Systematic functional genomics resource and annotation for poplar.
Identifieur interne : 001B23 ( Main/Exploration ); précédent : 001B22; suivant : 001B24Systematic functional genomics resource and annotation for poplar.
Auteurs : Jingna Si [République populaire de Chine] ; Xiyang Zhao [République populaire de Chine] ; Xinyin Zhao [République populaire de Chine] ; Rongling Wu [République populaire de Chine]Source :
- IET systems biology [ 1751-8849 ] ; 2015.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Plant Proteins.
- genetics : Genome, Plant, Populus, Salt-Tolerant Plants.
- methods : Chromosome Mapping, Genomics.
- Computer Simulation, Databases, Genetic, Models, Genetic.
Abstract
Poplar, as a model species for forestry research, has many excellent characteristics. Studies on functional genes have provided the foundation, at the molecular level, for improving genetic traits and cultivating elite lines. Although studies on functional genes have been performed for many years, large amounts of experimental data remain scattered across various reports and have not been unified via comprehensive statistical analysis. This problem can be addressed by employing bioinformatic methodology and technology to gather and organise data to construct a Poplar Functional Gene Database, containing data on 207 poplar functional genes. As an example, the authors investigated genes of Populus euphratica involved in the response to salt stress. Four small cDNA libraries were constructed and treated with 300 mM NaCl or pure water for 6 and 24 h. Using high-throughput sequencing, they identified conserved and novel miRNAs that were differentially expressed. Target genes were next predicted and detailed functional information derived using the Gene Ontology database and Kyoto Encyclopedia of Genes and Genomes pathway analysis. This information provides a primary visual schema allowing us to understand the dynamics of the regulatory gene network responding to salt stress in Populus.
DOI: 10.1049/iet-syb.2014.0047
PubMed: 26243833
Affiliations:
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last="Zhao">Xiyang Zhao</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040</wicri:regionArea><wicri:noRegion>Harbin 150040</wicri:noRegion></affiliation></author><author><name sortKey="Zhao, Xinyin" sort="Zhao, Xinyin" uniqKey="Zhao X" first="Xinyin" last="Zhao">Xinyin Zhao</name><affiliation wicri:level="1"><nlm:affiliation>Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Computational Biology, National 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Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, People's Republic of China. jingnasi@bjfu.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Zhao, Xiyang" sort="Zhao, Xiyang" uniqKey="Zhao X" first="Xiyang" last="Zhao">Xiyang Zhao</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040</wicri:regionArea><wicri:noRegion>Harbin 150040</wicri:noRegion></affiliation></author><author><name sortKey="Zhao, Xinyin" sort="Zhao, Xinyin" uniqKey="Zhao X" first="Xinyin" last="Zhao">Xinyin Zhao</name><affiliation wicri:level="1"><nlm:affiliation>Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Wu, Rongling" sort="Wu, Rongling" uniqKey="Wu R" first="Rongling" last="Wu">Rongling Wu</name><affiliation wicri:level="1"><nlm:affiliation>Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></analytic><series><title level="j">IET systems biology</title><idno type="ISSN">1751-8849</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosome Mapping (methods)</term><term>Computer Simulation (MeSH)</term><term>Databases, Genetic (MeSH)</term><term>Genome, Plant (genetics)</term><term>Genomics (methods)</term><term>Models, Genetic (MeSH)</term><term>Plant Proteins (genetics)</term><term>Populus (genetics)</term><term>Salt-Tolerant Plants (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Bases de données génétiques (MeSH)</term><term>Cartographie chromosomique (méthodes)</term><term>Génome végétal (génétique)</term><term>Génomique (méthodes)</term><term>Modèles génétiques (MeSH)</term><term>Plantes tolérantes au sel (génétique)</term><term>Populus (génétique)</term><term>Protéines végétales (génétique)</term><term>Simulation numérique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genome, Plant</term><term>Populus</term><term>Salt-Tolerant Plants</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Génome végétal</term><term>Plantes tolérantes au sel</term><term>Populus</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Chromosome Mapping</term><term>Genomics</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Cartographie chromosomique</term><term>Génomique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computer Simulation</term><term>Databases, Genetic</term><term>Models, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Bases de données génétiques</term><term>Modèles génétiques</term><term>Simulation numérique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Poplar, as a model species for forestry research, has many excellent characteristics. Studies on functional genes have provided the foundation, at the molecular level, for improving genetic traits and cultivating elite lines. Although studies on functional genes have been performed for many years, large amounts of experimental data remain scattered across various reports and have not been unified via comprehensive statistical analysis. This problem can be addressed by employing bioinformatic methodology and technology to gather and organise data to construct a Poplar Functional Gene Database, containing data on 207 poplar functional genes. As an example, the authors investigated genes of Populus euphratica involved in the response to salt stress. Four small cDNA libraries were constructed and treated with 300 mM NaCl or pure water for 6 and 24 h. Using high-throughput sequencing, they identified conserved and novel miRNAs that were differentially expressed. Target genes were next predicted and detailed functional information derived using the Gene Ontology database and Kyoto Encyclopedia of Genes and Genomes pathway analysis. This information provides a primary visual schema allowing us to understand the dynamics of the regulatory gene network responding to salt stress in Populus. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26243833</PMID><DateCompleted><Year>2015</Year><Month>11</Month><Day>20</Day></DateCompleted><DateRevised><Year>2015</Year><Month>08</Month><Day>05</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">1751-8849</ISSN><JournalIssue CitedMedium="Print"><Volume>9</Volume><Issue>4</Issue><PubDate><Year>2015</Year><Month>Aug</Month></PubDate></JournalIssue><Title>IET systems biology</Title><ISOAbbreviation>IET Syst Biol</ISOAbbreviation></Journal><ArticleTitle>Systematic functional genomics resource and annotation for poplar.</ArticleTitle><Pagination><MedlinePgn>164-71</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1049/iet-syb.2014.0047</ELocationID><Abstract><AbstractText>Poplar, as a model species for forestry research, has many excellent characteristics. Studies on functional genes have provided the foundation, at the molecular level, for improving genetic traits and cultivating elite lines. Although studies on functional genes have been performed for many years, large amounts of experimental data remain scattered across various reports and have not been unified via comprehensive statistical analysis. This problem can be addressed by employing bioinformatic methodology and technology to gather and organise data to construct a Poplar Functional Gene Database, containing data on 207 poplar functional genes. As an example, the authors investigated genes of Populus euphratica involved in the response to salt stress. Four small cDNA libraries were constructed and treated with 300 mM NaCl or pure water for 6 and 24 h. Using high-throughput sequencing, they identified conserved and novel miRNAs that were differentially expressed. Target genes were next predicted and detailed functional information derived using the Gene Ontology database and Kyoto Encyclopedia of Genes and Genomes pathway analysis. This information provides a primary visual schema allowing us to understand the dynamics of the regulatory gene network responding to salt stress in Populus. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Si</LastName><ForeName>Jingna</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, People's Republic of China. jingnasi@bjfu.edu.cn.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Xiyang</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Xinyin</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Rongling</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, People's Republic of 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></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>IET Syst Biol</MedlineTA><NlmUniqueID>101301198</NlmUniqueID><ISSNLinking>1751-8849</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D002874" MajorTopicYN="N">Chromosome Mapping</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003198" MajorTopicYN="N">Computer Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D030541" MajorTopicYN="Y">Databases, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008957" MajorTopicYN="Y">Models, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D055051" MajorTopicYN="N">Salt-Tolerant Plants</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>8</Month><Day>6</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>8</Month><Day>6</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>12</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26243833</ArticleId><ArticleId IdType="doi">10.1049/iet-syb.2014.0047</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country><settlement><li>Pékin</li></settlement></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Si, Jingna" sort="Si, Jingna" uniqKey="Si J" first="Jingna" last="Si">Jingna Si</name></noRegion><name sortKey="Wu, Rongling" sort="Wu, Rongling" uniqKey="Wu R" first="Rongling" last="Wu">Rongling Wu</name><name sortKey="Zhao, Xinyin" sort="Zhao, Xinyin" uniqKey="Zhao X" first="Xinyin" last="Zhao">Xinyin Zhao</name><name sortKey="Zhao, Xiyang" sort="Zhao, Xiyang" uniqKey="Zhao X" first="Xiyang" last="Zhao">Xiyang Zhao</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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