Transcriptome profiling of PeCRY1 transgenic Populus tomentosa.
Identifieur interne : 000C21 ( Main/Exploration ); précédent : 000C20; suivant : 000C22Transcriptome profiling of PeCRY1 transgenic Populus tomentosa.
Auteurs : Lina Wang [République populaire de Chine] ; Rongling Wu [République populaire de Chine] ; Wenhao Bo [République populaire de Chine]Source :
- Genes & genomics [ 2092-9293 ] ; 2018.
Descripteurs français
- KwdFr :
- Analyse de profil d'expression de gènes (méthodes), Analyse de séquence d'ARN (méthodes), Cryptochromes (génétique), Facteurs de transcription (génétique), Gènes de plante (génétique), Photosynthèse (génétique), Populus (génétique), Rythme circadien (génétique), Régulation de l'expression des gènes végétaux (génétique), Séquençage nucléotidique à haut débit (MeSH), Transcriptome (génétique), Voie des pentoses phosphates (génétique), Végétaux génétiquement modifiés (génétique).
- MESH :
- génétique : Cryptochromes, Facteurs de transcription, Gènes de plante, Photosynthèse, Populus, Rythme circadien, Régulation de l'expression des gènes végétaux, Transcriptome, Voie des pentoses phosphates, Végétaux génétiquement modifiés.
- méthodes : Analyse de profil d'expression de gènes, Analyse de séquence d'ARN.
- Séquençage nucléotidique à haut débit.
English descriptors
- KwdEn :
- Circadian Rhythm (genetics), Cryptochromes (genetics), Gene Expression Profiling (methods), Gene Expression Regulation, Plant (genetics), Genes, Plant (genetics), High-Throughput Nucleotide Sequencing (MeSH), Pentose Phosphate Pathway (genetics), Photosynthesis (genetics), Plants, Genetically Modified (genetics), Populus (genetics), Sequence Analysis, RNA (methods), Transcription Factors (genetics), Transcriptome (genetics).
- MESH :
- chemical , genetics : Cryptochromes, Transcription Factors.
- genetics : Circadian Rhythm, Gene Expression Regulation, Plant, Genes, Plant, Pentose Phosphate Pathway, Photosynthesis, Plants, Genetically Modified, Populus, Transcriptome.
- methods : Gene Expression Profiling, Sequence Analysis, RNA.
- High-Throughput Nucleotide Sequencing.
Abstract
Cryptochromes, a class of blue light photoreceptors, play vital roles in regulating growth and development in higher plants. Despite their control over various important traits, there have been few studies focusing on cryptochromes in forest trees to date. In this study, the Euphrates poplar (Populus euphratica) gene PeCRY1 (cryptochrome 1 of Populus euphratica) was isolated and heterologously expressed in Populus tomentosa. Three biological replicates of each of the PeCRY1 transgenic P. tomentosa (CRY1) and wild-type (WT) plants were processed for transcriptome profiling. We found 34792 commonly expressed transcripts among the 93868 detected unigenes. Using R package DESeq, we identified 357 differentially expressed genes (DEGs), including 132 upregulated and 225 downregulated genes. Gene ontology (GO) enrichment and KEGG pathway enrichment were used to better understand the functions of detected DEGs. Biosynthetic processes, such as starch and sucrose metabolism, which are closely related to growth and development, were highly enriched. Organic cyclic compound biosynthesis was downregulated, whereas carbohydrate metabolism was upregulated. Through KEGG pathway enrichment, we observed that the pentose phosphate pathway, photosynthesis, and circadian rhythm were significantly enriched. Another method of expression analysis based on quantitative reverse transcription polymerase chain reaction (qRT-PCR) validated our RNA sequencing (RNA-seq) results.
DOI: 10.1007/s13258-017-0631-7
PubMed: 29892838
Affiliations:
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scheme="MESH" xml:lang="fr"><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Cryptochromes, a class of blue light photoreceptors, play vital roles in regulating growth and development in higher plants. Despite their control over various important traits, there have been few studies focusing on cryptochromes in forest trees to date. In this study, the Euphrates poplar (Populus euphratica) gene PeCRY1 (cryptochrome 1 of Populus euphratica) was isolated and heterologously expressed in Populus tomentosa. Three biological replicates of each of the PeCRY1 transgenic P. tomentosa (CRY1) and wild-type (WT) plants were processed for transcriptome profiling. We found 34792 commonly expressed transcripts among the 93868 detected unigenes. Using R package DESeq, we identified 357 differentially expressed genes (DEGs), including 132 upregulated and 225 downregulated genes. Gene ontology (GO) enrichment and KEGG pathway enrichment were used to better understand the functions of detected DEGs. Biosynthetic processes, such as starch and sucrose metabolism, which are closely related to growth and development, were highly enriched. Organic cyclic compound biosynthesis was downregulated, whereas carbohydrate metabolism was upregulated. Through KEGG pathway enrichment, we observed that the pentose phosphate pathway, photosynthesis, and circadian rhythm were significantly enriched. Another method of expression analysis based on quantitative reverse transcription polymerase chain reaction (qRT-PCR) validated our RNA sequencing (RNA-seq) results.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29892838</PMID><DateCompleted><Year>2018</Year><Month>10</Month><Day>18</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>14</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">2092-9293</ISSN><JournalIssue CitedMedium="Internet"><Volume>40</Volume><Issue>4</Issue><PubDate><Year>2018</Year><Month>04</Month></PubDate></JournalIssue><Title>Genes & genomics</Title><ISOAbbreviation>Genes Genomics</ISOAbbreviation></Journal><ArticleTitle>Transcriptome profiling of PeCRY1 transgenic Populus tomentosa.</ArticleTitle><Pagination><MedlinePgn>349-359</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s13258-017-0631-7</ELocationID><Abstract><AbstractText>Cryptochromes, a class of blue light photoreceptors, play vital roles in regulating growth and development in higher plants. Despite their control over various important traits, there have been few studies focusing on cryptochromes in forest trees to date. In this study, the Euphrates poplar (Populus euphratica) gene PeCRY1 (cryptochrome 1 of Populus euphratica) was isolated and heterologously expressed in Populus tomentosa. Three biological replicates of each of the PeCRY1 transgenic P. tomentosa (CRY1) and wild-type (WT) plants were processed for transcriptome profiling. We found 34792 commonly expressed transcripts among the 93868 detected unigenes. Using R package DESeq, we identified 357 differentially expressed genes (DEGs), including 132 upregulated and 225 downregulated genes. Gene ontology (GO) enrichment and KEGG pathway enrichment were used to better understand the functions of detected DEGs. Biosynthetic processes, such as starch and sucrose metabolism, which are closely related to growth and development, were highly enriched. Organic cyclic compound biosynthesis was downregulated, whereas carbohydrate metabolism was upregulated. Through KEGG pathway enrichment, we observed that the pentose phosphate pathway, photosynthesis, and circadian rhythm were significantly enriched. Another method of expression analysis based on quantitative reverse transcription polymerase chain reaction (qRT-PCR) validated our RNA sequencing (RNA-seq) results.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Lina</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 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 Technology, Beijing Forestry University, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bo</LastName><ForeName>Wenhao</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China. bwh9620@gmail.com.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>201404102</GrantID><Agency>Special Fund for Forest Scientific Research in the Public Welfare</Agency><Country>International</Country></Grant><Grant><GrantID>NO.BLX2014-22</GrantID><Agency>the Fundamental Research Funds for the Central Universities</Agency><Country>International</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>11</Month><Day>25</Day></ArticleDate></Article><MedlineJournalInfo><Country>Korea (South)</Country><MedlineTA>Genes Genomics</MedlineTA><NlmUniqueID>101481027</NlmUniqueID><ISSNLinking>1976-9571</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D056931">Cryptochromes</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D002940" MajorTopicYN="N">Circadian Rhythm</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D056931" MajorTopicYN="N">Cryptochromes</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" 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MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D030821" MajorTopicYN="N">Plants, Genetically Modified</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017423" MajorTopicYN="N">Sequence Analysis, RNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014157" MajorTopicYN="N">Transcription Factors</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059467" MajorTopicYN="N">Transcriptome</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Cryptochromes</Keyword><Keyword MajorTopicYN="Y">Euphrates poplar</Keyword><Keyword MajorTopicYN="Y">Populus tomentosa</Keyword><Keyword MajorTopicYN="Y">RNA-seq</Keyword><Keyword MajorTopicYN="Y">Transcriptome</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>10</Month><Day>21</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>11</Month><Day>07</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2018</Year><Month>6</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>6</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>10</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId 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last="Wang">Lina Wang</name></noRegion><name sortKey="Bo, Wenhao" sort="Bo, Wenhao" uniqKey="Bo W" first="Wenhao" last="Bo">Wenhao Bo</name><name sortKey="Wu, Rongling" sort="Wu, Rongling" uniqKey="Wu R" first="Rongling" last="Wu">Rongling Wu</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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