RNA-SEQ Reveals Transcriptional Level Changes of Poplar Roots in Different Forms of Nitrogen Treatments.
Identifieur interne : 001693 ( Main/Exploration ); précédent : 001692; suivant : 001694RNA-SEQ Reveals Transcriptional Level Changes of Poplar Roots in Different Forms of Nitrogen Treatments.
Auteurs : Chun-Pu Qu [République populaire de Chine] ; Zhi-Ru Xu [République populaire de Chine] ; Yan-Bo Hu [République populaire de Chine] ; Yao Lu [République populaire de Chine] ; Cheng-Jun Yang [République populaire de Chine] ; Guang-Yu Sun [République populaire de Chine] ; Guan-Jun Liu [République populaire de Chine]Source :
- Frontiers in plant science [ 1664-462X ] ; 2016.
Abstract
Poplar has emerged as a model plant for better understanding cellular and molecular changes accompanying tree growth, development, and response to environment. Long-term application of different forms of nitrogen (such as [Formula: see text]-N and [Formula: see text]-N) may cause morphological changes of poplar roots; however, the molecular level changes are still not well-known. In this study, we analyzed the expression profiling of poplar roots treated by three forms of nitrogen: S1 ([Formula: see text]), S2 (NH4NO3), and S3 ([Formula: see text]) by using RNA-SEQ technique. We found 463 genes significantly differentially expressed in roots by different N treatments, of which a total of 112 genes were found to differentially express between S1 and S2, 171 genes between S2 and S3, and 319 genes between S1 and S3. A cluster analysis shows significant difference in many transcription factor families and functional genes family under different N forms. Through an analysis of Mapman metabolic pathway, we found that the significantly differentially expressed genes are associated with fermentation, glycolysis, and tricarboxylic acid cycle (TCA), secondary metabolism, hormone metabolism, and transport processing. Interestingly, we did not find significantly differentially expressed genes in N metabolism pathway, mitochondrial electron transport/ATP synthesis and mineral nutrition. We also found abundant candidate genes (20 transcription factors and 30 functional genes) regulating morphology changes of poplar roots under the three N forms. The results obtained are beneficial to a better understanding of the potential molecular and cellular mechanisms regulating root morphology changes under different N treatments.
DOI: 10.3389/fpls.2016.00051
PubMed: 26870068
PubMed Central: PMC4735414
Affiliations:
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College of Life Science, Northeast Forestry UniversityHarbin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry UniversityHarbin, China; College of Life Science, Northeast Forestry UniversityHarbin</wicri:regionArea><wicri:noRegion>Northeast Forestry UniversityHarbin</wicri:noRegion></affiliation></author><author><name sortKey="Hu, Yan Bo" sort="Hu, Yan Bo" uniqKey="Hu Y" first="Yan-Bo" last="Hu">Yan-Bo Hu</name><affiliation wicri:level="1"><nlm:affiliation>College of Life Science, Northeast Forestry University Harbin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Science, Northeast Forestry University Harbin</wicri:regionArea><wicri:noRegion>Northeast Forestry University Harbin</wicri:noRegion></affiliation></author><author><name sortKey="Lu, Yao" sort="Lu, Yao" uniqKey="Lu Y" first="Yao" last="Lu">Yao Lu</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University Harbin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University Harbin</wicri:regionArea><wicri:noRegion>Northeast Forestry University Harbin</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Cheng Jun" sort="Yang, Cheng Jun" uniqKey="Yang C" first="Cheng-Jun" last="Yang">Cheng-Jun Yang</name><affiliation wicri:level="1"><nlm:affiliation>School of Forestry, Northeast Forestry University Harbin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Forestry, Northeast Forestry University Harbin</wicri:regionArea><wicri:noRegion>Northeast Forestry University Harbin</wicri:noRegion></affiliation></author><author><name sortKey="Sun, Guang Yu" sort="Sun, Guang Yu" uniqKey="Sun G" first="Guang-Yu" last="Sun">Guang-Yu Sun</name><affiliation wicri:level="1"><nlm:affiliation>College of Life Science, Northeast Forestry University Harbin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Science, Northeast Forestry University Harbin</wicri:regionArea><wicri:noRegion>Northeast Forestry University Harbin</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Guan Jun" sort="Liu, Guan Jun" uniqKey="Liu G" first="Guan-Jun" last="Liu">Guan-Jun Liu</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University Harbin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University Harbin</wicri:regionArea><wicri:noRegion>Northeast Forestry University Harbin</wicri:noRegion></affiliation></author></analytic><series><title level="j">Frontiers in plant science</title><idno type="ISSN">1664-462X</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Poplar has emerged as a model plant for better understanding cellular and molecular changes accompanying tree growth, development, and response to environment. Long-term application of different forms of nitrogen (such as [Formula: see text]-N and [Formula: see text]-N) may cause morphological changes of poplar roots; however, the molecular level changes are still not well-known. In this study, we analyzed the expression profiling of poplar roots treated by three forms of nitrogen: S1 ([Formula: see text]), S2 (NH4NO3), and S3 ([Formula: see text]) by using RNA-SEQ technique. We found 463 genes significantly differentially expressed in roots by different N treatments, of which a total of 112 genes were found to differentially express between S1 and S2, 171 genes between S2 and S3, and 319 genes between S1 and S3. A cluster analysis shows significant difference in many transcription factor families and functional genes family under different N forms. Through an analysis of Mapman metabolic pathway, we found that the significantly differentially expressed genes are associated with fermentation, glycolysis, and tricarboxylic acid cycle (TCA), secondary metabolism, hormone metabolism, and transport processing. Interestingly, we did not find significantly differentially expressed genes in N metabolism pathway, mitochondrial electron transport/ATP synthesis and mineral nutrition. We also found abundant candidate genes (20 transcription factors and 30 functional genes) regulating morphology changes of poplar roots under the three N forms. The results obtained are beneficial to a better understanding of the potential molecular and cellular mechanisms regulating root morphology changes under different N treatments. </div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">26870068</PMID><DateCompleted><Year>2016</Year><Month>02</Month><Day>12</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-462X</ISSN><JournalIssue CitedMedium="Print"><Volume>7</Volume><PubDate><Year>2016</Year></PubDate></JournalIssue><Title>Frontiers in plant science</Title><ISOAbbreviation>Front Plant Sci</ISOAbbreviation></Journal><ArticleTitle>RNA-SEQ Reveals Transcriptional Level Changes of Poplar Roots in Different Forms of Nitrogen Treatments.</ArticleTitle><Pagination><MedlinePgn>51</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fpls.2016.00051</ELocationID><Abstract><AbstractText>Poplar has emerged as a model plant for better understanding cellular and molecular changes accompanying tree growth, development, and response to environment. Long-term application of different forms of nitrogen (such as [Formula: see text]-N and [Formula: see text]-N) may cause morphological changes of poplar roots; however, the molecular level changes are still not well-known. In this study, we analyzed the expression profiling of poplar roots treated by three forms of nitrogen: S1 ([Formula: see text]), S2 (NH4NO3), and S3 ([Formula: see text]) by using RNA-SEQ technique. We found 463 genes significantly differentially expressed in roots by different N treatments, of which a total of 112 genes were found to differentially express between S1 and S2, 171 genes between S2 and S3, and 319 genes between S1 and S3. A cluster analysis shows significant difference in many transcription factor families and functional genes family under different N forms. Through an analysis of Mapman metabolic pathway, we found that the significantly differentially expressed genes are associated with fermentation, glycolysis, and tricarboxylic acid cycle (TCA), secondary metabolism, hormone metabolism, and transport processing. Interestingly, we did not find significantly differentially expressed genes in N metabolism pathway, mitochondrial electron transport/ATP synthesis and mineral nutrition. We also found abundant candidate genes (20 transcription factors and 30 functional genes) regulating morphology changes of poplar roots under the three N forms. The results obtained are beneficial to a better understanding of the potential molecular and cellular mechanisms regulating root morphology changes under different N treatments. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Qu</LastName><ForeName>Chun-Pu</ForeName><Initials>CP</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University Harbin, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Zhi-Ru</ForeName><Initials>ZR</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry UniversityHarbin, China; College of Life Science, Northeast Forestry UniversityHarbin, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Yan-Bo</ForeName><Initials>YB</Initials><AffiliationInfo><Affiliation>College of Life Science, Northeast Forestry University Harbin, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lu</LastName><ForeName>Yao</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University Harbin, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Cheng-Jun</ForeName><Initials>CJ</Initials><AffiliationInfo><Affiliation>School of Forestry, Northeast Forestry University Harbin, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sun</LastName><ForeName>Guang-Yu</ForeName><Initials>GY</Initials><AffiliationInfo><Affiliation>College of Life Science, Northeast Forestry University Harbin, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Guan-Jun</ForeName><Initials>GJ</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University Harbin, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>02</Month><Day>02</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Plant Sci</MedlineTA><NlmUniqueID>101568200</NlmUniqueID><ISSNLinking>1664-462X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">RNA-SEQ</Keyword><Keyword MajorTopicYN="N">long-time nitrogen treatment</Keyword><Keyword MajorTopicYN="N">nitrogen forms</Keyword><Keyword MajorTopicYN="N">nitrogen metabolism</Keyword><Keyword MajorTopicYN="N">poplar</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate 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first="Guan-Jun" last="Liu">Guan-Jun Liu</name><name sortKey="Lu, Yao" sort="Lu, Yao" uniqKey="Lu Y" first="Yao" last="Lu">Yao Lu</name><name sortKey="Sun, Guang Yu" sort="Sun, Guang Yu" uniqKey="Sun G" first="Guang-Yu" last="Sun">Guang-Yu Sun</name><name sortKey="Xu, Zhi Ru" sort="Xu, Zhi Ru" uniqKey="Xu Z" first="Zhi-Ru" last="Xu">Zhi-Ru Xu</name><name sortKey="Yang, Cheng Jun" sort="Yang, Cheng Jun" uniqKey="Yang C" first="Cheng-Jun" last="Yang">Cheng-Jun Yang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:26870068" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PoplarV1
| This area was generated with Dilib version V0.6.37. |  |