Two evolutionarily distinct classes of paleopolyploidy.
Identifieur interne : 001F82 ( Main/Exploration ); précédent : 001F81; suivant : 001F83Two evolutionarily distinct classes of paleopolyploidy.
Auteurs : Olivier Garsmeur [France] ; James C. Schnable ; Ana Almeida ; Cyril Jourda ; Angélique D'Hont ; Michael FreelingSource :
- Molecular biology and evolution [ 1537-1719 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Musa, Plantes.
- classification : Duplication de gène, Gènes de plante, Génome végétal, Phylogenèse, Plantes, Polyploïdie, Spécificité d'espèce, Substitution d'acide aminé, Transcriptome, Évolution moléculaire.
English descriptors
- KwdEn :
- MESH :
- classification : Plants.
- genetics : Musa, Plants.
- Amino Acid Substitution, Evolution, Molecular, Gene Duplication, Genes, Plant, Genome, Plant, Phylogeny, Polyploidy, Species Specificity, Transcriptome.
Abstract
Whole genome duplications (WGDs) occurred in the distant evolutionary history of many lineages and are particularly frequent in the flowering plant lineages. Following paleopolyploidization in plants, most duplicated genes are deleted by intrachromosomal recombination, a process referred to as fractionation. In the examples studied so far, genes are disproportionately lost from one of the parental subgenomes (biased fractionation) and the subgenome having lost the lowest number of genes is more expressed (genome dominance). In the present study, we analyzed the pattern of gene deletion and gene expression following the most recent WGD in banana (alpha event) and extended our analyses to seven other sequenced plant genomes: poplar, soybean, medicago, arabidopsis, sorghum, brassica, and maize. We propose a new class of ancient WGD, with Musa (alpha), poplar, and soybean as members, where genes are both deleted and expressed to an equal extent (unbiased fractionation and genome equivalence). We suggest that WGDs with genome dominance and biased fractionation (Class I) may result from ancient allotetraploidies, while WGDs without genome dominance or biased fractionation (Class II) may result from ancient autotetraploidies.
DOI: 10.1093/molbev/mst230
PubMed: 24296661
Affiliations:
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Schnable</name></author><author><name sortKey="Almeida, Ana" sort="Almeida, Ana" uniqKey="Almeida A" first="Ana" last="Almeida">Ana Almeida</name></author><author><name sortKey="Jourda, Cyril" sort="Jourda, Cyril" uniqKey="Jourda C" first="Cyril" last="Jourda">Cyril Jourda</name></author><author><name sortKey="D Hont, Angelique" sort="D Hont, Angelique" uniqKey="D Hont A" first="Angélique" last="D'Hont">Angélique D'Hont</name></author><author><name sortKey="Freeling, Michael" sort="Freeling, Michael" uniqKey="Freeling M" first="Michael" last="Freeling">Michael Freeling</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:24296661</idno><idno type="pmid">24296661</idno><idno type="doi">10.1093/molbev/mst230</idno><idno type="wicri:Area/Main/Corpus">002388</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">002388</idno><idno type="wicri:Area/Main/Curation">002388</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">002388</idno><idno type="wicri:Area/Main/Exploration">002388</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Two evolutionarily distinct classes of paleopolyploidy.</title><author><name sortKey="Garsmeur, Olivier" sort="Garsmeur, Olivier" uniqKey="Garsmeur O" first="Olivier" last="Garsmeur">Olivier Garsmeur</name><affiliation wicri:level="3"><nlm:affiliation>Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), UMR AGAP, Montpellier, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), UMR AGAP, Montpellier</wicri:regionArea><placeName><region type="region">Occitanie (région administrative)</region><region type="old region">Languedoc-Roussillon</region><settlement type="city">Montpellier</settlement></placeName></affiliation></author><author><name sortKey="Schnable, James C" sort="Schnable, James C" uniqKey="Schnable J" first="James C" last="Schnable">James C. Schnable</name></author><author><name sortKey="Almeida, Ana" sort="Almeida, Ana" uniqKey="Almeida A" first="Ana" last="Almeida">Ana Almeida</name></author><author><name sortKey="Jourda, Cyril" sort="Jourda, Cyril" uniqKey="Jourda C" first="Cyril" last="Jourda">Cyril Jourda</name></author><author><name sortKey="D Hont, Angelique" sort="D Hont, Angelique" uniqKey="D Hont A" first="Angélique" last="D'Hont">Angélique D'Hont</name></author><author><name sortKey="Freeling, Michael" sort="Freeling, Michael" uniqKey="Freeling M" first="Michael" last="Freeling">Michael Freeling</name></author></analytic><series><title level="j">Molecular biology and evolution</title><idno type="eISSN">1537-1719</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Substitution (MeSH)</term><term>Evolution, Molecular (MeSH)</term><term>Gene Duplication (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Musa (genetics)</term><term>Phylogeny (MeSH)</term><term>Plants (classification)</term><term>Plants (genetics)</term><term>Polyploidy (MeSH)</term><term>Species Specificity (MeSH)</term><term>Transcriptome (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Duplication de gène (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Génome végétal (MeSH)</term><term>Musa (génétique)</term><term>Phylogenèse (MeSH)</term><term>Plantes (classification)</term><term>Plantes (génétique)</term><term>Polyploïdie (MeSH)</term><term>Spécificité d'espèce (MeSH)</term><term>Substitution d'acide aminé (MeSH)</term><term>Transcriptome (MeSH)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Plants</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Musa</term><term>Plants</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Musa</term><term>Plantes</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Substitution</term><term>Evolution, Molecular</term><term>Gene Duplication</term><term>Genes, Plant</term><term>Genome, Plant</term><term>Phylogeny</term><term>Polyploidy</term><term>Species Specificity</term><term>Transcriptome</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="fr"><term>Duplication de gène</term><term>Gènes de plante</term><term>Génome végétal</term><term>Phylogenèse</term><term>Plantes</term><term>Polyploïdie</term><term>Spécificité d'espèce</term><term>Substitution d'acide aminé</term><term>Transcriptome</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Whole genome duplications (WGDs) occurred in the distant evolutionary history of many lineages and are particularly frequent in the flowering plant lineages. Following paleopolyploidization in plants, most duplicated genes are deleted by intrachromosomal recombination, a process referred to as fractionation. In the examples studied so far, genes are disproportionately lost from one of the parental subgenomes (biased fractionation) and the subgenome having lost the lowest number of genes is more expressed (genome dominance). In the present study, we analyzed the pattern of gene deletion and gene expression following the most recent WGD in banana (alpha event) and extended our analyses to seven other sequenced plant genomes: poplar, soybean, medicago, arabidopsis, sorghum, brassica, and maize. We propose a new class of ancient WGD, with Musa (alpha), poplar, and soybean as members, where genes are both deleted and expressed to an equal extent (unbiased fractionation and genome equivalence). We suggest that WGDs with genome dominance and biased fractionation (Class I) may result from ancient allotetraploidies, while WGDs without genome dominance or biased fractionation (Class II) may result from ancient autotetraploidies. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24296661</PMID><DateCompleted><Year>2014</Year><Month>10</Month><Day>23</Day></DateCompleted><DateRevised><Year>2014</Year><Month>01</Month><Day>23</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1537-1719</ISSN><JournalIssue CitedMedium="Internet"><Volume>31</Volume><Issue>2</Issue><PubDate><Year>2014</Year><Month>Feb</Month></PubDate></JournalIssue><Title>Molecular biology and evolution</Title><ISOAbbreviation>Mol Biol Evol</ISOAbbreviation></Journal><ArticleTitle>Two evolutionarily distinct classes of paleopolyploidy.</ArticleTitle><Pagination><MedlinePgn>448-54</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/molbev/mst230</ELocationID><Abstract><AbstractText>Whole genome duplications (WGDs) occurred in the distant evolutionary history of many lineages and are particularly frequent in the flowering plant lineages. Following paleopolyploidization in plants, most duplicated genes are deleted by intrachromosomal recombination, a process referred to as fractionation. In the examples studied so far, genes are disproportionately lost from one of the parental subgenomes (biased fractionation) and the subgenome having lost the lowest number of genes is more expressed (genome dominance). In the present study, we analyzed the pattern of gene deletion and gene expression following the most recent WGD in banana (alpha event) and extended our analyses to seven other sequenced plant genomes: poplar, soybean, medicago, arabidopsis, sorghum, brassica, and maize. We propose a new class of ancient WGD, with Musa (alpha), poplar, and soybean as members, where genes are both deleted and expressed to an equal extent (unbiased fractionation and genome equivalence). We suggest that WGDs with genome dominance and biased fractionation (Class I) may result from ancient allotetraploidies, while WGDs without genome dominance or biased fractionation (Class II) may result from ancient autotetraploidies. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Garsmeur</LastName><ForeName>Olivier</ForeName><Initials>O</Initials><AffiliationInfo><Affiliation>Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), UMR AGAP, Montpellier, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schnable</LastName><ForeName>James C</ForeName><Initials>JC</Initials></Author><Author ValidYN="Y"><LastName>Almeida</LastName><ForeName>Ana</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Jourda</LastName><ForeName>Cyril</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>D'Hont</LastName><ForeName>Angélique</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Freeling</LastName><ForeName>Michael</ForeName><Initials>M</Initials></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>2013</Year><Month>12</Month><Day>01</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="D019943" MajorTopicYN="N">Amino Acid Substitution</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020440" MajorTopicYN="N">Gene Duplication</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D028521" MajorTopicYN="N">Musa</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010944" MajorTopicYN="N">Plants</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011123" MajorTopicYN="Y">Polyploidy</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013045" MajorTopicYN="N">Species Specificity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059467" MajorTopicYN="N">Transcriptome</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">evolution</Keyword><Keyword MajorTopicYN="N">gene fractionation</Keyword><Keyword MajorTopicYN="N">genome dominance</Keyword><Keyword MajorTopicYN="N">paleopolyploid</Keyword><Keyword MajorTopicYN="N">whole genome duplication</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2013</Year><Month>12</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2013</Year><Month>12</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>10</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">24296661</ArticleId><ArticleId IdType="pii">mst230</ArticleId><ArticleId IdType="doi">10.1093/molbev/mst230</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>France</li></country><region><li>Languedoc-Roussillon</li><li>Occitanie (région administrative)</li></region><settlement><li>Montpellier</li></settlement></list><tree><noCountry><name sortKey="Almeida, Ana" sort="Almeida, Ana" uniqKey="Almeida A" first="Ana" last="Almeida">Ana Almeida</name><name sortKey="D Hont, Angelique" sort="D Hont, Angelique" uniqKey="D Hont A" first="Angélique" last="D'Hont">Angélique D'Hont</name><name sortKey="Freeling, Michael" sort="Freeling, Michael" uniqKey="Freeling M" first="Michael" last="Freeling">Michael Freeling</name><name sortKey="Jourda, Cyril" sort="Jourda, Cyril" uniqKey="Jourda C" first="Cyril" last="Jourda">Cyril Jourda</name><name sortKey="Schnable, James C" sort="Schnable, James C" uniqKey="Schnable J" first="James C" last="Schnable">James C. Schnable</name></noCountry><country name="France"><region name="Occitanie (région administrative)"><name sortKey="Garsmeur, Olivier" sort="Garsmeur, Olivier" uniqKey="Garsmeur O" first="Olivier" last="Garsmeur">Olivier Garsmeur</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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