A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure.
Identifieur interne : 003016 ( Main/Exploration ); précédent : 003015; suivant : 003017A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure.
Auteurs : Andrea Zuccolo [États-Unis] ; John E. Bowers ; James C. Estill ; Zhiyong Xiong ; Meizhong Luo ; Aswathy Sebastian ; José Luis Goicoechea ; Kristi Collura ; Yeisoo Yu ; Yuannian Jiao ; Jill Duarte ; Haibao Tang ; Saravanaraj Ayyampalayam ; Steve Rounsley ; Dave Kudrna ; Andrew H. Paterson ; J Chris Pires ; Andre Chanderbali ; Douglas E. Soltis ; Srikar Chamala ; Brad Barbazuk ; Pamela S. Soltis ; Victor A. Albert ; Hong Ma ; Dina Mandoli ; Jody Banks ; John E. Carlson ; Jeffrey Tomkins ; Claude W. Depamphilis ; Rod A. Wing ; Jim Leebens-MackSource :
- Genome biology [ 1474-760X ] ; 2011.
Descripteurs français
- KwdFr :
- Analyse de séquence d'ADN (MeSH), Bases de données génétiques (MeSH), Cadres ouverts de lecture (génétique), Cartographie de contigs (méthodes), Génome végétal (MeSH), Génomique (méthodes), Magnoliopsida (classification), Magnoliopsida (génétique), Nouvelle-Calédonie (MeSH), Phylogenèse (MeSH), Phylogéographie (MeSH), Ploïdies (MeSH), Rétroéléments (MeSH), Synténie (MeSH), Évolution moléculaire (MeSH).
- MESH :
English descriptors
- KwdEn :
- Contig Mapping (methods), Databases, Genetic (MeSH), Evolution, Molecular (MeSH), Genome, Plant (MeSH), Genomics (methods), Magnoliopsida (classification), Magnoliopsida (genetics), New Caledonia (MeSH), Open Reading Frames (genetics), Phylogeny (MeSH), Phylogeography (MeSH), Ploidies (MeSH), Retroelements (MeSH), Sequence Analysis, DNA (MeSH), Synteny (MeSH).
- MESH :
- chemical : Retroelements.
- classification : Magnoliopsida.
- genetics : Magnoliopsida, Open Reading Frames.
- methods : Contig Mapping, Genomics.
- Databases, Genetic, Evolution, Molecular, Genome, Plant, New Caledonia, Phylogeny, Phylogeography, Ploidies, Sequence Analysis, DNA, Synteny.
Abstract
BACKGROUND
Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes because it can serve as an outgroup to root comparative analyses. A physical map, BAC end sequences and sample shotgun sequences provide a first view of the 870 Mbp Amborella genome.
RESULTS
Analysis of Amborella BAC ends sequenced from each contig suggests that the density of long terminal repeat retrotransposons is negatively correlated with that of protein coding genes. Syntenic, presumably ancestral, gene blocks were identified in comparisons of the Amborella BAC contigs and the sequenced Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa genomes. Parsimony mapping of the loss of synteny corroborates previous analyses suggesting that the rate of structural change has been more rapid on lineages leading to Arabidopsis and Oryza compared with lineages leading to Populus and Vitis. The gamma paleohexiploidy event identified in the Arabidopsis, Populus and Vitis genomes is shown to have occurred after the divergence of all other known angiosperms from the lineage leading to Amborella.
CONCLUSIONS
When placed in the context of a physical map, BAC end sequences representing just 5.4% of the Amborella genome have facilitated reconstruction of gene blocks that existed in the last common ancestor of all flowering plants. The Amborella genome is an invaluable reference for inferences concerning the ancestral angiosperm and subsequent genome evolution.
DOI: 10.1186/gb-2011-12-5-r48
PubMed: 21619600
PubMed Central: PMC3219971
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Bowers</name></author><author><name sortKey="Estill, James C" sort="Estill, James C" uniqKey="Estill J" first="James C" last="Estill">James C. Estill</name></author><author><name sortKey="Xiong, Zhiyong" sort="Xiong, Zhiyong" uniqKey="Xiong Z" first="Zhiyong" last="Xiong">Zhiyong Xiong</name></author><author><name sortKey="Luo, Meizhong" sort="Luo, Meizhong" uniqKey="Luo M" first="Meizhong" last="Luo">Meizhong Luo</name></author><author><name sortKey="Sebastian, Aswathy" sort="Sebastian, Aswathy" uniqKey="Sebastian A" first="Aswathy" last="Sebastian">Aswathy Sebastian</name></author><author><name sortKey="Goicoechea, Jose Luis" sort="Goicoechea, Jose Luis" uniqKey="Goicoechea J" first="José Luis" last="Goicoechea">José Luis Goicoechea</name></author><author><name sortKey="Collura, Kristi" sort="Collura, Kristi" uniqKey="Collura K" first="Kristi" last="Collura">Kristi Collura</name></author><author><name sortKey="Yu, Yeisoo" sort="Yu, Yeisoo" uniqKey="Yu Y" first="Yeisoo" last="Yu">Yeisoo Yu</name></author><author><name sortKey="Jiao, Yuannian" sort="Jiao, Yuannian" uniqKey="Jiao Y" first="Yuannian" last="Jiao">Yuannian Jiao</name></author><author><name sortKey="Duarte, Jill" sort="Duarte, Jill" uniqKey="Duarte J" first="Jill" last="Duarte">Jill Duarte</name></author><author><name sortKey="Tang, Haibao" sort="Tang, Haibao" uniqKey="Tang H" first="Haibao" last="Tang">Haibao Tang</name></author><author><name sortKey="Ayyampalayam, Saravanaraj" sort="Ayyampalayam, Saravanaraj" uniqKey="Ayyampalayam S" first="Saravanaraj" last="Ayyampalayam">Saravanaraj Ayyampalayam</name></author><author><name sortKey="Rounsley, Steve" sort="Rounsley, Steve" uniqKey="Rounsley S" first="Steve" last="Rounsley">Steve Rounsley</name></author><author><name sortKey="Kudrna, Dave" sort="Kudrna, Dave" uniqKey="Kudrna D" first="Dave" last="Kudrna">Dave Kudrna</name></author><author><name sortKey="Paterson, Andrew H" sort="Paterson, Andrew H" uniqKey="Paterson A" first="Andrew H" last="Paterson">Andrew H. Paterson</name></author><author><name sortKey="Pires, J Chris" sort="Pires, J Chris" uniqKey="Pires J" first="J Chris" last="Pires">J Chris Pires</name></author><author><name sortKey="Chanderbali, Andre" sort="Chanderbali, Andre" uniqKey="Chanderbali A" first="Andre" last="Chanderbali">Andre Chanderbali</name></author><author><name sortKey="Soltis, Douglas E" sort="Soltis, Douglas E" uniqKey="Soltis D" first="Douglas E" last="Soltis">Douglas E. Soltis</name></author><author><name sortKey="Chamala, Srikar" sort="Chamala, Srikar" uniqKey="Chamala S" first="Srikar" last="Chamala">Srikar Chamala</name></author><author><name sortKey="Barbazuk, Brad" sort="Barbazuk, Brad" uniqKey="Barbazuk B" first="Brad" last="Barbazuk">Brad Barbazuk</name></author><author><name sortKey="Soltis, Pamela S" sort="Soltis, Pamela S" uniqKey="Soltis P" first="Pamela S" last="Soltis">Pamela S. Soltis</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="Mandoli, Dina" sort="Mandoli, Dina" uniqKey="Mandoli D" first="Dina" last="Mandoli">Dina Mandoli</name></author><author><name sortKey="Banks, Jody" sort="Banks, Jody" uniqKey="Banks J" first="Jody" last="Banks">Jody Banks</name></author><author><name sortKey="Carlson, John E" sort="Carlson, John E" uniqKey="Carlson J" first="John E" last="Carlson">John E. Carlson</name></author><author><name sortKey="Tomkins, Jeffrey" sort="Tomkins, Jeffrey" uniqKey="Tomkins J" first="Jeffrey" last="Tomkins">Jeffrey Tomkins</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><author><name sortKey="Wing, Rod A" sort="Wing, Rod A" uniqKey="Wing R" first="Rod A" last="Wing">Rod A. Wing</name></author><author><name sortKey="Leebens Mack, Jim" sort="Leebens Mack, Jim" uniqKey="Leebens Mack J" first="Jim" last="Leebens-Mack">Jim Leebens-Mack</name></author></analytic><series><title level="j">Genome biology</title><idno type="eISSN">1474-760X</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Contig Mapping (methods)</term><term>Databases, Genetic (MeSH)</term><term>Evolution, Molecular (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Genomics (methods)</term><term>Magnoliopsida (classification)</term><term>Magnoliopsida (genetics)</term><term>New Caledonia (MeSH)</term><term>Open Reading Frames (genetics)</term><term>Phylogeny (MeSH)</term><term>Phylogeography (MeSH)</term><term>Ploidies (MeSH)</term><term>Retroelements (MeSH)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Synteny (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN (MeSH)</term><term>Bases de données génétiques (MeSH)</term><term>Cadres ouverts de lecture (génétique)</term><term>Cartographie de contigs (méthodes)</term><term>Génome végétal (MeSH)</term><term>Génomique (méthodes)</term><term>Magnoliopsida (classification)</term><term>Magnoliopsida (génétique)</term><term>Nouvelle-Calédonie (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Phylogéographie (MeSH)</term><term>Ploïdies (MeSH)</term><term>Rétroéléments (MeSH)</term><term>Synténie (MeSH)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Retroelements</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Magnoliopsida</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Magnoliopsida</term><term>Open Reading Frames</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Cadres ouverts de lecture</term><term>Magnoliopsida</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Contig Mapping</term><term>Genomics</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Cartographie de contigs</term><term>Génomique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Genetic</term><term>Evolution, Molecular</term><term>Genome, Plant</term><term>New Caledonia</term><term>Phylogeny</term><term>Phylogeography</term><term>Ploidies</term><term>Sequence Analysis, DNA</term><term>Synteny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Bases de données génétiques</term><term>Génome végétal</term><term>Magnoliopsida</term><term>Nouvelle-Calédonie</term><term>Phylogenèse</term><term>Phylogéographie</term><term>Ploïdies</term><term>Rétroéléments</term><term>Synténie</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes because it can serve as an outgroup to root comparative analyses. A physical map, BAC end sequences and sample shotgun sequences provide a first view of the 870 Mbp Amborella genome.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>Analysis of Amborella BAC ends sequenced from each contig suggests that the density of long terminal repeat retrotransposons is negatively correlated with that of protein coding genes. Syntenic, presumably ancestral, gene blocks were identified in comparisons of the Amborella BAC contigs and the sequenced Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa genomes. Parsimony mapping of the loss of synteny corroborates previous analyses suggesting that the rate of structural change has been more rapid on lineages leading to Arabidopsis and Oryza compared with lineages leading to Populus and Vitis. The gamma paleohexiploidy event identified in the Arabidopsis, Populus and Vitis genomes is shown to have occurred after the divergence of all other known angiosperms from the lineage leading to Amborella.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>When placed in the context of a physical map, BAC end sequences representing just 5.4% of the Amborella genome have facilitated reconstruction of gene blocks that existed in the last common ancestor of all flowering plants. The Amborella genome is an invaluable reference for inferences concerning the ancestral angiosperm and subsequent genome evolution.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21619600</PMID><DateCompleted><Year>2012</Year><Month>02</Month><Day>14</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1474-760X</ISSN><JournalIssue CitedMedium="Internet"><Volume>12</Volume><Issue>5</Issue><PubDate><Year>2011</Year></PubDate></JournalIssue><Title>Genome biology</Title><ISOAbbreviation>Genome Biol</ISOAbbreviation></Journal><ArticleTitle>A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure.</ArticleTitle><Pagination><MedlinePgn>R48</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/gb-2011-12-5-r48</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes because it can serve as an outgroup to root comparative analyses. A physical map, BAC end sequences and sample shotgun sequences provide a first view of the 870 Mbp Amborella genome.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Analysis of Amborella BAC ends sequenced from each contig suggests that the density of long terminal repeat retrotransposons is negatively correlated with that of protein coding genes. Syntenic, presumably ancestral, gene blocks were identified in comparisons of the Amborella BAC contigs and the sequenced Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa genomes. Parsimony mapping of the loss of synteny corroborates previous analyses suggesting that the rate of structural change has been more rapid on lineages leading to Arabidopsis and Oryza compared with lineages leading to Populus and Vitis. The gamma paleohexiploidy event identified in the Arabidopsis, Populus and Vitis genomes is shown to have occurred after the divergence of all other known angiosperms from the lineage leading to Amborella.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">When placed in the context of a physical map, BAC end sequences representing just 5.4% of the Amborella genome have facilitated reconstruction of gene blocks that existed in the last common ancestor of all flowering plants. The Amborella genome is an invaluable reference for inferences concerning the ancestral angiosperm and subsequent genome evolution.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zuccolo</LastName><ForeName>Andrea</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, 1657 East Helen Street, Tucson, AZ 85721, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bowers</LastName><ForeName>John E</ForeName><Initials>JE</Initials></Author><Author ValidYN="Y"><LastName>Estill</LastName><ForeName>James C</ForeName><Initials>JC</Initials></Author><Author ValidYN="Y"><LastName>Xiong</LastName><ForeName>Zhiyong</ForeName><Initials>Z</Initials></Author><Author ValidYN="Y"><LastName>Luo</LastName><ForeName>Meizhong</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Sebastian</LastName><ForeName>Aswathy</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Goicoechea</LastName><ForeName>José Luis</ForeName><Initials>JL</Initials></Author><Author ValidYN="Y"><LastName>Collura</LastName><ForeName>Kristi</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Yu</LastName><ForeName>Yeisoo</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Jiao</LastName><ForeName>Yuannian</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Duarte</LastName><ForeName>Jill</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Tang</LastName><ForeName>Haibao</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Ayyampalayam</LastName><ForeName>Saravanaraj</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Rounsley</LastName><ForeName>Steve</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Kudrna</LastName><ForeName>Dave</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Paterson</LastName><ForeName>Andrew H</ForeName><Initials>AH</Initials></Author><Author ValidYN="Y"><LastName>Pires</LastName><ForeName>J Chris</ForeName><Initials>JC</Initials></Author><Author ValidYN="Y"><LastName>Chanderbali</LastName><ForeName>Andre</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Soltis</LastName><ForeName>Douglas E</ForeName><Initials>DE</Initials></Author><Author ValidYN="Y"><LastName>Chamala</LastName><ForeName>Srikar</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Barbazuk</LastName><ForeName>Brad</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Soltis</LastName><ForeName>Pamela S</ForeName><Initials>PS</Initials></Author><Author ValidYN="Y"><LastName>Albert</LastName><ForeName>Victor A</ForeName><Initials>VA</Initials></Author><Author 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