Revealing Shared and Distinct Genes Responding to JA and SA Signaling in Arabidopsis by Meta-Analysis.
Identifieur interne : 000061 ( Main/Exploration ); précédent : 000060; suivant : 000062Revealing Shared and Distinct Genes Responding to JA and SA Signaling in Arabidopsis by Meta-Analysis.
Auteurs : Nailou Zhang [République populaire de Chine] ; Shuang Zhou [République populaire de Chine] ; Dongyan Yang [République populaire de Chine] ; Zhijin Fan [République populaire de Chine]Source :
- Frontiers in plant science [ 1664-462X ] ; 2020.
Abstract
Plant resistance against biotrophic and necrotrophic pathogens is mediated by mutually synergistic and antagonistic effects of salicylic acid (SA) and jasmonic acid (JA) signals. However, the unique and shared genes responding to the defense mediated by JA/SA signals were largely unclear. To reveal discrete, synergistic and antagonistic JA/SA responsive genes in Arabidopsis thaliana, Meta-Analysis was employed with 257 publicly available Arabidopsis thaliana RNA-Seq gene expression profiles following treatment of mock, JA or SA analogs. JA/SA signalings were found to co-induce broad-spectrum disease-response genes, co-repress the genes related to photosynthesis, auxin, and gibberellin, and reallocate resources of growth toward defense. JA might attenuate SA induced immune response by inhibiting the expression of resistance genes and receptor-like proteins/kinases. Strikingly, co-expression network analysis revealed that JA/SA uniquely regulated genes showing highly coordinated co-expression only in their respective treatment. Using principal component analysis, and hierarchical cluster analysis, JA/SA analogs were segregated into separate entities based on the global differential expression matrix rather than the expression matrix. To accurately classify JA/SA analogs with as few genes as possible, 87 genes, including the SA receptor NPR4, and JA biosynthesis gene AOC1 and JA response biomarkers VSP1/2, were identified by three feature selection algorithms as JA/SA markers. The results were confirmed by independent datasets and provided valuable resources for further functional analyses in JA- or SA- mediated plant defense. These methods would provide cues to build a promising approach for probing the mode of action of potential elicitors.
DOI: 10.3389/fpls.2020.00908
PubMed: 32670328
PubMed Central: PMC7333171
Affiliations:
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Zhou</name><affiliation wicri:level="3"><nlm:affiliation>State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin</wicri:regionArea><placeName><settlement type="city">Tianjin</settlement></placeName></affiliation></author><author><name sortKey="Yang, Dongyan" sort="Yang, Dongyan" uniqKey="Yang D" first="Dongyan" last="Yang">Dongyan Yang</name><affiliation wicri:level="3"><nlm:affiliation>State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin</wicri:regionArea><placeName><settlement type="city">Tianjin</settlement></placeName></affiliation></author><author><name sortKey="Fan, Zhijin" sort="Fan, Zhijin" uniqKey="Fan Z" first="Zhijin" last="Fan">Zhijin Fan</name><affiliation wicri:level="3"><nlm:affiliation>State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin</wicri:regionArea><placeName><settlement type="city">Tianjin</settlement></placeName></affiliation></author></analytic><series><title level="j">Frontiers in plant science</title><idno type="ISSN">1664-462X</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Plant resistance against biotrophic and necrotrophic pathogens is mediated by mutually synergistic and antagonistic effects of salicylic acid (SA) and jasmonic acid (JA) signals. However, the unique and shared genes responding to the defense mediated by JA/SA signals were largely unclear. To reveal discrete, synergistic and antagonistic JA/SA responsive genes in <i>Arabidopsis thaliana</i>, Meta-Analysis was employed with 257 publicly available <i>Arabidopsis thaliana</i> RNA-Seq gene expression profiles following treatment of mock, JA or SA analogs. JA/SA signalings were found to co-induce broad-spectrum disease-response genes, co-repress the genes related to photosynthesis, auxin, and gibberellin, and reallocate resources of growth toward defense. JA might attenuate SA induced immune response by inhibiting the expression of resistance genes and receptor-like proteins/kinases. Strikingly, co-expression network analysis revealed that JA/SA uniquely regulated genes showing highly coordinated co-expression only in their respective treatment. Using principal component analysis, and hierarchical cluster analysis, JA/SA analogs were segregated into separate entities based on the global differential expression matrix rather than the expression matrix. To accurately classify JA/SA analogs with as few genes as possible, 87 genes, including the SA receptor <i>NPR4</i>, and JA biosynthesis gene <i>AOC1</i> and JA response biomarkers <i>VSP1/2</i>, were identified by three feature selection algorithms as JA/SA markers. The results were confirmed by independent datasets and provided valuable resources for further functional analyses in JA- or SA- mediated plant defense. These methods would provide cues to build a promising approach for probing the mode of action of potential elicitors.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32670328</PMID><DateRevised><Year>2020</Year><Month>10</Month><Day>03</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-462X</ISSN><JournalIssue CitedMedium="Print"><Volume>11</Volume><PubDate><Year>2020</Year></PubDate></JournalIssue><Title>Frontiers in plant science</Title><ISOAbbreviation>Front Plant Sci</ISOAbbreviation></Journal><ArticleTitle>Revealing Shared and Distinct Genes Responding to JA and SA Signaling in Arabidopsis by Meta-Analysis.</ArticleTitle><Pagination><MedlinePgn>908</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fpls.2020.00908</ELocationID><Abstract><AbstractText>Plant resistance against biotrophic and necrotrophic pathogens is mediated by mutually synergistic and antagonistic effects of salicylic acid (SA) and jasmonic acid (JA) signals. However, the unique and shared genes responding to the defense mediated by JA/SA signals were largely unclear. To reveal discrete, synergistic and antagonistic JA/SA responsive genes in <i>Arabidopsis thaliana</i>, Meta-Analysis was employed with 257 publicly available <i>Arabidopsis thaliana</i> RNA-Seq gene expression profiles following treatment of mock, JA or SA analogs. JA/SA signalings were found to co-induce broad-spectrum disease-response genes, co-repress the genes related to photosynthesis, auxin, and gibberellin, and reallocate resources of growth toward defense. JA might attenuate SA induced immune response by inhibiting the expression of resistance genes and receptor-like proteins/kinases. Strikingly, co-expression network analysis revealed that JA/SA uniquely regulated genes showing highly coordinated co-expression only in their respective treatment. Using principal component analysis, and hierarchical cluster analysis, JA/SA analogs were segregated into separate entities based on the global differential expression matrix rather than the expression matrix. To accurately classify JA/SA analogs with as few genes as possible, 87 genes, including the SA receptor <i>NPR4</i>, and JA biosynthesis gene <i>AOC1</i> and JA response biomarkers <i>VSP1/2</i>, were identified by three feature selection algorithms as JA/SA markers. The results were confirmed by independent datasets and provided valuable resources for further functional analyses in JA- or SA- mediated plant defense. These methods would provide cues to build a promising approach for probing the mode of action of potential elicitors.</AbstractText><CopyrightInformation>Copyright © 2020 Zhang, Zhou, Yang and Fan.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Nailou</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhou</LastName><ForeName>Shuang</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Dongyan</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fan</LastName><ForeName>Zhijin</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>06</Month><Day>26</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Plant Sci</MedlineTA><NlmUniqueID>101568200</NlmUniqueID><ISSNLinking>1664-462X</ISSNLinking></MedlineJournalInfo><CommentsCorrectionsList><CommentsCorrections RefType="ErratumIn"><RefSource>Front Plant Sci. 2020 Sep 17;11:596349</RefSource><PMID Version="1">33042198</PMID></CommentsCorrections></CommentsCorrectionsList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">co-expression network</Keyword><Keyword MajorTopicYN="N">jasmonic acid</Keyword><Keyword MajorTopicYN="N">meta-analysis</Keyword><Keyword MajorTopicYN="N">molecular markers</Keyword><Keyword MajorTopicYN="N">plant immunity</Keyword><Keyword MajorTopicYN="N">salicylic acid</Keyword><Keyword MajorTopicYN="N">systems biology</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>11</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>06</Month><Day>03</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>7</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>7</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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Chine</li></country><settlement><li>Tianjin</li></settlement></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Zhang, Nailou" sort="Zhang, Nailou" uniqKey="Zhang N" first="Nailou" last="Zhang">Nailou Zhang</name></noRegion><name sortKey="Fan, Zhijin" sort="Fan, Zhijin" uniqKey="Fan Z" first="Zhijin" last="Fan">Zhijin Fan</name><name sortKey="Yang, Dongyan" sort="Yang, Dongyan" uniqKey="Yang D" first="Dongyan" last="Yang">Dongyan Yang</name><name sortKey="Zhou, Shuang" sort="Zhou, Shuang" uniqKey="Zhou S" first="Shuang" last="Zhou">Shuang Zhou</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/PlantImRecepV1/Data/Main/Exploration
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Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000061 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= PlantImRecepV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:32670328
|texte= Revealing Shared and Distinct Genes Responding to JA and SA Signaling in Arabidopsis by Meta-Analysis.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:32670328" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PlantImRecepV1
| This area was generated with Dilib version V0.6.38. |  |