High-Throughput Sequencing-Based Identification of Arabidopsis miRNAs Induced by Phytophthora capsici Infection.
Identifieur interne : 000171 ( Main/Exploration ); précédent : 000170; suivant : 000172High-Throughput Sequencing-Based Identification of Arabidopsis miRNAs Induced by Phytophthora capsici Infection.
Auteurs : Xiaoguo Zhu [République populaire de Chine] ; Shidan He [République populaire de Chine] ; Di Fang [République populaire de Chine] ; Liang Guo [République populaire de Chine] ; Xiaoyi Zhou [République populaire de Chine] ; Yushuang Guo [République populaire de Chine] ; Lei Gao [République populaire de Chine] ; Yongli Qiao [République populaire de Chine]Source :
- Frontiers in microbiology [ 1664-302X ] ; 2020.
Abstract
MicroRNAs (miRNAs) are a group of small non-coding endogenous RNAs. In plants, miRNAs play vital functions in regulating growth, development, and stress response. However, the role of miRNAs in Arabidopsis-Phytophthora capsici (P. capsici) model pathosystem is poorly understood. Here, we used a high-throughput sequencing approach to identify pathogen-responsive miRNAs using 15 small RNA (sRNA) libraries prepared from Arabidopsis thaliana leaves collected at 0, 3, 6, 12, and 24 h post-inoculation with P. capsici. A total of 293 known miRNAs and 6 potential novel sRNAs (miRNAs or siRNAs) were identified, of which 33 miRNAs were differentially expressed at four different infection stages. To verify the reliability of the sRNA-seq results, we investigated the expression of five sRNAs upregulated throughout the four infection stages and their potential target genes using northern blot analysis and/or stem-loop quantitative real-time polymerase chain reaction (qRT-PCR). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that the potential target genes of the differentially expressed miRNAs, both conserved and novel, were enriched in pathways such as starch and sugar metabolism, spliceosome, and plant-pathogen interaction, indicating that the splicing machinery and pathogenesis-related (PR) proteins play important roles in the response to P. capsici infection. Taken together, these results provide novel insights into the molecular mechanisms of pathogenesis by P. capsici. Additionally, these results will serve as a strong foundation for further in-depth analysis of miRNAs involved in the resistance to Phytophthora species in other crops.
DOI: 10.3389/fmicb.2020.01094
PubMed: 32655510
PubMed Central: PMC7324540
Affiliations:
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Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai</wicri:regionArea><wicri:noRegion>Shanghai</wicri:noRegion></affiliation></author><author><name sortKey="Fang, Di" sort="Fang, Di" uniqKey="Fang D" first="Di" last="Fang">Di Fang</name><affiliation wicri:level="1"><nlm:affiliation>Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai</wicri:regionArea><wicri:noRegion>Shanghai</wicri:noRegion></affiliation></author><author><name sortKey="Guo, Liang" sort="Guo, Liang" uniqKey="Guo L" first="Liang" last="Guo">Liang Guo</name><affiliation wicri:level="1"><nlm:affiliation>Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai</wicri:regionArea><wicri:noRegion>Shanghai</wicri:noRegion></affiliation></author><author><name sortKey="Zhou, Xiaoyi" sort="Zhou, Xiaoyi" uniqKey="Zhou X" first="Xiaoyi" last="Zhou">Xiaoyi Zhou</name><affiliation wicri:level="1"><nlm:affiliation>Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai</wicri:regionArea><wicri:noRegion>Shanghai</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>College of Agriculture, Yangtze University, Jingzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Agriculture, Yangtze University, Jingzhou</wicri:regionArea><wicri:noRegion>Jingzhou</wicri:noRegion></affiliation></author><author><name sortKey="Guo, Yushuang" sort="Guo, Yushuang" uniqKey="Guo Y" first="Yushuang" last="Guo">Yushuang Guo</name><affiliation wicri:level="1"><nlm:affiliation>Laboratory of Molecular Genetics, China National Tobacco Corporation, Guizhou Institute of Tobacco Science, Guiyang, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Laboratory of Molecular Genetics, China National Tobacco Corporation, Guizhou Institute of Tobacco Science, Guiyang</wicri:regionArea><wicri:noRegion>Guiyang</wicri:noRegion></affiliation></author><author><name sortKey="Gao, Lei" sort="Gao, Lei" uniqKey="Gao L" first="Lei" last="Gao">Lei Gao</name><affiliation wicri:level="3"><nlm:affiliation>Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen</wicri:regionArea><placeName><settlement type="city">Shenzhen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Qiao, Yongli" sort="Qiao, Yongli" uniqKey="Qiao Y" first="Yongli" last="Qiao">Yongli Qiao</name><affiliation wicri:level="1"><nlm:affiliation>Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai</wicri:regionArea><wicri:noRegion>Shanghai</wicri:noRegion></affiliation></author></analytic><series><title level="j">Frontiers in microbiology</title><idno type="ISSN">1664-302X</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">MicroRNAs (miRNAs) are a group of small non-coding endogenous RNAs. In plants, miRNAs play vital functions in regulating growth, development, and stress response. However, the role of miRNAs in <i>Arabidopsis</i>-<i>Phytophthora capsici</i> (<i>P. capsici</i>) model pathosystem is poorly understood. Here, we used a high-throughput sequencing approach to identify pathogen-responsive miRNAs using 15 small RNA (sRNA) libraries prepared from <i>Arabidopsis thaliana</i> leaves collected at 0, 3, 6, 12, and 24 h post-inoculation with <i>P. capsici</i>. A total of 293 known miRNAs and 6 potential novel sRNAs (miRNAs or siRNAs) were identified, of which 33 miRNAs were differentially expressed at four different infection stages. To verify the reliability of the sRNA-seq results, we investigated the expression of five sRNAs upregulated throughout the four infection stages and their potential target genes using northern blot analysis and/or stem-loop quantitative real-time polymerase chain reaction (qRT-PCR). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that the potential target genes of the differentially expressed miRNAs, both conserved and novel, were enriched in pathways such as starch and sugar metabolism, spliceosome, and plant-pathogen interaction, indicating that the splicing machinery and pathogenesis-related (PR) proteins play important roles in the response to <i>P. capsici</i> infection. Taken together, these results provide novel insights into the molecular mechanisms of pathogenesis by <i>P. capsici</i>. Additionally, these results will serve as a strong foundation for further in-depth analysis of miRNAs involved in the resistance to <i>Phytophthora</i> species in other crops.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32655510</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>28</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-302X</ISSN><JournalIssue CitedMedium="Print"><Volume>11</Volume><PubDate><Year>2020</Year></PubDate></JournalIssue><Title>Frontiers in microbiology</Title><ISOAbbreviation>Front Microbiol</ISOAbbreviation></Journal><ArticleTitle>High-Throughput Sequencing-Based Identification of Arabidopsis miRNAs Induced by <i>Phytophthora capsici</i> Infection.</ArticleTitle><Pagination><MedlinePgn>1094</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fmicb.2020.01094</ELocationID><Abstract><AbstractText>MicroRNAs (miRNAs) are a group of small non-coding endogenous RNAs. In plants, miRNAs play vital functions in regulating growth, development, and stress response. However, the role of miRNAs in <i>Arabidopsis</i>-<i>Phytophthora capsici</i> (<i>P. capsici</i>) model pathosystem is poorly understood. Here, we used a high-throughput sequencing approach to identify pathogen-responsive miRNAs using 15 small RNA (sRNA) libraries prepared from <i>Arabidopsis thaliana</i> leaves collected at 0, 3, 6, 12, and 24 h post-inoculation with <i>P. capsici</i>. A total of 293 known miRNAs and 6 potential novel sRNAs (miRNAs or siRNAs) were identified, of which 33 miRNAs were differentially expressed at four different infection stages. To verify the reliability of the sRNA-seq results, we investigated the expression of five sRNAs upregulated throughout the four infection stages and their potential target genes using northern blot analysis and/or stem-loop quantitative real-time polymerase chain reaction (qRT-PCR). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that the potential target genes of the differentially expressed miRNAs, both conserved and novel, were enriched in pathways such as starch and sugar metabolism, spliceosome, and plant-pathogen interaction, indicating that the splicing machinery and pathogenesis-related (PR) proteins play important roles in the response to <i>P. capsici</i> infection. Taken together, these results provide novel insights into the molecular mechanisms of pathogenesis by <i>P. capsici</i>. Additionally, these results will serve as a strong foundation for further in-depth analysis of miRNAs involved in the resistance to <i>Phytophthora</i> species in other crops.</AbstractText><CopyrightInformation>Copyright © 2020 Zhu, He, Fang, Guo, Zhou, Guo, Gao and Qiao.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhu</LastName><ForeName>Xiaoguo</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>He</LastName><ForeName>Shidan</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fang</LastName><ForeName>Di</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Guo</LastName><ForeName>Liang</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhou</LastName><ForeName>Xiaoyi</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>College of Agriculture, Yangtze University, Jingzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Guo</LastName><ForeName>Yushuang</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Laboratory of Molecular Genetics, China National Tobacco Corporation, Guizhou Institute of Tobacco Science, Guiyang, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gao</LastName><ForeName>Lei</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Qiao</LastName><ForeName>Yongli</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 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>23</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Microbiol</MedlineTA><NlmUniqueID>101548977</NlmUniqueID><ISSNLinking>1664-302X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Arabidopsis</Keyword><Keyword MajorTopicYN="N">Phytophthora capsici</Keyword><Keyword MajorTopicYN="N">high-throughput sequencing</Keyword><Keyword MajorTopicYN="N">host-pathogen interaction</Keyword><Keyword MajorTopicYN="N">microRNA</Keyword><Keyword MajorTopicYN="N">target gene</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>02</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>05</Month><Day>01</Day></PubMedPubDate><PubMedPubDate 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Chine</li></country><region><li>Guangdong</li></region><settlement><li>Shenzhen</li></settlement></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Zhu, Xiaoguo" sort="Zhu, Xiaoguo" uniqKey="Zhu X" first="Xiaoguo" last="Zhu">Xiaoguo Zhu</name></noRegion><name sortKey="Fang, Di" sort="Fang, Di" uniqKey="Fang D" first="Di" last="Fang">Di Fang</name><name sortKey="Gao, Lei" sort="Gao, Lei" uniqKey="Gao L" first="Lei" last="Gao">Lei Gao</name><name sortKey="Guo, Liang" sort="Guo, Liang" uniqKey="Guo L" first="Liang" last="Guo">Liang Guo</name><name sortKey="Guo, Yushuang" sort="Guo, Yushuang" uniqKey="Guo Y" first="Yushuang" last="Guo">Yushuang Guo</name><name sortKey="He, Shidan" sort="He, Shidan" uniqKey="He S" first="Shidan" last="He">Shidan He</name><name sortKey="Qiao, Yongli" sort="Qiao, Yongli" uniqKey="Qiao Y" first="Yongli" last="Qiao">Yongli Qiao</name><name sortKey="Zhou, Xiaoyi" sort="Zhou, Xiaoyi" uniqKey="Zhou X" first="Xiaoyi" last="Zhou">Xiaoyi Zhou</name><name sortKey="Zhou, Xiaoyi" sort="Zhou, Xiaoyi" uniqKey="Zhou X" first="Xiaoyi" last="Zhou">Xiaoyi Zhou</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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