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">001675</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation.</title><author><name sortKey="Pinosio, Sara" sort="Pinosio, Sara" uniqKey="Pinosio S" first="Sara" last="Pinosio">Sara Pinosio</name><affiliation wicri:level="1"><nlm:affiliation>Istituto di Bioscienze e Biorisorse, Consiglio Nazionale delle Ricerche, Sesto Fiorentino, Firenze, Italy Istituto di Genomica Applicata (IGA), Udine, Italy pinosio@appliedgenomics.org michele.morgante@uniud.it.</nlm:affiliation><country wicri:rule="url">Italie</country></affiliation></author><author><name sortKey="Giacomello, Stefania" sort="Giacomello, Stefania" uniqKey="Giacomello S" first="Stefania" last="Giacomello">Stefania Giacomello</name><affiliation wicri:level="1"><nlm:affiliation>Istituto di Genomica Applicata (IGA), Udine, Italy Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Istituto di Genomica Applicata (IGA), Udine, Italy Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine</wicri:regionArea></affiliation></author><author><name sortKey="Faivre Rampant, Patricia" sort="Faivre Rampant, Patricia" uniqKey="Faivre Rampant P" first="Patricia" last="Faivre-Rampant">Patricia Faivre-Rampant</name><affiliation wicri:level="1"><nlm:affiliation>INRA US 1279 EPGV/CEA/CNG, Evry, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA US 1279 EPGV/CEA/CNG, Evry</wicri:regionArea></affiliation></author><author><name sortKey="Taylor, Gail" sort="Taylor, Gail" uniqKey="Taylor G" first="Gail" last="Taylor">Gail Taylor</name><affiliation wicri:level="1"><nlm:affiliation>School of Biological Sciences, University of Southampton, Southampton, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>School of Biological Sciences, University of Southampton, Southampton</wicri:regionArea></affiliation></author><author><name sortKey="Jorge, Veronique" sort="Jorge, Veronique" uniqKey="Jorge V" first="Veronique" last="Jorge">Veronique Jorge</name><affiliation wicri:level="1"><nlm:affiliation>INRA, UR 0588 AGPF, Centre INRA Val de Loire, Orléans, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR 0588 AGPF, Centre INRA Val de Loire, Orléans</wicri:regionArea></affiliation></author><author><name sortKey="Le Paslier, Marie Christine" sort="Le Paslier, Marie Christine" uniqKey="Le Paslier M" first="Marie Christine" last="Le Paslier">Marie Christine Le Paslier</name><affiliation wicri:level="1"><nlm:affiliation>INRA US 1279 EPGV/CEA/CNG, Evry, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA US 1279 EPGV/CEA/CNG, Evry</wicri:regionArea></affiliation></author><author><name sortKey="Zaina, Giusi" sort="Zaina, Giusi" uniqKey="Zaina G" first="Giusi" last="Zaina">Giusi Zaina</name><affiliation wicri:level="1"><nlm:affiliation>Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine</wicri:regionArea></affiliation></author><author><name sortKey="Bastien, Catherine" sort="Bastien, Catherine" uniqKey="Bastien C" first="Catherine" last="Bastien">Catherine Bastien</name><affiliation wicri:level="1"><nlm:affiliation>INRA, UR 0588 AGPF, Centre INRA Val de Loire, Orléans, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR 0588 AGPF, Centre INRA Val de Loire, Orléans</wicri:regionArea></affiliation></author><author><name sortKey="Cattonaro, Federica" sort="Cattonaro, Federica" uniqKey="Cattonaro F" first="Federica" last="Cattonaro">Federica Cattonaro</name><affiliation wicri:level="1"><nlm:affiliation>IGA Technology Services (IGATS), Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>IGA Technology Services (IGATS), Udine</wicri:regionArea></affiliation></author><author><name sortKey="Marroni, Fabio" sort="Marroni, Fabio" uniqKey="Marroni F" first="Fabio" last="Marroni">Fabio Marroni</name><affiliation wicri:level="1"><nlm:affiliation>Istituto di Genomica Applicata (IGA), Udine, Italy Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Istituto di Genomica Applicata (IGA), Udine, Italy Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine</wicri:regionArea></affiliation></author><author><name sortKey="Morgante, Michele" sort="Morgante, Michele" uniqKey="Morgante M" first="Michele" last="Morgante">Michele Morgante</name><affiliation wicri:level="1"><nlm:affiliation>Istituto di Genomica Applicata (IGA), Udine, Italy Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy pinosio@appliedgenomics.org michele.morgante@uniud.it.</nlm:affiliation><country wicri:rule="url">Italie</country></affiliation></author></analytic><series><title level="j">Molecular biology and evolution</title><idno type="eISSN">1537-1719</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>DNA Copy Number Variations (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Genome-Wide Association Study (MeSH)</term><term>Genomics (MeSH)</term><term>INDEL Mutation (MeSH)</term><term>Populus (genetics)</term><term>Structure-Activity Relationship (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Gènes de plante (MeSH)</term><term>Génome végétal (MeSH)</term><term>Génomique (MeSH)</term><term>Mutation de type INDEL (MeSH)</term><term>Populus (génétique)</term><term>Relation structure-activité (MeSH)</term><term>Variations de nombre de copies de segment d'ADN (MeSH)</term><term>Étude d'association pangénomique (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>DNA Copy Number Variations</term><term>Genes, Plant</term><term>Genome, Plant</term><term>Genome-Wide Association Study</term><term>Genomics</term><term>INDEL Mutation</term><term>Structure-Activity Relationship</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Gènes de plante</term><term>Génome végétal</term><term>Génomique</term><term>Mutation de type INDEL</term><term>Relation structure-activité</term><term>Variations de nombre de copies de segment d'ADN</term><term>Étude d'association pangénomique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Many recent studies have emphasized the important role of structural variation (SV) in determining human genetic and phenotypic variation. In plants, studies aimed at elucidating the extent of SV are still in their infancy. Evidence has indicated a high presence and an active role of SV in driving plant genome evolution in different plant species.With the aim of characterizing the size and the composition of the poplar pan-genome, we performed a genome-wide analysis of structural variation in three intercrossable poplar species: Populus nigra, Populus deltoides, and Populus trichocarpa We detected a total of 7,889 deletions and 10,586 insertions relative to the P. trichocarpa reference genome, covering respectively 33.2 Mb and 62.9 Mb of genomic sequence, and 3,230 genes affected by copy number variation (CNV). The majority of the detected variants are inter-specific in agreement with a recent origin following separation of species.Insertions and deletions (INDELs) were preferentially located in low-gene density regions of the poplar genome and were, for the majority, associated with the activity of transposable elements. Genes affected by SV showed lower-than-average expression levels and higher levels of dN/dS, suggesting that they are subject to relaxed selective pressure or correspond to pseudogenes.Functional annotation of genes affected by INDELs showed over-representation of categories associated with transposable elements activity, while genes affected by genic CNVs showed enrichment in categories related to resistance to stress and pathogens. This study provides a genome-wide catalogue of SV and the first insight on functional and structural properties of the poplar pan-genome.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">27499133</PMID><DateCompleted><Year>2017</Year><Month>06</Month><Day>21</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1537-1719</ISSN><JournalIssue CitedMedium="Internet"><Volume>33</Volume><Issue>10</Issue><PubDate><Year>2016</Year><Month>10</Month></PubDate></JournalIssue><Title>Molecular biology and evolution</Title><ISOAbbreviation>Mol Biol Evol</ISOAbbreviation></Journal><ArticleTitle>Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation.</ArticleTitle><Pagination><MedlinePgn>2706-19</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/molbev/msw161</ELocationID><Abstract><AbstractText>Many recent studies have emphasized the important role of structural variation (SV) in determining human genetic and phenotypic variation. In plants, studies aimed at elucidating the extent of SV are still in their infancy. Evidence has indicated a high presence and an active role of SV in driving plant genome evolution in different plant species.With the aim of characterizing the size and the composition of the poplar pan-genome, we performed a genome-wide analysis of structural variation in three intercrossable poplar species: Populus nigra, Populus deltoides, and Populus trichocarpa We detected a total of 7,889 deletions and 10,586 insertions relative to the P. trichocarpa reference genome, covering respectively 33.2 Mb and 62.9 Mb of genomic sequence, and 3,230 genes affected by copy number variation (CNV). The majority of the detected variants are inter-specific in agreement with a recent origin following separation of species.Insertions and deletions (INDELs) were preferentially located in low-gene density regions of the poplar genome and were, for the majority, associated with the activity of transposable elements. Genes affected by SV showed lower-than-average expression levels and higher levels of dN/dS, suggesting that they are subject to relaxed selective pressure or correspond to pseudogenes.Functional annotation of genes affected by INDELs showed over-representation of categories associated with transposable elements activity, while genes affected by genic CNVs showed enrichment in categories related to resistance to stress and pathogens. This study provides a genome-wide catalogue of SV and the first insight on functional and structural properties of the poplar pan-genome.</AbstractText><CopyrightInformation>© The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Pinosio</LastName><ForeName>Sara</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Istituto di Bioscienze e Biorisorse, Consiglio Nazionale delle Ricerche, Sesto Fiorentino, Firenze, Italy Istituto di Genomica Applicata (IGA), Udine, Italy pinosio@appliedgenomics.org michele.morgante@uniud.it.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Giacomello</LastName><ForeName>Stefania</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Istituto di Genomica Applicata (IGA), Udine, Italy Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Faivre-Rampant</LastName><ForeName>Patricia</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>INRA US 1279 EPGV/CEA/CNG, Evry, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Taylor</LastName><ForeName>Gail</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>School of Biological Sciences, University of Southampton, Southampton, United Kingdom.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jorge</LastName><ForeName>Veronique</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>INRA, UR 0588 AGPF, Centre INRA Val de Loire, Orléans, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Le Paslier</LastName><ForeName>Marie Christine</ForeName><Initials>MC</Initials><AffiliationInfo><Affiliation>INRA US 1279 EPGV/CEA/CNG, Evry, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zaina</LastName><ForeName>Giusi</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bastien</LastName><ForeName>Catherine</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>INRA, UR 0588 AGPF, Centre INRA Val de Loire, Orléans, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cattonaro</LastName><ForeName>Federica</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>IGA Technology Services (IGATS), Udine, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Marroni</LastName><ForeName>Fabio</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Istituto di Genomica Applicata (IGA), Udine, Italy Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Morgante</LastName><ForeName>Michele</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Istituto di Genomica Applicata (IGA), Udine, Italy Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy pinosio@appliedgenomics.org michele.morgante@uniud.it.</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>07</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Mol Biol Evol</MedlineTA><NlmUniqueID>8501455</NlmUniqueID><ISSNLinking>0737-4038</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D056915" MajorTopicYN="N">DNA Copy Number Variations</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055106" MajorTopicYN="N">Genome-Wide Association Study</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D054643" MajorTopicYN="N">INDEL Mutation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013329" MajorTopicYN="N">Structure-Activity Relationship</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">pan-genome</Keyword><Keyword MajorTopicYN="Y">poplar</Keyword><Keyword MajorTopicYN="Y">structural variation</Keyword><Keyword MajorTopicYN="Y">transposable elements</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>8</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>8</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>6</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27499133</ArticleId><ArticleId IdType="pii">msw161</ArticleId><ArticleId IdType="doi">10.1093/molbev/msw161</ArticleId><ArticleId IdType="pmc">PMC5026262</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Genetics. 2001 Jun;158(2):787-809</Citation><ArticleIdList><ArticleId IdType="pubmed">11404342</ArticleId></ArticleIdList></Reference><Reference><Citation>Brief Bioinform. 2002 Mar;3(1):87-91</Citation><ArticleIdList><ArticleId IdType="pubmed">12002227</ArticleId></ArticleIdList></Reference><Reference><Citation>Brief Funct Genomics. 2014 Jul;13(4):296-307</Citation><ArticleIdList><ArticleId IdType="pubmed">24907366</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2015 Jan 15;31(2):166-9</Citation><ArticleIdList><ArticleId IdType="pubmed">25260700</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Biotechnol. 2011 Dec 11;30(1):105-11</Citation><ArticleIdList><ArticleId IdType="pubmed">22158310</ArticleId></ArticleIdList></Reference><Reference><Citation>J Mol Evol. 1993 Jan;36(1):96-9</Citation><ArticleIdList><ArticleId IdType="pubmed">8433381</ArticleId></ArticleIdList></Reference><Reference><Citation>Cytogenet Genome Res. 2008;123(1-4):244-52</Citation><ArticleIdList><ArticleId IdType="pubmed">19287161</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2011 Nov 21;12(11):R114</Citation><ArticleIdList><ArticleId IdType="pubmed">22104744</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 2004 Aug;167(4):1939-47</Citation><ArticleIdList><ArticleId IdType="pubmed">15342531</ArticleId></ArticleIdList></Reference><Reference><Citation>Annu Rev Plant Biol. 2014;65:505-30</Citation><ArticleIdList><ArticleId IdType="pubmed">24579996</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2011 Jun;21(6):813-20</Citation><ArticleIdList><ArticleId IdType="pubmed">21632748</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Genet. 1998 Sep;20(1):43-5</Citation><ArticleIdList><ArticleId IdType="pubmed">9731528</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Genet. 2005 Sep;37(9):997-1002</Citation><ArticleIdList><ArticleId IdType="pubmed">16056225</ArticleId></ArticleIdList></Reference><Reference><Citation>Trends Plant Sci. 2003 Dec;8(12):570-5</Citation><ArticleIdList><ArticleId IdType="pubmed">14659705</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant J. 2010 Sep;63(6):990-1003</Citation><ArticleIdList><ArticleId IdType="pubmed">20626650</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2011 Jan 31;6(1):e16526</Citation><ArticleIdList><ArticleId IdType="pubmed">21304975</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2013 Apr 25;14(4):R36</Citation><ArticleIdList><ArticleId IdType="pubmed">23618408</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Genet. 2006 Feb;2(2):e20</Citation><ArticleIdList><ArticleId IdType="pubmed">16482228</ArticleId></ArticleIdList></Reference><Reference><Citation>Curr Opin Plant Biol. 2014 Apr;18:31-6</Citation><ArticleIdList><ArticleId IdType="pubmed">24548794</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2010;11(10):R106</Citation><ArticleIdList><ArticleId IdType="pubmed">20979621</ArticleId></ArticleIdList></Reference><Reference><Citation>Cytogenet Genome Res. 2005;110(1-4):462-7</Citation><ArticleIdList><ArticleId IdType="pubmed">16093699</ArticleId></ArticleIdList></Reference><Reference><Citation>Curr Opin Plant Biol. 2007 Apr;10(2):149-55</Citation><ArticleIdList><ArticleId IdType="pubmed">17300983</ArticleId></ArticleIdList></Reference><Reference><Citation>Theor Appl Genet. 2005 Nov;111(7):1440-56</Citation><ArticleIdList><ArticleId IdType="pubmed">16211377</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2012 Mar;22(3):508-18</Citation><ArticleIdList><ArticleId IdType="pubmed">22106370</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Physiol. 2012 Aug;159(4):1295-308</Citation><ArticleIdList><ArticleId IdType="pubmed">22696021</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant J. 2011 Aug;67(4):736-45</Citation><ArticleIdList><ArticleId IdType="pubmed">21554453</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2011 Mar 15;27(6):764-70</Citation><ArticleIdList><ArticleId IdType="pubmed">21217122</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Mol Biol. 2000 Jan;42(1):251-69</Citation><ArticleIdList><ArticleId IdType="pubmed">10688140</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2010 Jan 19;107(3):1029-34</Citation><ArticleIdList><ArticleId IdType="pubmed">20018685</ArticleId></ArticleIdList></Reference><Reference><Citation>Trends Genet. 2004 Mar;20(3):116-22</Citation><ArticleIdList><ArticleId IdType="pubmed">15049302</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2007 Jul 20;317(5836):338-42</Citation><ArticleIdList><ArticleId IdType="pubmed">17641193</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2009 Aug 15;25(16):2078-9</Citation><ArticleIdList><ArticleId IdType="pubmed">19505943</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Rev Genet. 2002 May;3(5):329-41</Citation><ArticleIdList><ArticleId IdType="pubmed">11988759</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2014 Jan;31(1):59-69</Citation><ArticleIdList><ArticleId IdType="pubmed">24072814</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2012 Sep 15;28(18):i333-i339</Citation><ArticleIdList><ArticleId IdType="pubmed">22962449</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Genet. 2010 Dec;42(12):1053-9</Citation><ArticleIdList><ArticleId IdType="pubmed">21076406</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):7704-11</Citation><ArticleIdList><ArticleId IdType="pubmed">9223252</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2005 Sep 15;21(18):3674-6</Citation><ArticleIdList><ArticleId IdType="pubmed">16081474</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12404-10</Citation><ArticleIdList><ArticleId IdType="pubmed">15240870</ArticleId></ArticleIdList></Reference><Reference><Citation>Trends Genet. 2000 Jun;16(6):276-7</Citation><ArticleIdList><ArticleId IdType="pubmed">10827456</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Inform. 2005;16(1):106-15</Citation><ArticleIdList><ArticleId IdType="pubmed">16362912</ArticleId></ArticleIdList></Reference><Reference><Citation>Theor Appl Genet. 2014 Jan;127(1):1-18</Citation><ArticleIdList><ArticleId IdType="pubmed">23989647</ArticleId></ArticleIdList></Reference><Reference><Citation>J Mol Biol. 1990 Oct 5;215(3):403-10</Citation><ArticleIdList><ArticleId IdType="pubmed">2231712</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Rev Genet. 2010 Jun;11(6):446-50</Citation><ArticleIdList><ArticleId IdType="pubmed">20479774</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2006 Sep 15;313(5793):1596-604</Citation><ArticleIdList><ArticleId IdType="pubmed">16973872</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Mol Biol. 2008 Apr;66(6):619-36</Citation><ArticleIdList><ArticleId IdType="pubmed">18247136</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Genet. 2012 Jun 03;44(7):803-7</Citation><ArticleIdList><ArticleId IdType="pubmed">22660545</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Rev Genet. 2011 May;12(5):363-76</Citation><ArticleIdList><ArticleId IdType="pubmed">21358748</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Genet. 2010 Nov;42(11):1027-30</Citation><ArticleIdList><ArticleId IdType="pubmed">20972441</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2015 Oct;32(10):2760-74</Citation><ArticleIdList><ArticleId IdType="pubmed">26174143</ArticleId></ArticleIdList></Reference><Reference><Citation>J Mol Evol. 1980 Dec;16(2):111-20</Citation><ArticleIdList><ArticleId IdType="pubmed">7463489</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2009 Oct 8;461(7265):747-53</Citation><ArticleIdList><ArticleId IdType="pubmed">19812666</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Cell. 2015 Jun;27(6):1595-604</Citation><ArticleIdList><ArticleId IdType="pubmed">26002866</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Biotechnol. 2014 Oct;32(10):1045-52</Citation><ArticleIdList><ArticleId IdType="pubmed">25218520</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2008 Nov 27;9:565</Citation><ArticleIdList><ArticleId IdType="pubmed">19038031</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Plant Biol. 2004 Jun 01;4:10</Citation><ArticleIdList><ArticleId IdType="pubmed">15171794</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2013 Mar 26;110(13):5241-6</Citation><ArticleIdList><ArticleId IdType="pubmed">23479633</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Cell. 2012 Mar;24(3):1242-55</Citation><ArticleIdList><ArticleId IdType="pubmed">22427337</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Ecol Resour. 2016 Jul;16(4):1023-36</Citation><ArticleIdList><ArticleId IdType="pubmed">26929265</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2009 Jul 15;25(14):1754-60</Citation><ArticleIdList><ArticleId IdType="pubmed">19451168</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Cell. 2003 Apr;15(4):809-34</Citation><ArticleIdList><ArticleId IdType="pubmed">12671079</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2009 Nov 24;106(47):19922-7</Citation><ArticleIdList><ArticleId IdType="pubmed">19926865</ArticleId></ArticleIdList></Reference><Reference><Citation>New Phytol. 2011 Jan;189(1):106-21</Citation><ArticleIdList><ArticleId IdType="pubmed">21039557</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Rev Genet. 2010 Aug;11(8):589</Citation><ArticleIdList><ArticleId IdType="pubmed">20634813</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Cell. 2005 Feb;17(2):343-60</Citation><ArticleIdList><ArticleId IdType="pubmed">15659640</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2003 Aug 8;301(5634):793-7</Citation><ArticleIdList><ArticleId IdType="pubmed">12907789</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2009 Jun 15;25(12):i222-30</Citation><ArticleIdList><ArticleId IdType="pubmed">19477992</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/PoplarV1/Data/Main/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001675 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Curation/biblio.hfd -nk 001675 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= PoplarV1
|flux= Main
|étape= Curation
|type= RBID
|clé= pubmed:27499133
|texte= Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Curation/RBID.i -Sk "pubmed:27499133" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Curation/biblio.hfd \
| NlmPubMed2Wicri -a PoplarV1
| This area was generated with Dilib version V0.6.37. |  |