Aldehyde Dehydrogenase Gene Superfamily in Populus: Organization and Expression Divergence between Paralogous Gene Pairs.
Identifieur interne : 001F02 ( Main/Exploration ); précédent : 001F01; suivant : 001F03Aldehyde Dehydrogenase Gene Superfamily in Populus: Organization and Expression Divergence between Paralogous Gene Pairs.
Auteurs : Feng-Xia Tian [République populaire de Chine] ; Jian-Lei Zang [République populaire de Chine] ; Tan Wang [République populaire de Chine] ; Yu-Li Xie [République populaire de Chine] ; Jin Zhang [République populaire de Chine] ; Jian-Jun Hu [République populaire de Chine]Source :
- PloS one [ 1932-6203 ] ; 2015.
Descripteurs français
- KwdFr :
- Aldehyde dehydrogenase (classification), Aldehyde dehydrogenase (génétique), Analyse de profil d'expression de gènes (MeSH), Analyse de regroupements (MeSH), Bases de données d'acides nucléiques (MeSH), Biologie informatique (MeSH), Cartographie chromosomique (MeSH), Chromosomes de plante (MeSH), Duplication de gène (MeSH), Famille multigénique (MeSH), Génome végétal (MeSH), Phylogenèse (MeSH), Populus (classification), Populus (génétique), Régulation de l'expression des gènes végétaux (MeSH), Stress physiologique (génétique), Évolution moléculaire (MeSH).
- MESH :
- génétique : Aldehyde dehydrogenase, Populus, Stress physiologique.
- classification : Aldehyde dehydrogenase, Analyse de profil d'expression de gènes, Analyse de regroupements, Bases de données d'acides nucléiques, Biologie informatique, Cartographie chromosomique, Chromosomes de plante, Duplication de gène, Famille multigénique, Génome végétal, Phylogenèse, Régulation de l'expression des gènes végétaux, Évolution moléculaire.
English descriptors
- KwdEn :
- Aldehyde Dehydrogenase (classification), Aldehyde Dehydrogenase (genetics), Chromosome Mapping (MeSH), Chromosomes, Plant (MeSH), Cluster Analysis (MeSH), Computational Biology (MeSH), Databases, Nucleic Acid (MeSH), Evolution, Molecular (MeSH), Gene Duplication (MeSH), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (MeSH), Genome, Plant (MeSH), Multigene Family (MeSH), Phylogeny (MeSH), Populus (classification), Populus (genetics), Stress, Physiological (genetics).
- MESH :
- chemical , classification : Aldehyde Dehydrogenase.
- chemical , genetics : Aldehyde Dehydrogenase.
- classification : Populus.
- genetics : Populus, Stress, Physiological.
- Chromosome Mapping, Chromosomes, Plant, Cluster Analysis, Computational Biology, Databases, Nucleic Acid, Evolution, Molecular, Gene Duplication, Gene Expression Profiling, Gene Expression Regulation, Plant, Genome, Plant, Multigene Family, Phylogeny.
Abstract
Aldehyde dehydrogenases (ALDHs) constitute a superfamily of NAD(P)+-dependent enzymes that catalyze the irreversible oxidation of a wide range of reactive aldehydes to their corresponding nontoxic carboxylic acids. ALDHs have been studied in many organisms from bacteria to mammals; however, no systematic analyses incorporating genome organization, gene structure, expression profiles, and cis-acting elements have been conducted in the model tree species Populus trichocarpa thus far. In this study, a comprehensive analysis of the Populus ALDH gene superfamily was performed. A total of 26 Populus ALDH genes were found to be distributed across 12 chromosomes. Genomic organization analysis indicated that purifying selection may have played a pivotal role in the retention and maintenance of PtALDH gene families. The exon-intron organizations of PtALDHs were highly conserved within the same family, suggesting that the members of the same family also may have conserved functionalities. Microarray data and qRT-PCR analysis indicated that most PtALDHs had distinct tissue-specific expression patterns. The specificity of cis-acting elements in the promoter regions of the PtALDHs and the divergence of expression patterns between nine paralogous PtALDH gene pairs suggested that gene duplications may have freed the duplicate genes from the functional constraints. The expression levels of some ALDHs were up- or down-regulated by various abiotic stresses, implying that the products of these genes may be involved in the adaptation of Populus to abiotic stresses. Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the Populus ALDH gene superfamily and provide insights into the function and evolution of ALDH gene families in vascular plants.
DOI: 10.1371/journal.pone.0124669
PubMed: 25909656
PubMed Central: PMC4409362
Affiliations:
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State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Science and Technology, Nanyang Normal University, Nanyang, Henan, 473061, 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, 100091</wicri:regionArea><wicri:noRegion>100091</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Jin" sort="Zhang, Jin" uniqKey="Zhang J" first="Jin" last="Zhang">Jin Zhang</name><affiliation wicri:level="1"><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, 100091, China; Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>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, 100091, China; Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091</wicri:regionArea><wicri:noRegion>100091</wicri:noRegion></affiliation></author><author><name sortKey="Hu, Jian Jun" sort="Hu, Jian Jun" uniqKey="Hu J" first="Jian-Jun" last="Hu">Jian-Jun Hu</name><affiliation wicri:level="1"><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, 100091, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>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, 100091</wicri:regionArea><wicri:noRegion>100091</wicri:noRegion></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>Aldehyde Dehydrogenase (classification)</term><term>Aldehyde Dehydrogenase (genetics)</term><term>Chromosome Mapping (MeSH)</term><term>Chromosomes, Plant (MeSH)</term><term>Cluster Analysis (MeSH)</term><term>Computational Biology (MeSH)</term><term>Databases, Nucleic Acid (MeSH)</term><term>Evolution, Molecular (MeSH)</term><term>Gene Duplication (MeSH)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Multigene Family (MeSH)</term><term>Phylogeny (MeSH)</term><term>Populus (classification)</term><term>Populus (genetics)</term><term>Stress, Physiological (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Aldehyde dehydrogenase (classification)</term><term>Aldehyde dehydrogenase (génétique)</term><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Analyse de regroupements (MeSH)</term><term>Bases de données d'acides nucléiques (MeSH)</term><term>Biologie informatique (MeSH)</term><term>Cartographie chromosomique (MeSH)</term><term>Chromosomes de plante (MeSH)</term><term>Duplication de gène (MeSH)</term><term>Famille multigénique (MeSH)</term><term>Génome végétal (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Populus (classification)</term><term>Populus (génétique)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Stress physiologique (génétique)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="classification" xml:lang="en"><term>Aldehyde Dehydrogenase</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Aldehyde Dehydrogenase</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term><term>Stress, Physiological</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Aldehyde dehydrogenase</term><term>Populus</term><term>Stress physiologique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosome Mapping</term><term>Chromosomes, Plant</term><term>Cluster Analysis</term><term>Computational Biology</term><term>Databases, Nucleic Acid</term><term>Evolution, Molecular</term><term>Gene 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to their corresponding nontoxic carboxylic acids. ALDHs have been studied in many organisms from bacteria to mammals; however, no systematic analyses incorporating genome organization, gene structure, expression profiles, and cis-acting elements have been conducted in the model tree species Populus trichocarpa thus far. In this study, a comprehensive analysis of the Populus ALDH gene superfamily was performed. A total of 26 Populus ALDH genes were found to be distributed across 12 chromosomes. Genomic organization analysis indicated that purifying selection may have played a pivotal role in the retention and maintenance of PtALDH gene families. The exon-intron organizations of PtALDHs were highly conserved within the same family, suggesting that the members of the same family also may have conserved functionalities. Microarray data and qRT-PCR analysis indicated that most PtALDHs had distinct tissue-specific expression patterns. The specificity of cis-acting elements in the promoter regions of the PtALDHs and the divergence of expression patterns between nine paralogous PtALDH gene pairs suggested that gene duplications may have freed the duplicate genes from the functional constraints. The expression levels of some ALDHs were up- or down-regulated by various abiotic stresses, implying that the products of these genes may be involved in the adaptation of Populus to abiotic stresses. Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the Populus ALDH gene superfamily and provide insights into the function and evolution of ALDH gene families in vascular plants. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25909656</PMID><DateCompleted><Year>2016</Year><Month>01</Month><Day>19</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>06</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>Aldehyde Dehydrogenase Gene Superfamily in Populus: Organization and Expression Divergence between Paralogous Gene Pairs.</ArticleTitle><Pagination><MedlinePgn>e0124669</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0124669</ELocationID><Abstract><AbstractText>Aldehyde dehydrogenases (ALDHs) constitute a superfamily of NAD(P)+-dependent enzymes that catalyze the irreversible oxidation of a wide range of reactive aldehydes to their corresponding nontoxic carboxylic acids. ALDHs have been studied in many organisms from bacteria to mammals; however, no systematic analyses incorporating genome organization, gene structure, expression profiles, and cis-acting elements have been conducted in the model tree species Populus trichocarpa thus far. In this study, a comprehensive analysis of the Populus ALDH gene superfamily was performed. A total of 26 Populus ALDH genes were found to be distributed across 12 chromosomes. Genomic organization analysis indicated that purifying selection may have played a pivotal role in the retention and maintenance of PtALDH gene families. The exon-intron organizations of PtALDHs were highly conserved within the same family, suggesting that the members of the same family also may have conserved functionalities. Microarray data and qRT-PCR analysis indicated that most PtALDHs had distinct tissue-specific expression patterns. The specificity of cis-acting elements in the promoter regions of the PtALDHs and the divergence of expression patterns between nine paralogous PtALDH gene pairs suggested that gene duplications may have freed the duplicate genes from the functional constraints. The expression levels of some ALDHs were up- or down-regulated by various abiotic stresses, implying that the products of these genes may be involved in the adaptation of Populus to abiotic stresses. Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the Populus ALDH gene superfamily and provide insights into the function and evolution of ALDH gene families in vascular plants. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tian</LastName><ForeName>Feng-Xia</ForeName><Initials>FX</Initials><AffiliationInfo><Affiliation>College of Life Science and Technology, Nanyang Normal University, Nanyang, Henan, 473061, 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, 100091, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zang</LastName><ForeName>Jian-Lei</ForeName><Initials>JL</Initials><AffiliationInfo><Affiliation>College of Life Science and Technology, Nanyang Normal University, Nanyang, Henan, 473061, 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, 100091, 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, Nanyang, Henan, 473061, 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, 100091, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xie</LastName><ForeName>Yu-Li</ForeName><Initials>YL</Initials><AffiliationInfo><Affiliation>College of Life Science and Technology, Nanyang Normal University, Nanyang, Henan, 473061, 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, 100091, 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, 100091, China; Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Jian-Jun</ForeName><Initials>JJ</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, 100091, 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>24</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>EC 1.2.1.3</RegistryNumber><NameOfSubstance UI="D000444">Aldehyde Dehydrogenase</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000444" MajorTopicYN="N">Aldehyde Dehydrogenase</DescriptorName><QualifierName UI="Q000145" 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