Genome-Wide Identification of lncRNAs and Analysis of ceRNA Networks During Tomato Resistance to Phytophthora infestans.
Identifieur interne : 000184 ( Main/Exploration ); précédent : 000183; suivant : 000185Genome-Wide Identification of lncRNAs and Analysis of ceRNA Networks During Tomato Resistance to Phytophthora infestans.
Auteurs : Jun Cui [République populaire de Chine] ; Ning Jiang [République populaire de Chine] ; Xinxin Hou [République populaire de Chine] ; Sihan Wu [République populaire de Chine] ; Qiang Zhang [République populaire de Chine] ; Jun Meng ; Yushi Luan [République populaire de Chine]Source :
- Phytopathology [ 0031-949X ] ; 2020.
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Abstract
Our previous studies have revealed the function of long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) in tomato in response to Phytophthora infestans infection. However, the interaction relationships between lncRNAs and miRNAs during tomato resistance to P. infestans infection are unknown. In this study, 9,011 lncRNAs were identified from tomato plants, including 115 upregulated and 81 downregulated lncRNAs. Among these, 148 were found to be differentially expressed and might affect the expression of 771 genes, which are composed of 887 matched lncRNA-mRNA pairs. In total, 88 lncRNAs were identified as endogenous RNAs (ceRNAs) and predicted to decoy 46 miRNAs. Degradome sequencing revealed that 11 miRNAs that were decoyed by 20 lncRNAs could target 30 genes. These lncRNAs, miRNAs, and target genes were predicted to form 10 regulatory modules. Among them, lncRNA42705/lncRNA08711, lncRNA39896, and lncRNA11265/lncRNA15816 might modulate MYB, HD-Zip, and NAC transcription factors by decoying miR159, miR166b, and miR164a-5p, respectively. Upon P. infestans infection, the expression levels of lncRNA42705 and lncRNA08711 displayed a negative correlation with the expression level of miR159 and a positive correlation with the expression levels of MYB genes. Tomato plants in which lncRNA42705 and lncRNA08711 were silenced displayed increased levels of miR159 and decreased levels of MYB, respectively. The result demonstrated that lncRNAs might function as ceRNAs to decoy miRNAs and affect their target genes in tomato plants, increasing resistance to disease.
DOI: 10.1094/PHYTO-04-19-0137-R
PubMed: 31448997
Affiliations:
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University of Technology, Dalian, 116024, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Bioengineering, Dalian University of Technology, Dalian, 116024</wicri:regionArea><wicri:noRegion>116024</wicri:noRegion></affiliation></author><author><name sortKey="Hou, Xinxin" sort="Hou, Xinxin" uniqKey="Hou X" first="Xinxin" last="Hou">Xinxin Hou</name><affiliation wicri:level="1"><nlm:affiliation>School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Bioengineering, Dalian University of Technology, Dalian, 116024</wicri:regionArea><wicri:noRegion>116024</wicri:noRegion></affiliation></author><author><name sortKey="Wu, Sihan" sort="Wu, Sihan" uniqKey="Wu S" first="Sihan" last="Wu">Sihan Wu</name><affiliation wicri:level="1"><nlm:affiliation>School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Bioengineering, Dalian University of Technology, Dalian, 116024</wicri:regionArea><wicri:noRegion>116024</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Qiang" sort="Zhang, Qiang" uniqKey="Zhang Q" first="Qiang" last="Zhang">Qiang Zhang</name><affiliation wicri:level="1"><nlm:affiliation>School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Bioengineering, Dalian University of Technology, Dalian, 116024</wicri:regionArea><wicri:noRegion>116024</wicri:noRegion></affiliation></author><author><name sortKey="Meng, Jun" sort="Meng, Jun" uniqKey="Meng J" first="Jun" last="Meng">Jun Meng</name><affiliation><nlm:affiliation>School of Computer Science and Technology, Dalian University of Technology.</nlm:affiliation><wicri:noCountry code="subField">Dalian University of Technology</wicri:noCountry></affiliation></author><author><name sortKey="Luan, Yushi" sort="Luan, Yushi" uniqKey="Luan Y" first="Yushi" last="Luan">Yushi Luan</name><affiliation wicri:level="1"><nlm:affiliation>School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Bioengineering, Dalian University of Technology, Dalian, 116024</wicri:regionArea><wicri:noRegion>116024</wicri:noRegion></affiliation></author></analytic><series><title level="j">Phytopathology</title><idno type="ISSN">0031-949X</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Gene Expression Regulation, Neoplastic (MeSH)</term><term>Gene Regulatory Networks (MeSH)</term><term>Lycopersicon esculentum (MeSH)</term><term>MicroRNAs (MeSH)</term><term>Phytophthora infestans (MeSH)</term><term>Plant Diseases (MeSH)</term><term>RNA, Long Noncoding (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN long non codant (MeSH)</term><term>Lycopersicon esculentum (MeSH)</term><term>Maladies des plantes (MeSH)</term><term>Phytophthora infestans (MeSH)</term><term>Régulation de l'expression des gènes tumoraux (MeSH)</term><term>Réseaux de régulation génique (MeSH)</term><term>microARN (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>MicroRNAs</term><term>RNA, Long Noncoding</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Regulation, Neoplastic</term><term>Gene Regulatory Networks</term><term>Lycopersicon esculentum</term><term>Phytophthora infestans</term><term>Plant Diseases</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ARN long non codant</term><term>Lycopersicon esculentum</term><term>Maladies des plantes</term><term>Phytophthora infestans</term><term>Régulation de l'expression des gènes tumoraux</term><term>Réseaux de régulation génique</term><term>microARN</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Our previous studies have revealed the function of long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) in tomato in response to <i>Phytophthora infestans</i> infection. However, the interaction relationships between lncRNAs and miRNAs during tomato resistance to <i>P. infestans</i> infection are unknown. In this study, 9,011 lncRNAs were identified from tomato plants, including 115 upregulated and 81 downregulated lncRNAs. Among these, 148 were found to be differentially expressed and might affect the expression of 771 genes, which are composed of 887 matched lncRNA-mRNA pairs. In total, 88 lncRNAs were identified as endogenous RNAs (ceRNAs) and predicted to decoy 46 miRNAs. Degradome sequencing revealed that 11 miRNAs that were decoyed by 20 lncRNAs could target 30 genes. These lncRNAs, miRNAs, and target genes were predicted to form 10 regulatory modules. Among them, lncRNA42705/lncRNA08711, lncRNA39896, and lncRNA11265/lncRNA15816 might modulate MYB, HD-Zip, and NAC transcription factors by decoying miR159, miR166b, and miR164a-5p, respectively. Upon <i>P. infestans</i> infection, the expression levels of lncRNA42705 and lncRNA08711 displayed a negative correlation with the expression level of miR159 and a positive correlation with the expression levels of <i>MYB</i> genes. Tomato plants in which lncRNA42705 and lncRNA08711 were silenced displayed increased levels of miR159 and decreased levels of MYB, respectively. The result demonstrated that lncRNAs might function as ceRNAs to decoy miRNAs and affect their target genes in tomato plants, increasing resistance to disease.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Automated" Owner="NLM"><PMID Version="1">31448997</PMID><DateCompleted><Year>2020</Year><Month>02</Month><Day>21</Day></DateCompleted><DateRevised><Year>2020</Year><Month>02</Month><Day>21</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0031-949X</ISSN><JournalIssue CitedMedium="Print"><Volume>110</Volume><Issue>2</Issue><PubDate><Year>2020</Year><Month>Feb</Month></PubDate></JournalIssue><Title>Phytopathology</Title><ISOAbbreviation>Phytopathology</ISOAbbreviation></Journal><ArticleTitle>Genome-Wide Identification of lncRNAs and Analysis of ceRNA Networks During Tomato Resistance to <i>Phytophthora infestans</i>.</ArticleTitle><Pagination><MedlinePgn>456-464</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1094/PHYTO-04-19-0137-R</ELocationID><Abstract><AbstractText>Our previous studies have revealed the function of long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) in tomato in response to <i>Phytophthora infestans</i> infection. However, the interaction relationships between lncRNAs and miRNAs during tomato resistance to <i>P. infestans</i> infection are unknown. In this study, 9,011 lncRNAs were identified from tomato plants, including 115 upregulated and 81 downregulated lncRNAs. Among these, 148 were found to be differentially expressed and might affect the expression of 771 genes, which are composed of 887 matched lncRNA-mRNA pairs. In total, 88 lncRNAs were identified as endogenous RNAs (ceRNAs) and predicted to decoy 46 miRNAs. Degradome sequencing revealed that 11 miRNAs that were decoyed by 20 lncRNAs could target 30 genes. These lncRNAs, miRNAs, and target genes were predicted to form 10 regulatory modules. Among them, lncRNA42705/lncRNA08711, lncRNA39896, and lncRNA11265/lncRNA15816 might modulate MYB, HD-Zip, and NAC transcription factors by decoying miR159, miR166b, and miR164a-5p, respectively. Upon <i>P. infestans</i> infection, the expression levels of lncRNA42705 and lncRNA08711 displayed a negative correlation with the expression level of miR159 and a positive correlation with the expression levels of <i>MYB</i> genes. Tomato plants in which lncRNA42705 and lncRNA08711 were silenced displayed increased levels of miR159 and decreased levels of MYB, respectively. The result demonstrated that lncRNAs might function as ceRNAs to decoy miRNAs and affect their target genes in tomato plants, increasing resistance to disease.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Cui</LastName><ForeName>Jun</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Ning</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hou</LastName><ForeName>Xinxin</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Sihan</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Qiang</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Meng</LastName><ForeName>Jun</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>School of Computer Science and Technology, Dalian University of Technology.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Luan</LastName><ForeName>Yushi</ForeName><Initials>Y</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-9397-9171</Identifier><AffiliationInfo><Affiliation>School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>11</Month><Day>12</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Phytopathology</MedlineTA><NlmUniqueID>9427222</NlmUniqueID><ISSNLinking>0031-949X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D035683">MicroRNAs</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D062085">RNA, Long Noncoding</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D015972" MajorTopicYN="N">Gene Expression Regulation, Neoplastic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D053263" MajorTopicYN="N">Gene Regulatory Networks</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018551" MajorTopicYN="Y">Lycopersicon esculentum</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D035683" MajorTopicYN="Y">MicroRNAs</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055750" MajorTopicYN="Y">Phytophthora infestans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D062085" MajorTopicYN="Y">RNA, Long Noncoding</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Phytophthora</Keyword><Keyword MajorTopicYN="N">ceRNA</Keyword><Keyword MajorTopicYN="N">genetics and resistance</Keyword><Keyword MajorTopicYN="N">interaction network</Keyword><Keyword MajorTopicYN="N">lncRNA</Keyword><Keyword MajorTopicYN="N">tomato</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>8</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>2</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>8</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31448997</ArticleId><ArticleId IdType="doi">10.1094/PHYTO-04-19-0137-R</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><noCountry><name sortKey="Meng, Jun" sort="Meng, Jun" uniqKey="Meng J" first="Jun" last="Meng">Jun Meng</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Cui, Jun" sort="Cui, Jun" uniqKey="Cui J" first="Jun" last="Cui">Jun Cui</name></noRegion><name sortKey="Hou, Xinxin" sort="Hou, Xinxin" uniqKey="Hou X" first="Xinxin" last="Hou">Xinxin Hou</name><name sortKey="Jiang, Ning" sort="Jiang, Ning" uniqKey="Jiang N" first="Ning" last="Jiang">Ning Jiang</name><name sortKey="Luan, Yushi" sort="Luan, Yushi" uniqKey="Luan Y" first="Yushi" last="Luan">Yushi Luan</name><name sortKey="Wu, Sihan" sort="Wu, Sihan" uniqKey="Wu S" first="Sihan" last="Wu">Sihan Wu</name><name sortKey="Zhang, Qiang" sort="Zhang, Qiang" uniqKey="Zhang Q" first="Qiang" last="Zhang">Qiang Zhang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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