Genome-wide analysis of the MADS-box gene family in cucumber.
Identifieur interne : 002A65 ( Main/Exploration ); précédent : 002A64; suivant : 002A66Genome-wide analysis of the MADS-box gene family in cucumber.
Auteurs : Lifang Hu [République populaire de Chine] ; Shiqiang LiuSource :
- Genome [ 1480-3321 ] ; 2012.
Descripteurs français
- KwdFr :
- Alignement de séquences (MeSH), Amorces ADN (génétique), Analyse de profil d'expression de gènes (MeSH), Analyse de regroupements (MeSH), Biologie informatique (MeSH), Cucumis sativus (génétique), Génome végétal (génétique), Modèles génétiques (MeSH), Phylogenèse (MeSH), Protéines à domaine MADS (génétique), Protéines à domaine MADS (métabolisme), Régulation de l'expression des gènes végétaux (génétique), Spécificité d'espèce (MeSH), Séquence nucléotidique (MeSH).
- MESH :
- génétique : Amorces ADN, Cucumis sativus, Génome végétal, Protéines à domaine MADS, Régulation de l'expression des gènes végétaux.
- métabolisme : Protéines à domaine MADS.
- Alignement de séquences, Analyse de profil d'expression de gènes, Analyse de regroupements, Biologie informatique, Modèles génétiques, Phylogenèse, Spécificité d'espèce, Séquence nucléotidique.
English descriptors
- KwdEn :
- Base Sequence (MeSH), Cluster Analysis (MeSH), Computational Biology (MeSH), Cucumis sativus (genetics), DNA Primers (genetics), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (genetics), Genome, Plant (genetics), MADS Domain Proteins (genetics), MADS Domain Proteins (metabolism), Models, Genetic (MeSH), Phylogeny (MeSH), Sequence Alignment (MeSH), Species Specificity (MeSH).
- MESH :
- chemical , genetics : DNA Primers, MADS Domain Proteins.
- genetics : Cucumis sativus, Gene Expression Regulation, Plant, Genome, Plant.
- chemical , metabolism : MADS Domain Proteins.
- Base Sequence, Cluster Analysis, Computational Biology, Gene Expression Profiling, Models, Genetic, Phylogeny, Sequence Alignment, Species Specificity.
Abstract
MADS-box transcription factors are known to be involved in many important processes during plant growth and development. To date, few cucumber MADS-box genes and little tissue expression profiling have been reported. Recent completion of the cucumber whole-genome sequencing has allowed genome-wide analysis of the MADS-box gene family in cucumber as well as its comparison with other species. Here, we performed comprehensive analyses of the 43 cucumber MADS-box genes and compared them with those in Arabidopsis, poplar, and grapevine. The phylogenetic analysis showed that most cucumber members were comparable with those in other species, with the exception of AG members. At the same time, the three subfamilies FLC, AGL12, and Bs were absent in the cucumber genome. The conserved motif analysis revealed that most motifs outside the MADS domain were distributed only in specific groups. The analysis of chromosomal localization suggested that tandem duplication might contribute to the MADS-box gene expansion. Expression analysis revealed that 42 of 43 cucumber MADS-box members were expressed in multiple plant tissues, thereby implying their various roles in plants.
DOI: 10.1139/g2012-009
PubMed: 22376137
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome-wide analysis of the MADS-box gene family in cucumber.</title><author><name sortKey="Hu, Lifang" sort="Hu, Lifang" uniqKey="Hu L" first="Lifang" last="Hu">Lifang Hu</name><affiliation wicri:level="1"><nlm:affiliation>School of Sciences, Jiangxi Agricultural University, 330045 Nanchang, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Sciences, Jiangxi Agricultural University, 330045 Nanchang</wicri:regionArea><placeName><settlement type="city">Nanchang</settlement><region type="province">Jiangxi</region></placeName></affiliation></author><author><name sortKey="Liu, Shiqiang" sort="Liu, Shiqiang" uniqKey="Liu S" first="Shiqiang" last="Liu">Shiqiang Liu</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2012">2012</date><idno type="RBID">pubmed:22376137</idno><idno type="pmid">22376137</idno><idno type="doi">10.1139/g2012-009</idno><idno type="wicri:Area/Main/Corpus">002B20</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">002B20</idno><idno type="wicri:Area/Main/Curation">002B20</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">002B20</idno><idno type="wicri:Area/Main/Exploration">002B20</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Genome-wide analysis of the MADS-box gene family in cucumber.</title><author><name sortKey="Hu, Lifang" sort="Hu, Lifang" uniqKey="Hu L" first="Lifang" last="Hu">Lifang Hu</name><affiliation wicri:level="1"><nlm:affiliation>School of Sciences, Jiangxi Agricultural University, 330045 Nanchang, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Sciences, Jiangxi Agricultural University, 330045 Nanchang</wicri:regionArea><placeName><settlement type="city">Nanchang</settlement><region type="province">Jiangxi</region></placeName></affiliation></author><author><name sortKey="Liu, Shiqiang" sort="Liu, Shiqiang" uniqKey="Liu S" first="Shiqiang" last="Liu">Shiqiang Liu</name></author></analytic><series><title level="j">Genome</title><idno type="eISSN">1480-3321</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence (MeSH)</term><term>Cluster Analysis (MeSH)</term><term>Computational Biology (MeSH)</term><term>Cucumis sativus (genetics)</term><term>DNA Primers (genetics)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation, Plant (genetics)</term><term>Genome, Plant (genetics)</term><term>MADS Domain Proteins (genetics)</term><term>MADS Domain Proteins (metabolism)</term><term>Models, Genetic (MeSH)</term><term>Phylogeny (MeSH)</term><term>Sequence Alignment (MeSH)</term><term>Species Specificity (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Alignement de séquences (MeSH)</term><term>Amorces ADN (génétique)</term><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Analyse de regroupements (MeSH)</term><term>Biologie informatique (MeSH)</term><term>Cucumis sativus (génétique)</term><term>Génome végétal (génétique)</term><term>Modèles génétiques (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Protéines à domaine MADS (génétique)</term><term>Protéines à domaine MADS (métabolisme)</term><term>Régulation de l'expression des gènes végétaux (génétique)</term><term>Spécificité d'espèce (MeSH)</term><term>Séquence nucléotidique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA Primers</term><term>MADS Domain Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Cucumis sativus</term><term>Gene Expression Regulation, Plant</term><term>Genome, Plant</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Amorces ADN</term><term>Cucumis sativus</term><term>Génome végétal</term><term>Protéines à domaine MADS</term><term>Régulation de l'expression des gènes végétaux</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>MADS Domain Proteins</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Protéines à domaine MADS</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Cluster Analysis</term><term>Computational Biology</term><term>Gene Expression Profiling</term><term>Models, Genetic</term><term>Phylogeny</term><term>Sequence Alignment</term><term>Species Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Analyse de profil d'expression de gènes</term><term>Analyse de regroupements</term><term>Biologie informatique</term><term>Modèles génétiques</term><term>Phylogenèse</term><term>Spécificité d'espèce</term><term>Séquence nucléotidique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">MADS-box transcription factors are known to be involved in many important processes during plant growth and development. To date, few cucumber MADS-box genes and little tissue expression profiling have been reported. Recent completion of the cucumber whole-genome sequencing has allowed genome-wide analysis of the MADS-box gene family in cucumber as well as its comparison with other species. Here, we performed comprehensive analyses of the 43 cucumber MADS-box genes and compared them with those in Arabidopsis, poplar, and grapevine. The phylogenetic analysis showed that most cucumber members were comparable with those in other species, with the exception of AG members. At the same time, the three subfamilies FLC, AGL12, and Bs were absent in the cucumber genome. The conserved motif analysis revealed that most motifs outside the MADS domain were distributed only in specific groups. The analysis of chromosomal localization suggested that tandem duplication might contribute to the MADS-box gene expansion. Expression analysis revealed that 42 of 43 cucumber MADS-box members were expressed in multiple plant tissues, thereby implying their various roles in plants.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22376137</PMID><DateCompleted><Year>2012</Year><Month>07</Month><Day>09</Day></DateCompleted><DateRevised><Year>2016</Year><Month>10</Month><Day>20</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1480-3321</ISSN><JournalIssue CitedMedium="Internet"><Volume>55</Volume><Issue>3</Issue><PubDate><Year>2012</Year><Month>Mar</Month></PubDate></JournalIssue><Title>Genome</Title><ISOAbbreviation>Genome</ISOAbbreviation></Journal><ArticleTitle>Genome-wide analysis of the MADS-box gene family in cucumber.</ArticleTitle><Pagination><MedlinePgn>245-56</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1139/g2012-009</ELocationID><Abstract><AbstractText>MADS-box transcription factors are known to be involved in many important processes during plant growth and development. To date, few cucumber MADS-box genes and little tissue expression profiling have been reported. Recent completion of the cucumber whole-genome sequencing has allowed genome-wide analysis of the MADS-box gene family in cucumber as well as its comparison with other species. Here, we performed comprehensive analyses of the 43 cucumber MADS-box genes and compared them with those in Arabidopsis, poplar, and grapevine. The phylogenetic analysis showed that most cucumber members were comparable with those in other species, with the exception of AG members. At the same time, the three subfamilies FLC, AGL12, and Bs were absent in the cucumber genome. The conserved motif analysis revealed that most motifs outside the MADS domain were distributed only in specific groups. The analysis of chromosomal localization suggested that tandem duplication might contribute to the MADS-box gene expansion. Expression analysis revealed that 42 of 43 cucumber MADS-box members were expressed in multiple plant tissues, thereby implying their various roles in plants.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Lifang</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>School of Sciences, Jiangxi Agricultural University, 330045 Nanchang, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Shiqiang</ForeName><Initials>S</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></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2012</Year><Month>02</Month><Day>29</Day></ArticleDate></Article><MedlineJournalInfo><Country>Canada</Country><MedlineTA>Genome</MedlineTA><NlmUniqueID>8704544</NlmUniqueID><ISSNLinking>0831-2796</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D017931">DNA Primers</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D026161">MADS Domain Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016000" MajorTopicYN="N">Cluster Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018553" MajorTopicYN="N">Cucumis sativus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017931" MajorTopicYN="N">DNA Primers</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D026161" MajorTopicYN="N">MADS Domain Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008957" MajorTopicYN="N">Models, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="Y">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016415" MajorTopicYN="N">Sequence Alignment</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013045" MajorTopicYN="N">Species Specificity</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2012</Year><Month>3</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2012</Year><Month>3</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2012</Year><Month>7</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">22376137</ArticleId><ArticleId IdType="doi">10.1139/g2012-009</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country><region><li>Jiangxi</li></region><settlement><li>Nanchang</li></settlement></list><tree><noCountry><name sortKey="Liu, Shiqiang" sort="Liu, Shiqiang" uniqKey="Liu S" first="Shiqiang" last="Liu">Shiqiang Liu</name></noCountry><country name="République populaire de Chine"><region name="Jiangxi"><name sortKey="Hu, Lifang" sort="Hu, Lifang" uniqKey="Hu L" first="Lifang" last="Hu">Lifang Hu</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/PoplarV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002A65 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 002A65 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= PoplarV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:22376137
|texte= Genome-wide analysis of the MADS-box gene family in cucumber.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:22376137" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PoplarV1
| This area was generated with Dilib version V0.6.37. |  |