Genome-wide identification, classification and analysis of HD-ZIP gene family in citrus, and its potential roles in somatic embryogenesis regulation.
Identifieur interne : 001C49 ( Ncbi/Merge ); précédent : 001C48; suivant : 001C50Genome-wide identification, classification and analysis of HD-ZIP gene family in citrus, and its potential roles in somatic embryogenesis regulation.
Auteurs : Xiao-Xia Ge [République populaire de Chine] ; Zheng Liu [République populaire de Chine] ; Xiao-Meng Wu [République populaire de Chine] ; Li-Jun Chai [République populaire de Chine] ; Wen-Wu Guo [République populaire de Chine]Source :
- Gene [ 1879-0038 ] ; 2015.
English descriptors
- KwdEn :
- Base Sequence, Citrus (genetics), Gene Expression Regulation, Plant (genetics), Genes, Homeobox (genetics), Genome, Plant (genetics), Homeodomain Proteins (genetics), Leucine Zippers (genetics), Molecular Sequence Data, Plant Proteins (genetics), Transcription Factors (genetics), Up-Regulation (genetics).
- MESH :
- chemical , genetics : Homeodomain Proteins, Plant Proteins, Transcription Factors.
- genetics : Citrus, Gene Expression Regulation, Plant, Genes, Homeobox, Genome, Plant, Leucine Zippers, Up-Regulation.
- Base Sequence, Molecular Sequence Data.
Abstract
The homeodomain-leucine zipper (HD-Zip) transcription factors, which belong to a class of Homeobox proteins, has been reported to be involved in different biological processes of plants, including growth and development, photomorphogenesis, flowering, fruit ripening and adaptation responses to environmental stresses. In this study, 27 HD-Zip genes (CsHBs) were identified in Citrus. Based on the phylogenetic analysis and characteristics of individual gene or protein, the HD-Zip gene family in Citrus can be classified into 4 subfamilies, i.e. HD-Zip I, HD-Zip II, HD-Zip III, and HD-Zip IV containing 16, 2, 4, and 5 members respectively. The digital expression patterns of 27 HD-Zip genes were analyzed in the callus, flower, leaf and fruit of Citrus sinensis. The qRT-PCR and RT-PCR analyses of six selected HD-Zip genes were performed in six citrus cultivars with different embryogenic competence and in the embryo induction stages, which revealed that these genes were differentially expressed and might be involved in citrus somatic embryogenesis (SE). The results exhibited that the expression of CsHB1 was up-regulated in somatic embryo induction process, and its expression was higher in citrus cultivars with high embryogenic capacity than in cultivars recalcitrant to form somatic embryos. Moreover, a microsatellite site of three nucleotide repeats was found in CsHB1 gene among eighteen citrus genotypes, indicating the possible association of CsHB1 gene to the capacity of callus induction.
DOI: 10.1016/j.gene.2015.07.079
PubMed: 26232336
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Electronic address: gexiaoxia15@aliyun.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan 430415</wicri:regionArea><wicri:noRegion>Wuhan 430415</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Zheng" sort="Liu, Zheng" uniqKey="Liu Z" first="Zheng" last="Liu">Zheng Liu</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070</wicri:regionArea><wicri:noRegion>Wuhan 430070</wicri:noRegion></affiliation></author><author><name sortKey="Wu, Xiao Meng" sort="Wu, Xiao Meng" uniqKey="Wu X" first="Xiao-Meng" last="Wu">Xiao-Meng Wu</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070</wicri:regionArea><wicri:noRegion>Wuhan 430070</wicri:noRegion></affiliation></author><author><name sortKey="Chai, Li Jun" sort="Chai, Li Jun" uniqKey="Chai L" first="Li-Jun" last="Chai">Li-Jun Chai</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070</wicri:regionArea><wicri:noRegion>Wuhan 430070</wicri:noRegion></affiliation></author><author><name sortKey="Guo, Wen Wu" sort="Guo, Wen Wu" uniqKey="Guo W" first="Wen-Wu" last="Guo">Wen-Wu Guo</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China. Electronic address: guoww@mail.hzau.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070</wicri:regionArea><wicri:noRegion>Wuhan 430070</wicri:noRegion></affiliation></author></analytic><series><title level="j">Gene</title><idno type="eISSN">1879-0038</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>Citrus (genetics)</term><term>Gene Expression Regulation, Plant (genetics)</term><term>Genes, Homeobox (genetics)</term><term>Genome, Plant (genetics)</term><term>Homeodomain Proteins (genetics)</term><term>Leucine Zippers (genetics)</term><term>Molecular Sequence Data</term><term>Plant Proteins (genetics)</term><term>Transcription Factors (genetics)</term><term>Up-Regulation (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Homeodomain Proteins</term><term>Plant Proteins</term><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Citrus</term><term>Gene Expression Regulation, Plant</term><term>Genes, Homeobox</term><term>Genome, Plant</term><term>Leucine Zippers</term><term>Up-Regulation</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Molecular Sequence Data</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The homeodomain-leucine zipper (HD-Zip) transcription factors, which belong to a class of Homeobox proteins, has been reported to be involved in different biological processes of plants, including growth and development, photomorphogenesis, flowering, fruit ripening and adaptation responses to environmental stresses. In this study, 27 HD-Zip genes (CsHBs) were identified in Citrus. Based on the phylogenetic analysis and characteristics of individual gene or protein, the HD-Zip gene family in Citrus can be classified into 4 subfamilies, i.e. HD-Zip I, HD-Zip II, HD-Zip III, and HD-Zip IV containing 16, 2, 4, and 5 members respectively. The digital expression patterns of 27 HD-Zip genes were analyzed in the callus, flower, leaf and fruit of Citrus sinensis. The qRT-PCR and RT-PCR analyses of six selected HD-Zip genes were performed in six citrus cultivars with different embryogenic competence and in the embryo induction stages, which revealed that these genes were differentially expressed and might be involved in citrus somatic embryogenesis (SE). The results exhibited that the expression of CsHB1 was up-regulated in somatic embryo induction process, and its expression was higher in citrus cultivars with high embryogenic capacity than in cultivars recalcitrant to form somatic embryos. Moreover, a microsatellite site of three nucleotide repeats was found in CsHB1 gene among eighteen citrus genotypes, indicating the possible association of CsHB1 gene to the capacity of callus induction.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26232336</PMID><DateCreated><Year>2015</Year><Month>10</Month><Day>12</Day></DateCreated><DateCompleted><Year>2016</Year><Month>01</Month><Day>08</Day></DateCompleted><DateRevised><Year>2015</Year><Month>10</Month><Day>12</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1879-0038</ISSN><JournalIssue CitedMedium="Internet"><Volume>574</Volume><Issue>1</Issue><PubDate><Year>2015</Year><Month>Dec</Month><Day>10</Day></PubDate></JournalIssue><Title>Gene</Title><ISOAbbreviation>Gene</ISOAbbreviation></Journal><ArticleTitle>Genome-wide identification, classification and analysis of HD-ZIP gene family in citrus, and its potential roles in somatic embryogenesis regulation.</ArticleTitle><Pagination><MedlinePgn>61-8</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.gene.2015.07.079</ELocationID><ELocationID EIdType="pii" ValidYN="Y">S0378-1119(15)00920-8</ELocationID><Abstract><AbstractText>The homeodomain-leucine zipper (HD-Zip) transcription factors, which belong to a class of Homeobox proteins, has been reported to be involved in different biological processes of plants, including growth and development, photomorphogenesis, flowering, fruit ripening and adaptation responses to environmental stresses. In this study, 27 HD-Zip genes (CsHBs) were identified in Citrus. Based on the phylogenetic analysis and characteristics of individual gene or protein, the HD-Zip gene family in Citrus can be classified into 4 subfamilies, i.e. HD-Zip I, HD-Zip II, HD-Zip III, and HD-Zip IV containing 16, 2, 4, and 5 members respectively. The digital expression patterns of 27 HD-Zip genes were analyzed in the callus, flower, leaf and fruit of Citrus sinensis. The qRT-PCR and RT-PCR analyses of six selected HD-Zip genes were performed in six citrus cultivars with different embryogenic competence and in the embryo induction stages, which revealed that these genes were differentially expressed and might be involved in citrus somatic embryogenesis (SE). The results exhibited that the expression of CsHB1 was up-regulated in somatic embryo induction process, and its expression was higher in citrus cultivars with high embryogenic capacity than in cultivars recalcitrant to form somatic embryos. Moreover, a microsatellite site of three nucleotide repeats was found in CsHB1 gene among eighteen citrus genotypes, indicating the possible association of CsHB1 gene to the capacity of callus induction.</AbstractText><CopyrightInformation>Copyright © 2015 Elsevier B.V. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ge</LastName><ForeName>Xiao-Xia</ForeName><Initials>XX</Initials><AffiliationInfo><Affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan 430415, China. Electronic address: gexiaoxia15@aliyun.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Zheng</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Xiao-Meng</ForeName><Initials>XM</Initials><AffiliationInfo><Affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chai</LastName><ForeName>Li-Jun</ForeName><Initials>LJ</Initials><AffiliationInfo><Affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Guo</LastName><ForeName>Wen-Wu</ForeName><Initials>WW</Initials><AffiliationInfo><Affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China. Electronic address: guoww@mail.hzau.edu.cn.</Affiliation></AffiliationInfo></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>2015</Year><Month>Jul</Month><Day>29</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="D018398">Homeodomain Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002957" MajorTopicYN="N">Citrus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005801" MajorTopicYN="N">Genes, Homeobox</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="D018398" MajorTopicYN="N">Homeodomain Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016350" MajorTopicYN="N">Leucine Zippers</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014157" MajorTopicYN="N">Transcription Factors</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015854" MajorTopicYN="N">Up-Regulation</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Citrus</Keyword><Keyword MajorTopicYN="N">HD-Zip genes</Keyword><Keyword MajorTopicYN="N">Somatic embryogenesis</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>4</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2015</Year><Month>7</Month><Day>22</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>7</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>8</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>8</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>1</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26232336</ArticleId><ArticleId IdType="pii">S0378-1119(15)00920-8</ArticleId><ArticleId IdType="doi">10.1016/j.gene.2015.07.079</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Ge, Xiao Xia" sort="Ge, Xiao Xia" uniqKey="Ge X" first="Xiao-Xia" last="Ge">Xiao-Xia Ge</name></noRegion><name sortKey="Chai, Li Jun" sort="Chai, Li Jun" uniqKey="Chai L" first="Li-Jun" last="Chai">Li-Jun Chai</name><name sortKey="Guo, Wen Wu" sort="Guo, Wen Wu" uniqKey="Guo W" first="Wen-Wu" last="Guo">Wen-Wu Guo</name><name sortKey="Liu, Zheng" sort="Liu, Zheng" uniqKey="Liu Z" first="Zheng" last="Liu">Zheng Liu</name><name sortKey="Wu, Xiao Meng" sort="Wu, Xiao Meng" uniqKey="Wu X" first="Xiao-Meng" last="Wu">Xiao-Meng Wu</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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