Widespread genome duplications throughout the history of flowering plants.
Identifieur interne : 003C87 ( Main/Exploration ); précédent : 003C86; suivant : 003C88Widespread genome duplications throughout the history of flowering plants.
Auteurs : Liying Cui [États-Unis] ; P Kerr Wall ; James H. Leebens-Mack ; Bruce G. Lindsay ; Douglas E. Soltis ; Jeff J. Doyle ; Pamela S. Soltis ; John E. Carlson ; Kathiravetpilla Arumuganathan ; Abdelali Barakat ; Victor A. Albert ; Hong Ma ; Claude W. DepamphilisSource :
- Genome research [ 1088-9051 ] ; 2006.
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Abstract
Genomic comparisons provide evidence for ancient genome-wide duplications in a diverse array of animals and plants. We developed a birth-death model to identify evidence for genome duplication in EST data, and applied a mixture model to estimate the age distribution of paralogous pairs identified in EST sets for species representing the basal-most extant flowering plant lineages. We found evidence for episodes of ancient genome-wide duplications in the basal angiosperm lineages including Nuphar advena (yellow water lily: Nymphaeaceae) and the magnoliids Persea americana (avocado: Lauraceae), Liriodendron tulipifera (tulip poplar: Magnoliaceae), and Saruma henryi (Aristolochiaceae). In addition, we detected independent genome duplications in the basal eudicot Eschscholzia californica (California poppy: Papaveraceae) and the basal monocot Acorus americanus (Acoraceae), both of which were distinct from duplications documented for ancestral grass (Poaceae) and core eudicot lineages. Among gymnosperms, we found equivocal evidence for ancient polyploidy in Welwitschia mirabilis (Gnetales) and no evidence for polyploidy in pine, although gymnosperms generally have much larger genomes than the angiosperms investigated. Cross-species sequence divergence estimates suggest that synonymous substitution rates in the basal angiosperms are less than half those previously reported for core eudicots and members of Poaceae. These lower substitution rates permit inference of older duplication events. We hypothesize that evidence of an ancient duplication observed in the Nuphar data may represent a genome duplication in the common ancestor of all or most extant angiosperms, except Amborella.
DOI: 10.1101/gr.4825606
PubMed: 16702410
PubMed Central: PMC1479859
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Carlson</name></author><author><name sortKey="Arumuganathan, Kathiravetpilla" sort="Arumuganathan, Kathiravetpilla" uniqKey="Arumuganathan K" first="Kathiravetpilla" last="Arumuganathan">Kathiravetpilla Arumuganathan</name></author><author><name sortKey="Barakat, Abdelali" sort="Barakat, Abdelali" uniqKey="Barakat A" first="Abdelali" last="Barakat">Abdelali Barakat</name></author><author><name sortKey="Albert, Victor A" sort="Albert, Victor A" uniqKey="Albert V" first="Victor A" last="Albert">Victor A. Albert</name></author><author><name sortKey="Ma, Hong" sort="Ma, Hong" uniqKey="Ma H" first="Hong" last="Ma">Hong Ma</name></author><author><name sortKey="Depamphilis, Claude W" sort="Depamphilis, Claude W" uniqKey="Depamphilis C" first="Claude W" last="Depamphilis">Claude W. Depamphilis</name></author></analytic><series><title level="j">Genome research</title><idno type="ISSN">1088-9051</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Cycadopsida (genetics)</term><term>Evolution, Molecular (MeSH)</term><term>Gene Duplication (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Magnoliopsida (genetics)</term><term>Models, Genetic (MeSH)</term><term>Models, Statistical (MeSH)</term><term>Phylogeny (MeSH)</term><term>Polyploidy (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Cycadopsida (génétique)</term><term>Duplication de gène (MeSH)</term><term>Génome végétal (MeSH)</term><term>Magnoliopsida (génétique)</term><term>Modèles génétiques (MeSH)</term><term>Modèles statistiques (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Polyploïdie (MeSH)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Cycadopsida</term><term>Magnoliopsida</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Cycadopsida</term><term>Magnoliopsida</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Evolution, Molecular</term><term>Gene Duplication</term><term>Genome, Plant</term><term>Models, Genetic</term><term>Models, Statistical</term><term>Phylogeny</term><term>Polyploidy</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Duplication de gène</term><term>Génome végétal</term><term>Modèles génétiques</term><term>Modèles statistiques</term><term>Phylogenèse</term><term>Polyploïdie</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Genomic comparisons provide evidence for ancient genome-wide duplications in a diverse array of animals and plants. We developed a birth-death model to identify evidence for genome duplication in EST data, and applied a mixture model to estimate the age distribution of paralogous pairs identified in EST sets for species representing the basal-most extant flowering plant lineages. We found evidence for episodes of ancient genome-wide duplications in the basal angiosperm lineages including Nuphar advena (yellow water lily: Nymphaeaceae) and the magnoliids Persea americana (avocado: Lauraceae), Liriodendron tulipifera (tulip poplar: Magnoliaceae), and Saruma henryi (Aristolochiaceae). In addition, we detected independent genome duplications in the basal eudicot Eschscholzia californica (California poppy: Papaveraceae) and the basal monocot Acorus americanus (Acoraceae), both of which were distinct from duplications documented for ancestral grass (Poaceae) and core eudicot lineages. Among gymnosperms, we found equivocal evidence for ancient polyploidy in Welwitschia mirabilis (Gnetales) and no evidence for polyploidy in pine, although gymnosperms generally have much larger genomes than the angiosperms investigated. Cross-species sequence divergence estimates suggest that synonymous substitution rates in the basal angiosperms are less than half those previously reported for core eudicots and members of Poaceae. These lower substitution rates permit inference of older duplication events. We hypothesize that evidence of an ancient duplication observed in the Nuphar data may represent a genome duplication in the common ancestor of all or most extant angiosperms, except Amborella.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16702410</PMID><DateCompleted><Year>2006</Year><Month>07</Month><Day>13</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">1088-9051</ISSN><JournalIssue CitedMedium="Print"><Volume>16</Volume><Issue>6</Issue><PubDate><Year>2006</Year><Month>Jun</Month></PubDate></JournalIssue><Title>Genome research</Title><ISOAbbreviation>Genome Res</ISOAbbreviation></Journal><ArticleTitle>Widespread genome duplications throughout the history of flowering plants.</ArticleTitle><Pagination><MedlinePgn>738-49</MedlinePgn></Pagination><Abstract><AbstractText>Genomic comparisons provide evidence for ancient genome-wide duplications in a diverse array of animals and plants. We developed a birth-death model to identify evidence for genome duplication in EST data, and applied a mixture model to estimate the age distribution of paralogous pairs identified in EST sets for species representing the basal-most extant flowering plant lineages. We found evidence for episodes of ancient genome-wide duplications in the basal angiosperm lineages including Nuphar advena (yellow water lily: Nymphaeaceae) and the magnoliids Persea americana (avocado: Lauraceae), Liriodendron tulipifera (tulip poplar: Magnoliaceae), and Saruma henryi (Aristolochiaceae). In addition, we detected independent genome duplications in the basal eudicot Eschscholzia californica (California poppy: Papaveraceae) and the basal monocot Acorus americanus (Acoraceae), both of which were distinct from duplications documented for ancestral grass (Poaceae) and core eudicot lineages. Among gymnosperms, we found equivocal evidence for ancient polyploidy in Welwitschia mirabilis (Gnetales) and no evidence for polyploidy in pine, although gymnosperms generally have much larger genomes than the angiosperms investigated. Cross-species sequence divergence estimates suggest that synonymous substitution rates in the basal angiosperms are less than half those previously reported for core eudicots and members of Poaceae. These lower substitution rates permit inference of older duplication events. We hypothesize that evidence of an ancient duplication observed in the Nuphar data may represent a genome duplication in the common ancestor of all or most extant angiosperms, except Amborella.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Cui</LastName><ForeName>Liying</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Department of Biology, The Pennsylvania State University, University Park 16802, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wall</LastName><ForeName>P Kerr</ForeName><Initials>PK</Initials></Author><Author ValidYN="Y"><LastName>Leebens-Mack</LastName><ForeName>James H</ForeName><Initials>JH</Initials></Author><Author ValidYN="Y"><LastName>Lindsay</LastName><ForeName>Bruce G</ForeName><Initials>BG</Initials></Author><Author ValidYN="Y"><LastName>Soltis</LastName><ForeName>Douglas E</ForeName><Initials>DE</Initials></Author><Author ValidYN="Y"><LastName>Doyle</LastName><ForeName>Jeff J</ForeName><Initials>JJ</Initials></Author><Author ValidYN="Y"><LastName>Soltis</LastName><ForeName>Pamela S</ForeName><Initials>PS</Initials></Author><Author ValidYN="Y"><LastName>Carlson</LastName><ForeName>John E</ForeName><Initials>JE</Initials></Author><Author ValidYN="Y"><LastName>Arumuganathan</LastName><ForeName>Kathiravetpilla</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Barakat</LastName><ForeName>Abdelali</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Albert</LastName><ForeName>Victor A</ForeName><Initials>VA</Initials></Author><Author ValidYN="Y"><LastName>Ma</LastName><ForeName>Hong</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>dePamphilis</LastName><ForeName>Claude W</ForeName><Initials>CW</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2006</Year><Month>05</Month><Day>15</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Genome Res</MedlineTA><NlmUniqueID>9518021</NlmUniqueID><ISSNLinking>1088-9051</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D032462" MajorTopicYN="N">Cycadopsida</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020440" MajorTopicYN="Y">Gene Duplication</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019684" MajorTopicYN="N">Magnoliopsida</DescriptorName><QualifierName UI="Q000235" 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Victor A" sort="Albert, Victor A" uniqKey="Albert V" first="Victor A" last="Albert">Victor A. Albert</name><name sortKey="Arumuganathan, Kathiravetpilla" sort="Arumuganathan, Kathiravetpilla" uniqKey="Arumuganathan K" first="Kathiravetpilla" last="Arumuganathan">Kathiravetpilla Arumuganathan</name><name sortKey="Barakat, Abdelali" sort="Barakat, Abdelali" uniqKey="Barakat A" first="Abdelali" last="Barakat">Abdelali Barakat</name><name sortKey="Carlson, John E" sort="Carlson, John E" uniqKey="Carlson J" first="John E" last="Carlson">John E. Carlson</name><name sortKey="Depamphilis, Claude W" sort="Depamphilis, Claude W" uniqKey="Depamphilis C" first="Claude W" last="Depamphilis">Claude W. Depamphilis</name><name sortKey="Doyle, Jeff J" sort="Doyle, Jeff J" uniqKey="Doyle J" first="Jeff J" last="Doyle">Jeff J. Doyle</name><name sortKey="Leebens Mack, James H" sort="Leebens Mack, James H" uniqKey="Leebens Mack J" first="James H" last="Leebens-Mack">James H. Leebens-Mack</name><name sortKey="Lindsay, Bruce G" sort="Lindsay, Bruce G" uniqKey="Lindsay B" first="Bruce G" last="Lindsay">Bruce G. Lindsay</name><name sortKey="Ma, Hong" sort="Ma, Hong" uniqKey="Ma H" first="Hong" last="Ma">Hong Ma</name><name sortKey="Soltis, Douglas E" sort="Soltis, Douglas E" uniqKey="Soltis D" first="Douglas E" last="Soltis">Douglas E. Soltis</name><name sortKey="Soltis, Pamela S" sort="Soltis, Pamela S" uniqKey="Soltis P" first="Pamela S" last="Soltis">Pamela S. Soltis</name><name sortKey="Wall, P Kerr" sort="Wall, P Kerr" uniqKey="Wall P" first="P Kerr" last="Wall">P Kerr Wall</name></noCountry><country name="États-Unis"><region name="Pennsylvanie"><name sortKey="Cui, Liying" sort="Cui, Liying" uniqKey="Cui L" first="Liying" last="Cui">Liying Cui</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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