Comparison of gene order of GIGANTEA loci in yellow-poplar, monocots, and eudicots.
Identifieur interne : 003327 ( Main/Exploration ); précédent : 003326; suivant : 003328Comparison of gene order of GIGANTEA loci in yellow-poplar, monocots, and eudicots.
Auteurs : Haiying Liang [États-Unis] ; Abdelali Barakat ; Scott E. Schlarbaum ; Dina F. Mandoli ; John E. CarlsonSource :
- Genome [ 1480-3321 ] ; 2010.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA, Plant, Plant Proteins.
- classification : Magnoliopsida.
- genetics : Liriodendron, Magnoliopsida.
- Chromosomes, Artificial, Bacterial, Evolution, Molecular, Gene Order, Genome, Plant, Phylogeny.
Abstract
GIGANTEA plays an important role in the control of circadian rhythms and photoperiodic flowering. The GIGANTEA gene has been studied in various species, but not in basal angiosperms. Moreover, to the best of our knowledge, no study of the genome organization of a basal angiosperm has yet been published. In this study, we sequenced a bacterial artificial chromosome (BAC) harboring GIGANTEA from yellow-poplar (Liriodendron tulipifera L.) and compared the genomic organization of this gene in yellow-poplar with that in other species from various angiosperm clades. This is the first report on the gene structure and organization of a large contig in any basal angiosperm species. The BAC clone, covering a region of approximately 122 kb from the yellow-poplar genome, was sequenced and assembled by coupling the 454 pyrosequencing technology with ABI capillary sequencing. In addition to GIGANTEA, the gene RPS18.A (encoding ribosomal protein S18.A) was found in this segment of the genome. We found that gene content and order in this region of the yellow-poplar genome were similar to those in the corresponding region in eudicots but not in Oryza sativa and Sorghum bicolor, implying that clustering of the GIGANTEA and RPS18.A genes is ancestral and separation of the genes occurred after the phylogenetic split of monocots from dicots. Phylogenetic analysis of GIGANTEA amino acid sequences placed yellow-poplar closer to eudicots than to monocots. In addition, evidence for transposition and large insertions and duplications was found, suggesting multiple and complex mechanisms of basal angiosperm genome evolution.
DOI: 10.1139/g10-031
PubMed: 20616875
Affiliations:
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Schlarbaum</name></author><author><name sortKey="Mandoli, Dina F" sort="Mandoli, Dina F" uniqKey="Mandoli D" first="Dina F" last="Mandoli">Dina F. Mandoli</name></author><author><name sortKey="Carlson, John E" sort="Carlson, John E" uniqKey="Carlson J" first="John E" last="Carlson">John E. 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Schlarbaum</name></author><author><name sortKey="Mandoli, Dina F" sort="Mandoli, Dina F" uniqKey="Mandoli D" first="Dina F" last="Mandoli">Dina F. Mandoli</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></analytic><series><title level="j">Genome</title><idno type="eISSN">1480-3321</idno><imprint><date when="2010" type="published">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosomes, Artificial, Bacterial (MeSH)</term><term>DNA, Plant (genetics)</term><term>Evolution, Molecular (MeSH)</term><term>Gene Order (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Liriodendron (genetics)</term><term>Magnoliopsida (classification)</term><term>Magnoliopsida (genetics)</term><term>Phylogeny (MeSH)</term><term>Plant Proteins (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des plantes (génétique)</term><term>Chromosomes artificiels de bactérie (MeSH)</term><term>Génome végétal (MeSH)</term><term>Liriodendron (génétique)</term><term>Magnoliopsida (classification)</term><term>Magnoliopsida (génétique)</term><term>Ordre des gènes (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Protéines végétales (génétique)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Plant</term><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Magnoliopsida</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Liriodendron</term><term>Magnoliopsida</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN des plantes</term><term>Liriodendron</term><term>Magnoliopsida</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosomes, Artificial, Bacterial</term><term>Evolution, Molecular</term><term>Gene Order</term><term>Genome, Plant</term><term>Phylogeny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Chromosomes artificiels de bactérie</term><term>Génome végétal</term><term>Ordre des gènes</term><term>Phylogenèse</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">GIGANTEA plays an important role in the control of circadian rhythms and photoperiodic flowering. The GIGANTEA gene has been studied in various species, but not in basal angiosperms. Moreover, to the best of our knowledge, no study of the genome organization of a basal angiosperm has yet been published. In this study, we sequenced a bacterial artificial chromosome (BAC) harboring GIGANTEA from yellow-poplar (Liriodendron tulipifera L.) and compared the genomic organization of this gene in yellow-poplar with that in other species from various angiosperm clades. This is the first report on the gene structure and organization of a large contig in any basal angiosperm species. The BAC clone, covering a region of approximately 122 kb from the yellow-poplar genome, was sequenced and assembled by coupling the 454 pyrosequencing technology with ABI capillary sequencing. In addition to GIGANTEA, the gene RPS18.A (encoding ribosomal protein S18.A) was found in this segment of the genome. We found that gene content and order in this region of the yellow-poplar genome were similar to those in the corresponding region in eudicots but not in Oryza sativa and Sorghum bicolor, implying that clustering of the GIGANTEA and RPS18.A genes is ancestral and separation of the genes occurred after the phylogenetic split of monocots from dicots. Phylogenetic analysis of GIGANTEA amino acid sequences placed yellow-poplar closer to eudicots than to monocots. In addition, evidence for transposition and large insertions and duplications was found, suggesting multiple and complex mechanisms of basal angiosperm genome evolution.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">20616875</PMID><DateCompleted><Year>2010</Year><Month>11</Month><Day>05</Day></DateCompleted><DateRevised><Year>2017</Year><Month>11</Month><Day>16</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1480-3321</ISSN><JournalIssue CitedMedium="Internet"><Volume>53</Volume><Issue>7</Issue><PubDate><Year>2010</Year><Month>Jul</Month></PubDate></JournalIssue><Title>Genome</Title><ISOAbbreviation>Genome</ISOAbbreviation></Journal><ArticleTitle>Comparison of gene order of GIGANTEA loci in yellow-poplar, monocots, and eudicots.</ArticleTitle><Pagination><MedlinePgn>533-44</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1139/g10-031</ELocationID><Abstract><AbstractText>GIGANTEA plays an important role in the control of circadian rhythms and photoperiodic flowering. The GIGANTEA gene has been studied in various species, but not in basal angiosperms. Moreover, to the best of our knowledge, no study of the genome organization of a basal angiosperm has yet been published. In this study, we sequenced a bacterial artificial chromosome (BAC) harboring GIGANTEA from yellow-poplar (Liriodendron tulipifera L.) and compared the genomic organization of this gene in yellow-poplar with that in other species from various angiosperm clades. This is the first report on the gene structure and organization of a large contig in any basal angiosperm species. The BAC clone, covering a region of approximately 122 kb from the yellow-poplar genome, was sequenced and assembled by coupling the 454 pyrosequencing technology with ABI capillary sequencing. In addition to GIGANTEA, the gene RPS18.A (encoding ribosomal protein S18.A) was found in this segment of the genome. We found that gene content and order in this region of the yellow-poplar genome were similar to those in the corresponding region in eudicots but not in Oryza sativa and Sorghum bicolor, implying that clustering of the GIGANTEA and RPS18.A genes is ancestral and separation of the genes occurred after the phylogenetic split of monocots from dicots. Phylogenetic analysis of GIGANTEA amino acid sequences placed yellow-poplar closer to eudicots than to monocots. In addition, evidence for transposition and large insertions and duplications was found, suggesting multiple and complex mechanisms of basal angiosperm genome evolution.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Liang</LastName><ForeName>Haiying</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>School of Forest Resources and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA. hliang@clemson.edu</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Barakat</LastName><ForeName>Abdelali</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Schlarbaum</LastName><ForeName>Scott E</ForeName><Initials>SE</Initials></Author><Author ValidYN="Y"><LastName>Mandoli</LastName><ForeName>Dina F</ForeName><Initials>DF</Initials></Author><Author ValidYN="Y"><LastName>Carlson</LastName><ForeName>John E</ForeName><Initials>JE</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>Canada</Country><MedlineTA>Genome</MedlineTA><NlmUniqueID>8704544</NlmUniqueID><ISSNLinking>0831-2796</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018744">DNA, Plant</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D022202" MajorTopicYN="N">Chromosomes, Artificial, Bacterial</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018744" MajorTopicYN="N">DNA, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023061" MajorTopicYN="Y">Gene Order</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D031567" MajorTopicYN="N">Liriodendron</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019684" MajorTopicYN="N">Magnoliopsida</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2010</Year><Month>7</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2010</Year><Month>7</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2010</Year><Month>11</Month><Day>6</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">20616875</ArticleId><ArticleId IdType="pii">g10-031</ArticleId><ArticleId IdType="doi">10.1139/g10-031</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Pennsylvanie</li></region><settlement><li>University Park (Pennsylvanie)</li></settlement><orgName><li>Université d'État de Pennsylvanie</li></orgName></list><tree><noCountry><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="Mandoli, Dina F" sort="Mandoli, Dina F" uniqKey="Mandoli D" first="Dina F" last="Mandoli">Dina F. Mandoli</name><name sortKey="Schlarbaum, Scott E" sort="Schlarbaum, Scott E" uniqKey="Schlarbaum S" first="Scott E" last="Schlarbaum">Scott E. Schlarbaum</name></noCountry><country name="États-Unis"><region name="Pennsylvanie"><name sortKey="Liang, Haiying" sort="Liang, Haiying" uniqKey="Liang H" first="Haiying" last="Liang">Haiying Liang</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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