Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family.
Identifieur interne : 003906 ( Main/Exploration ); précédent : 003905; suivant : 003907Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family.
Auteurs : An-Yuan Guo [République populaire de Chine] ; Qi-Hui Zhu ; Xiaocheng Gu ; Song Ge ; Ji Yang ; Jingchu LuoSource :
- Gene [ 0378-1119 ] ; 2008.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , analysis : MicroRNAs.
- Binding Sites, Conserved Sequence, Evolution, Molecular, Genes, Plant, Genome, Plant, Multigene Family, Phylogeny, Transcription Factors, Zinc Fingers.
Abstract
We made genome-wide analyses to explore the evolutionary process of the SBP-box gene family. We identified 120 SBP-box genes from nine species representing the main green plant lineages: green alga, moss, lycophyte, gymnosperm and angiosperm. A maximum-likelihood phylogenetic tree was constructed using the protein sequences of the DNA-binding domain of SBP-box genes (SBP-domain). Our results revealed that all SBP-box genes of green alga clustered into a single clade (CR group), while all genes from land-plants fell into two distinct groups. Group I had a single copy in each species except for poplar while group II had several members in each species and can be divided into several subgroups. The SBP-domain encoded by all SBP-box genes possesses two zinc fingers. The C-terminal zinc finger of both group I and group II had the same C2HC motif while their N-terminal zinc finger showed different signatures, C4 in group I and C3H in group II. The patterns of exon-intron structure in Arabidopsis and rice SBP-box genes were consistent with the phylogenetic results. A target site of microRNA miR156 was highly conserved among land-plant SBP-box genes. Our results suggested that the SBP-box gene family might have originated from a common ancestor of green plants, followed by duplication and divergence in each lineage including exon-intron loss processes.
DOI: 10.1016/j.gene.2008.03.016
PubMed: 18495384
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family.</title>
<author><name sortKey="Guo, An Yuan" sort="Guo, An Yuan" uniqKey="Guo A" first="An-Yuan" last="Guo">An-Yuan Guo</name>
<affiliation wicri:level="4"><nlm:affiliation>College of Life Sciences, Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing, 100871, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>College of Life Sciences, Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing, 100871</wicri:regionArea>
<orgName type="university">Université de Pékin</orgName>
<placeName><settlement type="city">Pékin</settlement>
<region type="capitale">Pékin</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Zhu, Qi Hui" sort="Zhu, Qi Hui" uniqKey="Zhu Q" first="Qi-Hui" last="Zhu">Qi-Hui Zhu</name>
</author>
<author><name sortKey="Gu, Xiaocheng" sort="Gu, Xiaocheng" uniqKey="Gu X" first="Xiaocheng" last="Gu">Xiaocheng Gu</name>
</author>
<author><name sortKey="Ge, Song" sort="Ge, Song" uniqKey="Ge S" first="Song" last="Ge">Song Ge</name>
</author>
<author><name sortKey="Yang, Ji" sort="Yang, Ji" uniqKey="Yang J" first="Ji" last="Yang">Ji Yang</name>
</author>
<author><name sortKey="Luo, Jingchu" sort="Luo, Jingchu" uniqKey="Luo J" first="Jingchu" last="Luo">Jingchu Luo</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2008">2008</date>
<idno type="RBID">pubmed:18495384</idno>
<idno type="pmid">18495384</idno>
<idno type="doi">10.1016/j.gene.2008.03.016</idno>
<idno type="wicri:Area/Main/Corpus">003885</idno>
<idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">003885</idno>
<idno type="wicri:Area/Main/Curation">003885</idno>
<idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">003885</idno>
<idno type="wicri:Area/Main/Exploration">003885</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family.</title>
<author><name sortKey="Guo, An Yuan" sort="Guo, An Yuan" uniqKey="Guo A" first="An-Yuan" last="Guo">An-Yuan Guo</name>
<affiliation wicri:level="4"><nlm:affiliation>College of Life Sciences, Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing, 100871, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>College of Life Sciences, Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing, 100871</wicri:regionArea>
<orgName type="university">Université de Pékin</orgName>
<placeName><settlement type="city">Pékin</settlement>
<region type="capitale">Pékin</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Zhu, Qi Hui" sort="Zhu, Qi Hui" uniqKey="Zhu Q" first="Qi-Hui" last="Zhu">Qi-Hui Zhu</name>
</author>
<author><name sortKey="Gu, Xiaocheng" sort="Gu, Xiaocheng" uniqKey="Gu X" first="Xiaocheng" last="Gu">Xiaocheng Gu</name>
</author>
<author><name sortKey="Ge, Song" sort="Ge, Song" uniqKey="Ge S" first="Song" last="Ge">Song Ge</name>
</author>
<author><name sortKey="Yang, Ji" sort="Yang, Ji" uniqKey="Yang J" first="Ji" last="Yang">Ji Yang</name>
</author>
<author><name sortKey="Luo, Jingchu" sort="Luo, Jingchu" uniqKey="Luo J" first="Jingchu" last="Luo">Jingchu Luo</name>
</author>
</analytic>
<series><title level="j">Gene</title>
<idno type="ISSN">0378-1119</idno>
<imprint><date when="2008" type="published">2008</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Binding Sites (MeSH)</term>
<term>Conserved Sequence (MeSH)</term>
<term>Evolution, Molecular (MeSH)</term>
<term>Genes, Plant (MeSH)</term>
<term>Genome, Plant (MeSH)</term>
<term>MicroRNAs (analysis)</term>
<term>Multigene Family (MeSH)</term>
<term>Phylogeny (MeSH)</term>
<term>Transcription Factors (MeSH)</term>
<term>Zinc Fingers (MeSH)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Doigts de zinc (MeSH)</term>
<term>Facteurs de transcription (MeSH)</term>
<term>Famille multigénique (MeSH)</term>
<term>Gènes de plante (MeSH)</term>
<term>Génome végétal (MeSH)</term>
<term>Phylogenèse (MeSH)</term>
<term>Sites de fixation (MeSH)</term>
<term>Séquence conservée (MeSH)</term>
<term>microARN (analyse)</term>
<term>Évolution moléculaire (MeSH)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>MicroRNAs</term>
</keywords>
<keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>microARN</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term>
<term>Conserved Sequence</term>
<term>Evolution, Molecular</term>
<term>Genes, Plant</term>
<term>Genome, Plant</term>
<term>Multigene Family</term>
<term>Phylogeny</term>
<term>Transcription Factors</term>
<term>Zinc Fingers</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Doigts de zinc</term>
<term>Facteurs de transcription</term>
<term>Famille multigénique</term>
<term>Gènes de plante</term>
<term>Génome végétal</term>
<term>Phylogenèse</term>
<term>Sites de fixation</term>
<term>Séquence conservée</term>
<term>Évolution moléculaire</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">We made genome-wide analyses to explore the evolutionary process of the SBP-box gene family. We identified 120 SBP-box genes from nine species representing the main green plant lineages: green alga, moss, lycophyte, gymnosperm and angiosperm. A maximum-likelihood phylogenetic tree was constructed using the protein sequences of the DNA-binding domain of SBP-box genes (SBP-domain). Our results revealed that all SBP-box genes of green alga clustered into a single clade (CR group), while all genes from land-plants fell into two distinct groups. Group I had a single copy in each species except for poplar while group II had several members in each species and can be divided into several subgroups. The SBP-domain encoded by all SBP-box genes possesses two zinc fingers. The C-terminal zinc finger of both group I and group II had the same C2HC motif while their N-terminal zinc finger showed different signatures, C4 in group I and C3H in group II. The patterns of exon-intron structure in Arabidopsis and rice SBP-box genes were consistent with the phylogenetic results. A target site of microRNA miR156 was highly conserved among land-plant SBP-box genes. Our results suggested that the SBP-box gene family might have originated from a common ancestor of green plants, followed by duplication and divergence in each lineage including exon-intron loss processes.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18495384</PMID>
<DateCompleted><Year>2008</Year>
<Month>08</Month>
<Day>15</Day>
</DateCompleted>
<DateRevised><Year>2008</Year>
<Month>06</Month>
<Day>16</Day>
</DateRevised>
<Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0378-1119</ISSN>
<JournalIssue CitedMedium="Print"><Volume>418</Volume>
<Issue>1-2</Issue>
<PubDate><Year>2008</Year>
<Month>Jul</Month>
<Day>15</Day>
</PubDate>
</JournalIssue>
<Title>Gene</Title>
<ISOAbbreviation>Gene</ISOAbbreviation>
</Journal>
<ArticleTitle>Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family.</ArticleTitle>
<Pagination><MedlinePgn>1-8</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1016/j.gene.2008.03.016</ELocationID>
<Abstract><AbstractText>We made genome-wide analyses to explore the evolutionary process of the SBP-box gene family. We identified 120 SBP-box genes from nine species representing the main green plant lineages: green alga, moss, lycophyte, gymnosperm and angiosperm. A maximum-likelihood phylogenetic tree was constructed using the protein sequences of the DNA-binding domain of SBP-box genes (SBP-domain). Our results revealed that all SBP-box genes of green alga clustered into a single clade (CR group), while all genes from land-plants fell into two distinct groups. Group I had a single copy in each species except for poplar while group II had several members in each species and can be divided into several subgroups. The SBP-domain encoded by all SBP-box genes possesses two zinc fingers. The C-terminal zinc finger of both group I and group II had the same C2HC motif while their N-terminal zinc finger showed different signatures, C4 in group I and C3H in group II. The patterns of exon-intron structure in Arabidopsis and rice SBP-box genes were consistent with the phylogenetic results. A target site of microRNA miR156 was highly conserved among land-plant SBP-box genes. Our results suggested that the SBP-box gene family might have originated from a common ancestor of green plants, followed by duplication and divergence in each lineage including exon-intron loss processes.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Guo</LastName>
<ForeName>An-Yuan</ForeName>
<Initials>AY</Initials>
<AffiliationInfo><Affiliation>College of Life Sciences, Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing, 100871, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Zhu</LastName>
<ForeName>Qi-Hui</ForeName>
<Initials>QH</Initials>
</Author>
<Author ValidYN="Y"><LastName>Gu</LastName>
<ForeName>Xiaocheng</ForeName>
<Initials>X</Initials>
</Author>
<Author ValidYN="Y"><LastName>Ge</LastName>
<ForeName>Song</ForeName>
<Initials>S</Initials>
</Author>
<Author ValidYN="Y"><LastName>Yang</LastName>
<ForeName>Ji</ForeName>
<Initials>J</Initials>
</Author>
<Author ValidYN="Y"><LastName>Luo</LastName>
<ForeName>Jingchu</ForeName>
<Initials>J</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>2008</Year>
<Month>04</Month>
<Day>09</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>Netherlands</Country>
<MedlineTA>Gene</MedlineTA>
<NlmUniqueID>7706761</NlmUniqueID>
<ISSNLinking>0378-1119</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D035683">MicroRNAs</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList><MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017124" MajorTopicYN="N">Conserved Sequence</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D019143" MajorTopicYN="Y">Evolution, Molecular</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017343" MajorTopicYN="Y">Genes, Plant</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D035683" MajorTopicYN="N">MicroRNAs</DescriptorName>
<QualifierName UI="Q000032" MajorTopicYN="Y">analysis</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D005810" MajorTopicYN="Y">Multigene Family</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D014157" MajorTopicYN="Y">Transcription Factors</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016335" MajorTopicYN="N">Zinc Fingers</DescriptorName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2007</Year>
<Month>07</Month>
<Day>13</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="revised"><Year>2008</Year>
<Month>03</Month>
<Day>18</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted"><Year>2008</Year>
<Month>03</Month>
<Day>26</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed"><Year>2008</Year>
<Month>5</Month>
<Day>23</Day>
<Hour>9</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline"><Year>2008</Year>
<Month>8</Month>
<Day>16</Day>
<Hour>9</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez"><Year>2008</Year>
<Month>5</Month>
<Day>23</Day>
<Hour>9</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList><ArticleId IdType="pubmed">18495384</ArticleId>
<ArticleId IdType="pii">S0378-1119(08)00136-4</ArticleId>
<ArticleId IdType="doi">10.1016/j.gene.2008.03.016</ArticleId>
</ArticleIdList>
</PubmedData>
</pubmed>
<affiliations><list><country><li>République populaire de Chine</li>
</country>
<region><li>Pékin</li>
</region>
<settlement><li>Pékin</li>
</settlement>
<orgName><li>Université de Pékin</li>
</orgName>
</list>
<tree><noCountry><name sortKey="Ge, Song" sort="Ge, Song" uniqKey="Ge S" first="Song" last="Ge">Song Ge</name>
<name sortKey="Gu, Xiaocheng" sort="Gu, Xiaocheng" uniqKey="Gu X" first="Xiaocheng" last="Gu">Xiaocheng Gu</name>
<name sortKey="Luo, Jingchu" sort="Luo, Jingchu" uniqKey="Luo J" first="Jingchu" last="Luo">Jingchu Luo</name>
<name sortKey="Yang, Ji" sort="Yang, Ji" uniqKey="Yang J" first="Ji" last="Yang">Ji Yang</name>
<name sortKey="Zhu, Qi Hui" sort="Zhu, Qi Hui" uniqKey="Zhu Q" first="Qi-Hui" last="Zhu">Qi-Hui Zhu</name>
</noCountry>
<country name="République populaire de Chine"><region name="Pékin"><name sortKey="Guo, An Yuan" sort="Guo, An Yuan" uniqKey="Guo A" first="An-Yuan" last="Guo">An-Yuan Guo</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 003906 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 003906 | 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:18495384 |texte= Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:18495384" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \ | NlmPubMed2Wicri -a PoplarV1
![]() | This area was generated with Dilib version V0.6.37. | ![]() |