Genome-wide identification, classification, and expression analysis of 14-3-3 gene family in Populus.
Identifieur interne : 001D32 ( Main/Exploration ); précédent : 001D31; suivant : 001D33Genome-wide identification, classification, and expression analysis of 14-3-3 gene family in Populus.
Auteurs : Fengxia Tian [République populaire de Chine] ; Tan Wang [République populaire de Chine] ; Yuli Xie [République populaire de Chine] ; Jin Zhang [République populaire de Chine] ; Jianjun Hu [République populaire de Chine]Source :
- PloS one [ 1932-6203 ] ; 2015.
Descripteurs français
- KwdFr :
- Analyse de profil d'expression de gènes (MeSH), Cartographie chromosomique (MeSH), Chromosomes de plante (MeSH), Données de séquences moléculaires (MeSH), Gènes de plante (MeSH), Phylogenèse (MeSH), Populus (classification), Populus (génétique), Protéines 14-3-3 (composition chimique), Protéines 14-3-3 (génétique), Similitude de séquences d'acides aminés (MeSH), Séquence d'acides aminés (MeSH), Étude d'association pangénomique (MeSH), Évolution moléculaire (MeSH).
- MESH :
- composition chimique : Populus, Protéines 14-3-3.
- génétique : Populus, Protéines 14-3-3.
- Analyse de profil d'expression de gènes, Cartographie chromosomique, Chromosomes de plante, Données de séquences moléculaires, Gènes de plante, Phylogenèse, Similitude de séquences d'acides aminés, Séquence d'acides aminés, Étude d'association pangénomique, Évolution moléculaire.
English descriptors
- KwdEn :
- 14-3-3 Proteins (chemistry), 14-3-3 Proteins (genetics), Amino Acid Sequence (MeSH), Chromosome Mapping (MeSH), Chromosomes, Plant (MeSH), Evolution, Molecular (MeSH), Gene Expression Profiling (MeSH), Genes, Plant (MeSH), Genome-Wide Association Study (MeSH), Molecular Sequence Data (MeSH), Phylogeny (MeSH), Populus (classification), Populus (genetics), Sequence Homology, Amino Acid (MeSH).
- MESH :
- chemical , chemistry : 14-3-3 Proteins.
- chemical , genetics : 14-3-3 Proteins.
- classification : Populus.
- genetics : Populus.
- Amino Acid Sequence, Chromosome Mapping, Chromosomes, Plant, Evolution, Molecular, Gene Expression Profiling, Genes, Plant, Genome-Wide Association Study, Molecular Sequence Data, Phylogeny, Sequence Homology, Amino Acid.
Abstract
BACKGROUND
In plants, 14-3-3 proteins are encoded by a large multigene family and are involved in signaling pathways to regulate plant development and protection from stress. Although twelve Populus 14-3-3s were identified based on the Populus trichocarpa genome V1.1 in a previous study, no systematic analysis including genome organization, gene structure, duplication relationship, evolutionary analysis and expression compendium has been conducted in Populus based on the latest P. trichocarpa genome V3.0.
PRINCIPAL FINDINGS
Here, a comprehensive analysis of Populus 14-3-3 family is presented. Two new 14-3-3 genes were identified based on the latest P. trichocarpa genome. In P. trichocarpa, fourteen 14-3-3 genes were grouped into ε and non-ε group. Exon-intron organizations of Populus 14-3-3s are highly conserved within the same group. Genomic organization analysis indicated that purifying selection plays a pivotal role in the retention and maintenance of Populus 14-3-3 family. Protein conformational analysis indicated that Populus 14-3-3 consists of a bundle of nine α-helices (α1-α9); the first four are essential for formation of the dimer, while α3, α5, α7, and α9 form a conserved peptide-binding groove. In addition, α1, α3, α5, α7, and α9 were evolving at a lower rate, while α2, α4, and α6 were evolving at a relatively faster rate. Microarray analyses showed that most Populus 14-3-3s are differentially expressed across tissues and upon exposure to various stresses.
CONCLUSIONS
The gene structures and their coding protein structures of Populus 14-3-3s are highly conserved among group members, suggesting that members of the same group might also have conserved functions. Microarray and qRT-PCR analyses showed that most Populus 14-3-3s were differentially expressed in various tissues and were induced by various stresses. Our investigation provided a better understanding of the complexity of the 14-3-3 gene family in poplars.
DOI: 10.1371/journal.pone.0123225
PubMed: 25867623
PubMed Central: PMC4395111
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Chinese Academy of Forestry, Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Science and Technology, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, China; State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Wang, Tan" sort="Wang, Tan" uniqKey="Wang T" first="Tan" last="Wang">Tan Wang</name><affiliation wicri:level="3"><nlm:affiliation>College of Life Science and Technology, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, China; State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Science and Technology, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, China; State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Xie, Yuli" sort="Xie, Yuli" uniqKey="Xie Y" first="Yuli" last="Xie">Yuli Xie</name><affiliation wicri:level="3"><nlm:affiliation>College of Life Science and Technology, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, China; State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Science and Technology, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, China; State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Zhang, Jin" sort="Zhang, Jin" uniqKey="Zhang J" first="Jin" last="Zhang">Jin Zhang</name><affiliation wicri:level="3"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de 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Academy of Forestry, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>14-3-3 Proteins (chemistry)</term><term>14-3-3 Proteins (genetics)</term><term>Amino Acid Sequence (MeSH)</term><term>Chromosome Mapping (MeSH)</term><term>Chromosomes, Plant (MeSH)</term><term>Evolution, Molecular (MeSH)</term><term>Gene Expression Profiling (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Genome-Wide Association Study (MeSH)</term><term>Molecular Sequence Data (MeSH)</term><term>Phylogeny (MeSH)</term><term>Populus (classification)</term><term>Populus (genetics)</term><term>Sequence Homology, Amino Acid (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Cartographie chromosomique (MeSH)</term><term>Chromosomes de plante (MeSH)</term><term>Données de séquences moléculaires (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Populus (classification)</term><term>Populus (génétique)</term><term>Protéines 14-3-3 (composition chimique)</term><term>Protéines 14-3-3 (génétique)</term><term>Similitude de séquences d'acides aminés (MeSH)</term><term>Séquence d'acides aminés (MeSH)</term><term>Étude d'association pangénomique (MeSH)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>14-3-3 Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>14-3-3 Proteins</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Populus</term><term>Protéines 14-3-3</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Populus</term><term>Protéines 14-3-3</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Chromosome Mapping</term><term>Chromosomes, Plant</term><term>Evolution, Molecular</term><term>Gene Expression Profiling</term><term>Genes, Plant</term><term>Genome-Wide Association Study</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Sequence Homology, Amino Acid</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Cartographie chromosomique</term><term>Chromosomes de plante</term><term>Données de séquences moléculaires</term><term>Gènes de plante</term><term>Phylogenèse</term><term>Similitude de séquences d'acides aminés</term><term>Séquence d'acides aminés</term><term>Étude d'association pangénomique</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>In plants, 14-3-3 proteins are encoded by a large multigene family and are involved in signaling pathways to regulate plant development and protection from stress. Although twelve Populus 14-3-3s were identified based on the Populus trichocarpa genome V1.1 in a previous study, no systematic analysis including genome organization, gene structure, duplication relationship, evolutionary analysis and expression compendium has been conducted in Populus based on the latest P. trichocarpa genome V3.0.</p></div><div type="abstract" xml:lang="en"><p><b>PRINCIPAL FINDINGS</b></p><p>Here, a comprehensive analysis of Populus 14-3-3 family is presented. Two new 14-3-3 genes were identified based on the latest P. trichocarpa genome. In P. trichocarpa, fourteen 14-3-3 genes were grouped into ε and non-ε group. Exon-intron organizations of Populus 14-3-3s are highly conserved within the same group. Genomic organization analysis indicated that purifying selection plays a pivotal role in the retention and maintenance of Populus 14-3-3 family. Protein conformational analysis indicated that Populus 14-3-3 consists of a bundle of nine α-helices (α1-α9); the first four are essential for formation of the dimer, while α3, α5, α7, and α9 form a conserved peptide-binding groove. In addition, α1, α3, α5, α7, and α9 were evolving at a lower rate, while α2, α4, and α6 were evolving at a relatively faster rate. Microarray analyses showed that most Populus 14-3-3s are differentially expressed across tissues and upon exposure to various stresses.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>The gene structures and their coding protein structures of Populus 14-3-3s are highly conserved among group members, suggesting that members of the same group might also have conserved functions. Microarray and qRT-PCR analyses showed that most Populus 14-3-3s were differentially expressed in various tissues and were induced by various stresses. Our investigation provided a better understanding of the complexity of the 14-3-3 gene family in poplars.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25867623</PMID><DateCompleted><Year>2016</Year><Month>03</Month><Day>26</Day></DateCompleted><DateRevised><Year>2019</Year><Month>02</Month><Day>23</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>10</Volume><Issue>4</Issue><PubDate><Year>2015</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>Genome-wide identification, classification, and expression analysis of 14-3-3 gene family in Populus.</ArticleTitle><Pagination><MedlinePgn>e0123225</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0123225</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">In plants, 14-3-3 proteins are encoded by a large multigene family and are involved in signaling pathways to regulate plant development and protection from stress. Although twelve Populus 14-3-3s were identified based on the Populus trichocarpa genome V1.1 in a previous study, no systematic analysis including genome organization, gene structure, duplication relationship, evolutionary analysis and expression compendium has been conducted in Populus based on the latest P. trichocarpa genome V3.0.</AbstractText><AbstractText Label="PRINCIPAL FINDINGS" NlmCategory="RESULTS">Here, a comprehensive analysis of Populus 14-3-3 family is presented. Two new 14-3-3 genes were identified based on the latest P. trichocarpa genome. In P. trichocarpa, fourteen 14-3-3 genes were grouped into ε and non-ε group. Exon-intron organizations of Populus 14-3-3s are highly conserved within the same group. Genomic organization analysis indicated that purifying selection plays a pivotal role in the retention and maintenance of Populus 14-3-3 family. Protein conformational analysis indicated that Populus 14-3-3 consists of a bundle of nine α-helices (α1-α9); the first four are essential for formation of the dimer, while α3, α5, α7, and α9 form a conserved peptide-binding groove. In addition, α1, α3, α5, α7, and α9 were evolving at a lower rate, while α2, α4, and α6 were evolving at a relatively faster rate. Microarray analyses showed that most Populus 14-3-3s are differentially expressed across tissues and upon exposure to various stresses.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">The gene structures and their coding protein structures of Populus 14-3-3s are highly conserved among group members, suggesting that members of the same group might also have conserved functions. Microarray and qRT-PCR analyses showed that most Populus 14-3-3s were differentially expressed in various tissues and were induced by various stresses. Our investigation provided a better understanding of the complexity of the 14-3-3 gene family in poplars.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tian</LastName><ForeName>Fengxia</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>College of Life Science and Technology, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, China; State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Tan</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>College of Life Science and Technology, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, China; State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xie</LastName><ForeName>Yuli</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>College of Life Science and Technology, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, China; State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Jin</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Jianjun</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</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>04</Month><Day>13</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D048948">14-3-3 Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D048948" MajorTopicYN="N">14-3-3 Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002874" MajorTopicYN="N">Chromosome Mapping</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032461" MajorTopicYN="N">Chromosomes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, 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