Transcriptomic analysis reveals importance of ROS and phytohormones in response to short-term salinity stress in Populus tomentosa.
Identifieur interne : 001A84 ( Main/Exploration ); précédent : 001A83; suivant : 001A85Transcriptomic analysis reveals importance of ROS and phytohormones in response to short-term salinity stress in Populus tomentosa.
Auteurs : Lingyu Zheng [République populaire de Chine] ; Yu Meng [République populaire de Chine] ; Jing Ma [République populaire de Chine] ; Xiulian Zhao [République populaire de Chine] ; Tielong Cheng [République populaire de Chine] ; Jing Ji [République populaire de Chine] ; Ermei Chang [République populaire de Chine] ; Chen Meng [Allemagne] ; Nan Deng [République populaire de Chine] ; Lanzhen Chen [République populaire de Chine] ; Shengqing Shi [République populaire de Chine] ; Zeping Jiang [République populaire de Chine]Source :
- Frontiers in plant science [ 1664-462X ] ; 2015.
Abstract
Populus tomentosa (Chinese white poplar) is well adapted to various extreme environments, and is considered an important species to study the effects of salinity stress on poplar trees. To decipher the mechanism of poplar's rapid response to short-term salinity stress, we firstly detected the changes in H2O2 and hormone, and then profiled the gene expression pattern of 10-week-old seedling roots treated with 200 mM NaCl for 0, 6, 12, and 24 h (h) by RNA-seq on the Illumina-Solexa platform. Physiological determination showed that the significant increase in H2O2 began at 6 h, while that in hormone ABA was at 24 h, under salt stress. Compared with controls (0 h), 3991, 4603, and 4903 genes were up regulated, and 1408, 2206, and 3461 genes were down regulated (adjusted P ≤ 0.05 and |log2Ratio|≥1) at 6, 12, and 24 h time points, respectively. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation revealed that the differentially expressed genes (DEGs) were highly enriched in hormone- and reactive oxygen species-related biological processes, including "response to oxidative stress or abiotic stimulus," "peroxidase activity," "regulation of transcription," "hormone synthetic and metabolic process," "hormone signal transduction," "antioxidant activity," and "transcription factor activity." Moreover, K-means clustering demonstrated that DEGs (total RPKM value>12 from four time points) could be categorized into four kinds of expression trends: quick up/down over 6 or 12 h, and slow up/down over 24 h. Of these, DEGs involved in H2O2- and hormone- producing and signal-related genes were further enriched in this analysis, which indicated that the two kinds of small molecules, hormones and H2O2, play pivotal roles in the short-term salt stress response in poplar. This study provides a basis for future studies of the molecular adaptation of poplar and other tree species to salinity stress.
DOI: 10.3389/fpls.2015.00678
PubMed: 26442002
PubMed Central: PMC4569970
Affiliations:
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and Travel, Agricultural University of Hebei Baoding, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Landscape and Travel, Agricultural University of Hebei Baoding</wicri:regionArea><wicri:noRegion>Agricultural University of Hebei Baoding</wicri:noRegion></affiliation></author><author><name sortKey="Ma, Jing" sort="Ma, Jing" uniqKey="Ma J" first="Jing" last="Ma">Jing Ma</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing</wicri:regionArea><wicri:noRegion>Chinese Academy of Forestry Beijing</wicri:noRegion></affiliation></author><author><name sortKey="Zhao, Xiulian" sort="Zhao, 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Freising</wicri:noRegion></affiliation></author><author><name sortKey="Deng, Nan" sort="Deng, Nan" uniqKey="Deng N" first="Nan" last="Deng">Nan Deng</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing</wicri:regionArea><wicri:noRegion>Chinese Academy of Forestry Beijing</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Lanzhen" sort="Chen, Lanzhen" uniqKey="Chen L" first="Lanzhen" last="Chen">Lanzhen Chen</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Apicultural Research, Chinese Academy of Agricultural Sciences Beijing, China ; Risk Assessment Laboratory for Bee Products, Quality and Safety of Ministry of Agriculture Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Apicultural Research, Chinese Academy of Agricultural Sciences Beijing, China ; Risk Assessment Laboratory for Bee Products, Quality and Safety of Ministry of Agriculture Beijing</wicri:regionArea><wicri:noRegion>Quality and Safety of Ministry of Agriculture Beijing</wicri:noRegion></affiliation></author><author><name sortKey="Shi, Shengqing" sort="Shi, Shengqing" uniqKey="Shi S" first="Shengqing" last="Shi">Shengqing Shi</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry 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Research Institute of Forestry, Chinese Academy of Forestry Beijing</wicri:regionArea><wicri:noRegion>Chinese Academy of Forestry Beijing</wicri:noRegion></affiliation></author><author><name sortKey="Meng, Yu" sort="Meng, Yu" uniqKey="Meng Y" first="Yu" last="Meng">Yu Meng</name><affiliation wicri:level="1"><nlm:affiliation>College of Landscape and Travel, Agricultural University of Hebei Baoding, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Landscape and Travel, Agricultural University of Hebei Baoding</wicri:regionArea><wicri:noRegion>Agricultural University of Hebei Baoding</wicri:noRegion></affiliation></author><author><name sortKey="Ma, Jing" sort="Ma, Jing" uniqKey="Ma J" first="Jing" last="Ma">Jing Ma</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing</wicri:regionArea><wicri:noRegion>Chinese Academy of Forestry Beijing</wicri:noRegion></affiliation></author><author><name sortKey="Zhao, Xiulian" sort="Zhao, Xiulian" uniqKey="Zhao X" first="Xiulian" last="Zhao">Xiulian Zhao</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing</wicri:regionArea><wicri:noRegion>Chinese Academy of Forestry Beijing</wicri:noRegion></affiliation></author><author><name sortKey="Cheng, Tielong" sort="Cheng, Tielong" uniqKey="Cheng T" first="Tielong" last="Cheng">Tielong Cheng</name><affiliation wicri:level="1"><nlm:affiliation>College of Biology and the Environment, Nanjing Forestry University Nanjing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Biology and the Environment, Nanjing Forestry University Nanjing</wicri:regionArea><wicri:noRegion>Nanjing Forestry University Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Ji, Jing" sort="Ji, Jing" uniqKey="Ji J" first="Jing" last="Ji">Jing Ji</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing</wicri:regionArea><wicri:noRegion>Chinese Academy of Forestry Beijing</wicri:noRegion></affiliation></author><author><name sortKey="Chang, Ermei" sort="Chang, Ermei" uniqKey="Chang E" first="Ermei" last="Chang">Ermei Chang</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing</wicri:regionArea><wicri:noRegion>Chinese Academy of Forestry Beijing</wicri:noRegion></affiliation></author><author><name sortKey="Meng, Chen" sort="Meng, Chen" uniqKey="Meng C" first="Chen" last="Meng">Chen Meng</name><affiliation wicri:level="1"><nlm:affiliation>Chair of Proteomics and Bioanalytics, Technische Universität München Freising, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Chair of Proteomics and Bioanalytics, Technische Universität München Freising</wicri:regionArea><wicri:noRegion>Technische Universität München Freising</wicri:noRegion><wicri:noRegion>Technische Universität München Freising</wicri:noRegion><wicri:noRegion>Technische Universität München Freising</wicri:noRegion></affiliation></author><author><name sortKey="Deng, Nan" sort="Deng, Nan" uniqKey="Deng N" first="Nan" last="Deng">Nan Deng</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing</wicri:regionArea><wicri:noRegion>Chinese Academy of Forestry Beijing</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Lanzhen" sort="Chen, Lanzhen" uniqKey="Chen L" first="Lanzhen" last="Chen">Lanzhen Chen</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Apicultural Research, Chinese Academy of Agricultural Sciences Beijing, China ; Risk Assessment Laboratory for Bee Products, Quality and Safety of Ministry of Agriculture Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Apicultural Research, Chinese Academy of Agricultural Sciences Beijing, China ; Risk Assessment Laboratory for Bee Products, Quality and Safety of Ministry of Agriculture Beijing</wicri:regionArea><wicri:noRegion>Quality and Safety of Ministry of Agriculture Beijing</wicri:noRegion></affiliation></author><author><name sortKey="Shi, Shengqing" sort="Shi, Shengqing" uniqKey="Shi S" first="Shengqing" last="Shi">Shengqing Shi</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing</wicri:regionArea><wicri:noRegion>Chinese Academy of Forestry Beijing</wicri:noRegion></affiliation></author><author><name sortKey="Jiang, Zeping" sort="Jiang, Zeping" uniqKey="Jiang Z" first="Zeping" last="Jiang">Zeping Jiang</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing</wicri:regionArea><wicri:noRegion>Chinese Academy of Forestry Beijing</wicri:noRegion></affiliation></author></analytic><series><title level="j">Frontiers in plant science</title><idno type="ISSN">1664-462X</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Populus tomentosa (Chinese white poplar) is well adapted to various extreme environments, and is considered an important species to study the effects of salinity stress on poplar trees. To decipher the mechanism of poplar's rapid response to short-term salinity stress, we firstly detected the changes in H2O2 and hormone, and then profiled the gene expression pattern of 10-week-old seedling roots treated with 200 mM NaCl for 0, 6, 12, and 24 h (h) by RNA-seq on the Illumina-Solexa platform. Physiological determination showed that the significant increase in H2O2 began at 6 h, while that in hormone ABA was at 24 h, under salt stress. Compared with controls (0 h), 3991, 4603, and 4903 genes were up regulated, and 1408, 2206, and 3461 genes were down regulated (adjusted P ≤ 0.05 and |log2Ratio|≥1) at 6, 12, and 24 h time points, respectively. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation revealed that the differentially expressed genes (DEGs) were highly enriched in hormone- and reactive oxygen species-related biological processes, including "response to oxidative stress or abiotic stimulus," "peroxidase activity," "regulation of transcription," "hormone synthetic and metabolic process," "hormone signal transduction," "antioxidant activity," and "transcription factor activity." Moreover, K-means clustering demonstrated that DEGs (total RPKM value>12 from four time points) could be categorized into four kinds of expression trends: quick up/down over 6 or 12 h, and slow up/down over 24 h. Of these, DEGs involved in H2O2- and hormone- producing and signal-related genes were further enriched in this analysis, which indicated that the two kinds of small molecules, hormones and H2O2, play pivotal roles in the short-term salt stress response in poplar. This study provides a basis for future studies of the molecular adaptation of poplar and other tree species to salinity stress. </div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">26442002</PMID><DateCompleted><Year>2015</Year><Month>10</Month><Day>07</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>6</Volume><PubDate><Year>2015</Year></PubDate></JournalIssue><Title>Frontiers in plant science</Title><ISOAbbreviation>Front Plant Sci</ISOAbbreviation></Journal><ArticleTitle>Transcriptomic analysis reveals importance of ROS and phytohormones in response to short-term salinity stress in Populus tomentosa.</ArticleTitle><Pagination><MedlinePgn>678</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fpls.2015.00678</ELocationID><Abstract><AbstractText>Populus tomentosa (Chinese white poplar) is well adapted to various extreme environments, and is considered an important species to study the effects of salinity stress on poplar trees. To decipher the mechanism of poplar's rapid response to short-term salinity stress, we firstly detected the changes in H2O2 and hormone, and then profiled the gene expression pattern of 10-week-old seedling roots treated with 200 mM NaCl for 0, 6, 12, and 24 h (h) by RNA-seq on the Illumina-Solexa platform. Physiological determination showed that the significant increase in H2O2 began at 6 h, while that in hormone ABA was at 24 h, under salt stress. Compared with controls (0 h), 3991, 4603, and 4903 genes were up regulated, and 1408, 2206, and 3461 genes were down regulated (adjusted P ≤ 0.05 and |log2Ratio|≥1) at 6, 12, and 24 h time points, respectively. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation revealed that the differentially expressed genes (DEGs) were highly enriched in hormone- and reactive oxygen species-related biological processes, including "response to oxidative stress or abiotic stimulus," "peroxidase activity," "regulation of transcription," "hormone synthetic and metabolic process," "hormone signal transduction," "antioxidant activity," and "transcription factor activity." Moreover, K-means clustering demonstrated that DEGs (total RPKM value>12 from four time points) could be categorized into four kinds of expression trends: quick up/down over 6 or 12 h, and slow up/down over 24 h. Of these, DEGs involved in H2O2- and hormone- producing and signal-related genes were further enriched in this analysis, which indicated that the two kinds of small molecules, hormones and H2O2, play pivotal roles in the short-term salt stress response in poplar. This study provides a basis for future studies of the molecular adaptation of poplar and other tree species to salinity stress. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zheng</LastName><ForeName>Lingyu</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Meng</LastName><ForeName>Yu</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>College of Landscape and Travel, Agricultural University of Hebei Baoding, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ma</LastName><ForeName>Jing</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Xiulian</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cheng</LastName><ForeName>Tielong</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>College of Biology and the Environment, Nanjing Forestry University Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ji</LastName><ForeName>Jing</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chang</LastName><ForeName>Ermei</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Meng</LastName><ForeName>Chen</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Chair of Proteomics and Bioanalytics, Technische Universität München Freising, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Deng</LastName><ForeName>Nan</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Lanzhen</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Institute of Apicultural Research, Chinese Academy of Agricultural Sciences Beijing, China ; Risk Assessment Laboratory for Bee Products, Quality and Safety of Ministry of Agriculture Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shi</LastName><ForeName>Shengqing</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Zeping</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2015</Year><Month>09</Month><Day>15</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">H2O2</Keyword><Keyword MajorTopicYN="N">Populus tomentosa</Keyword><Keyword MajorTopicYN="N">differentially expressed genes</Keyword><Keyword MajorTopicYN="N">hormone</Keyword><Keyword MajorTopicYN="N">salt stress</Keyword><Keyword MajorTopicYN="N">transcriptomic analysis</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>01</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>08</Month><Day>17</Day></PubMedPubDate><PubMedPubDate 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