Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops.
Identifieur interne : 001C73 ( Main/Exploration ); précédent : 001C72; suivant : 001C74Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops.
Auteurs : Florent Murat [France] ; Rongzhi Zhang [France] ; Sébastien Guizard [France] ; Haris Gavranovi [Bosnie-Herzégovine] ; Raphael Flores [France] ; Delphine Steinbach [France] ; Hadi Quesneville [France] ; Eric Tannier [France] ; Jérôme Salse [France]Source :
- Genome biology and evolution [ 1759-6653 ] ; 2015.
Descripteurs français
- KwdFr :
- Caryotype (MeSH), Chromosomes de plante (MeSH), Duplication de gène (MeSH), Génome végétal (MeSH), Génomique (MeSH), Magnoliopsida (classification), Magnoliopsida (génétique), Ordre des gènes (MeSH), Phylogenèse (MeSH), Polyploïdie (MeSH), Produits agricoles (génétique), Synténie (MeSH), Évolution moléculaire (MeSH).
- MESH :
- génétique : Magnoliopsida, Produits agricoles.
- classification : Caryotype, Chromosomes de plante, Duplication de gène, Génome végétal, Génomique, Magnoliopsida, Ordre des gènes, Phylogenèse, Polyploïdie, Synténie, Évolution moléculaire.
English descriptors
- KwdEn :
- MESH :
- classification : Magnoliopsida.
- genetics : Crops, Agricultural, Magnoliopsida.
- Chromosomes, Plant, Evolution, Molecular, Gene Duplication, Gene Order, Genome, Plant, Genomics, Karyotype, Phylogeny, Polyploidy, Synteny.
Abstract
We used nine complete genome sequences, from grape, poplar, Arabidopsis, soybean, lotus, apple, strawberry, cacao, and papaya, to investigate the paleohistory of rosid crops. We characterized an ancestral rosid karyotype, structured into 7/21 protochomosomes, with a minimal set of 6,250 ordered protogenes and a minimum physical coding gene space of 50 megabases. We also proposed ancestral karyotypes for the Caricaceae, Brassicaceae, Malvaceae, Fabaceae, Rosaceae, Salicaceae, and Vitaceae families with 9, 8, 10, 6, 12, 9, 12, and 19 protochromosomes, respectively. On the basis of these ancestral karyotypes and present-day species comparisons, we proposed a two-step evolutionary scenario based on allohexaploidization involving the newly characterized A, B, and C diploid progenitors leading to dominant (stable) and sensitive (plastic) genomic compartments in any modern rosid crops. Finally, a new user-friendly online tool, "DicotSyntenyViewer" (available from http://urgi.versailles.inra.fr/synteny-dicot), has been made available for accurate translational genomics in rosids.
DOI: 10.1093/gbe/evv014
PubMed: 25637221
PubMed Central: PMC5322550
Affiliations:
- Bosnie-Herzégovine, France
- Auvergne (région administrative), Auvergne-Rhône-Alpes, Île-de-France
- Clermont-Ferrand, Versailles
Links toward previous steps (curation, corpus...)
Le document en format XML
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genome plasticity of modern rosid crops.</title><author><name sortKey="Murat, Florent" sort="Murat, Florent" uniqKey="Murat F" first="Florent" last="Murat">Florent Murat</name><affiliation wicri:level="3"><nlm:affiliation>INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Clermont Ferrand, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Clermont Ferrand</wicri:regionArea><placeName><region type="region">Auvergne-Rhône-Alpes</region><region type="old region">Auvergne (région administrative)</region><settlement type="city">Clermont-Ferrand</settlement></placeName></affiliation></author><author><name sortKey="Zhang, Rongzhi" sort="Zhang, Rongzhi" uniqKey="Zhang R" first="Rongzhi" last="Zhang">Rongzhi Zhang</name><affiliation wicri:level="3"><nlm:affiliation>INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Clermont Ferrand, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Clermont Ferrand</wicri:regionArea><placeName><region type="region">Auvergne-Rhône-Alpes</region><region type="old region">Auvergne (région administrative)</region><settlement type="city">Clermont-Ferrand</settlement></placeName></affiliation></author><author><name sortKey="Guizard, Sebastien" sort="Guizard, Sebastien" uniqKey="Guizard S" first="Sébastien" last="Guizard">Sébastien Guizard</name><affiliation wicri:level="3"><nlm:affiliation>INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Clermont Ferrand, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Clermont Ferrand</wicri:regionArea><placeName><region type="region">Auvergne-Rhône-Alpes</region><region type="old region">Auvergne (région administrative)</region><settlement type="city">Clermont-Ferrand</settlement></placeName></affiliation></author><author><name sortKey="Gavranovi, Haris" sort="Gavranovi, Haris" uniqKey="Gavranovi H" first="Haris" last="Gavranovi">Haris Gavranovi</name><affiliation wicri:level="1"><nlm:affiliation>Faculty of Engineering and Natural Sciences, International University of Sarajevo, Sarajevo, Bosnia and Herzegovina.</nlm:affiliation><country xml:lang="fr">Bosnie-Herzégovine</country><wicri:regionArea>Faculty of Engineering and Natural Sciences, International University of Sarajevo, Sarajevo</wicri:regionArea><wicri:noRegion>Sarajevo</wicri:noRegion></affiliation></author><author><name sortKey="Flores, Raphael" sort="Flores, Raphael" uniqKey="Flores R" first="Raphael" last="Flores">Raphael Flores</name><affiliation wicri:level="3"><nlm:affiliation>INRA 'Unité de Recherche en Génomique et Informatique', Centre INRA de Versailles, Versailles, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA 'Unité de Recherche en Génomique et Informatique', Centre INRA de Versailles, Versailles</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Versailles</settlement></placeName></affiliation></author><author><name sortKey="Steinbach, Delphine" sort="Steinbach, Delphine" uniqKey="Steinbach D" first="Delphine" last="Steinbach">Delphine Steinbach</name><affiliation wicri:level="3"><nlm:affiliation>INRA 'Unité de Recherche en Génomique et Informatique', Centre INRA de Versailles, Versailles, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA 'Unité de Recherche en Génomique et Informatique', Centre INRA de Versailles, Versailles</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Versailles</settlement></placeName></affiliation></author><author><name sortKey="Quesneville, Hadi" sort="Quesneville, Hadi" uniqKey="Quesneville H" first="Hadi" last="Quesneville">Hadi Quesneville</name><affiliation wicri:level="3"><nlm:affiliation>INRA 'Unité de Recherche en Génomique et Informatique', Centre INRA de Versailles, Versailles, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA 'Unité de Recherche en Génomique et Informatique', Centre INRA de Versailles, Versailles</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Versailles</settlement></placeName></affiliation></author><author><name sortKey="Tannier, Eric" sort="Tannier, Eric" uniqKey="Tannier E" first="Eric" last="Tannier">Eric Tannier</name><affiliation wicri:level="1"><nlm:affiliation>INRIA Rhône-Alpes, Université de Lyon 1, CNRS UMR5558, Laboratoire Biométrie et Biologie Évolutive, Villeurbanne Cedex, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRIA Rhône-Alpes, Université de Lyon 1, CNRS UMR5558, Laboratoire Biométrie et Biologie Évolutive, Villeurbanne Cedex</wicri:regionArea><wicri:noRegion>Villeurbanne Cedex</wicri:noRegion><wicri:noRegion>Villeurbanne Cedex</wicri:noRegion></affiliation></author><author><name sortKey="Salse, Jerome" sort="Salse, Jerome" uniqKey="Salse J" first="Jérôme" last="Salse">Jérôme Salse</name><affiliation wicri:level="3"><nlm:affiliation>INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Clermont Ferrand, France jsalse@clermont.inra.fr.</nlm:affiliation><country wicri:rule="url">France</country><wicri:regionArea>INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Clermont Ferrand</wicri:regionArea><placeName><region type="region">Auvergne-Rhône-Alpes</region><region type="old region">Auvergne (région administrative)</region><settlement type="city">Clermont-Ferrand</settlement></placeName></affiliation></author></analytic><series><title level="j">Genome biology and evolution</title><idno type="eISSN">1759-6653</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosomes, Plant (MeSH)</term><term>Crops, Agricultural (genetics)</term><term>Evolution, Molecular (MeSH)</term><term>Gene Duplication (MeSH)</term><term>Gene Order (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Genomics (MeSH)</term><term>Karyotype (MeSH)</term><term>Magnoliopsida (classification)</term><term>Magnoliopsida (genetics)</term><term>Phylogeny (MeSH)</term><term>Polyploidy (MeSH)</term><term>Synteny (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Caryotype (MeSH)</term><term>Chromosomes de plante (MeSH)</term><term>Duplication de gène (MeSH)</term><term>Génome végétal (MeSH)</term><term>Génomique (MeSH)</term><term>Magnoliopsida (classification)</term><term>Magnoliopsida (génétique)</term><term>Ordre des gènes (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Polyploïdie (MeSH)</term><term>Produits agricoles (génétique)</term><term>Synténie (MeSH)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Magnoliopsida</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Crops, Agricultural</term><term>Magnoliopsida</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Magnoliopsida</term><term>Produits agricoles</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosomes, Plant</term><term>Evolution, Molecular</term><term>Gene Duplication</term><term>Gene Order</term><term>Genome, Plant</term><term>Genomics</term><term>Karyotype</term><term>Phylogeny</term><term>Polyploidy</term><term>Synteny</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="fr"><term>Caryotype</term><term>Chromosomes de plante</term><term>Duplication de gène</term><term>Génome végétal</term><term>Génomique</term><term>Magnoliopsida</term><term>Ordre des gènes</term><term>Phylogenèse</term><term>Polyploïdie</term><term>Synténie</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We used nine complete genome sequences, from grape, poplar, Arabidopsis, soybean, lotus, apple, strawberry, cacao, and papaya, to investigate the paleohistory of rosid crops. We characterized an ancestral rosid karyotype, structured into 7/21 protochomosomes, with a minimal set of 6,250 ordered protogenes and a minimum physical coding gene space of 50 megabases. We also proposed ancestral karyotypes for the Caricaceae, Brassicaceae, Malvaceae, Fabaceae, Rosaceae, Salicaceae, and Vitaceae families with 9, 8, 10, 6, 12, 9, 12, and 19 protochromosomes, respectively. On the basis of these ancestral karyotypes and present-day species comparisons, we proposed a two-step evolutionary scenario based on allohexaploidization involving the newly characterized A, B, and C diploid progenitors leading to dominant (stable) and sensitive (plastic) genomic compartments in any modern rosid crops. Finally, a new user-friendly online tool, "DicotSyntenyViewer" (available from http://urgi.versailles.inra.fr/synteny-dicot), has been made available for accurate translational genomics in rosids. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25637221</PMID><DateCompleted><Year>2015</Year><Month>10</Month><Day>20</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1759-6653</ISSN><JournalIssue CitedMedium="Internet"><Volume>7</Volume><Issue>3</Issue><PubDate><Year>2015</Year><Month>Jan</Month><Day>29</Day></PubDate></JournalIssue><Title>Genome biology and evolution</Title><ISOAbbreviation>Genome Biol Evol</ISOAbbreviation></Journal><ArticleTitle>Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops.</ArticleTitle><Pagination><MedlinePgn>735-49</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/gbe/evv014</ELocationID><Abstract><AbstractText>We used nine complete genome sequences, from grape, poplar, Arabidopsis, soybean, lotus, apple, strawberry, cacao, and papaya, to investigate the paleohistory of rosid crops. We characterized an ancestral rosid karyotype, structured into 7/21 protochomosomes, with a minimal set of 6,250 ordered protogenes and a minimum physical coding gene space of 50 megabases. We also proposed ancestral karyotypes for the Caricaceae, Brassicaceae, Malvaceae, Fabaceae, Rosaceae, Salicaceae, and Vitaceae families with 9, 8, 10, 6, 12, 9, 12, and 19 protochromosomes, respectively. On the basis of these ancestral karyotypes and present-day species comparisons, we proposed a two-step evolutionary scenario based on allohexaploidization involving the newly characterized A, B, and C diploid progenitors leading to dominant (stable) and sensitive (plastic) genomic compartments in any modern rosid crops. Finally, a new user-friendly online tool, "DicotSyntenyViewer" (available from http://urgi.versailles.inra.fr/synteny-dicot), has been made available for accurate translational genomics in rosids. </AbstractText><CopyrightInformation>© The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Murat</LastName><ForeName>Florent</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Clermont Ferrand, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Rongzhi</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Clermont Ferrand, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Guizard</LastName><ForeName>Sébastien</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Clermont Ferrand, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gavranović</LastName><ForeName>Haris</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Faculty of Engineering and Natural Sciences, International University of Sarajevo, Sarajevo, Bosnia and Herzegovina.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Flores</LastName><ForeName>Raphael</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>INRA 'Unité de Recherche en Génomique et Informatique', Centre INRA de Versailles, Versailles, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Steinbach</LastName><ForeName>Delphine</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>INRA 'Unité de Recherche en Génomique et Informatique', Centre INRA de Versailles, Versailles, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Quesneville</LastName><ForeName>Hadi</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>INRA 'Unité de Recherche en Génomique et Informatique', Centre INRA de Versailles, Versailles, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tannier</LastName><ForeName>Eric</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>INRIA Rhône-Alpes, Université de Lyon 1, CNRS UMR5558, Laboratoire Biométrie et Biologie Évolutive, Villeurbanne Cedex, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Salse</LastName><ForeName>Jérôme</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Clermont Ferrand, France jsalse@clermont.inra.fr.</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>01</Month><Day>29</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Genome Biol Evol</MedlineTA><NlmUniqueID>101509707</NlmUniqueID><ISSNLinking>1759-6653</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D032461" MajorTopicYN="N">Chromosomes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018556" MajorTopicYN="N">Crops, Agricultural</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="Y">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020440" MajorTopicYN="N">Gene Duplication</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023061" MajorTopicYN="Y">Gene Order</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, 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