Integrative analysis of the RNA interference toolbox in two Salicaceae willow species, and their roles in stress response in poplar (Populus trichocarpa Torr. & Gray).
Identifieur interne : 000312 ( Main/Exploration ); précédent : 000311; suivant : 000313Integrative analysis of the RNA interference toolbox in two Salicaceae willow species, and their roles in stress response in poplar (Populus trichocarpa Torr. & Gray).
Auteurs : Yunpeng Cao [République populaire de Chine] ; Xiangqin Xu [République populaire de Chine] ; Lan Jiang [République populaire de Chine]Source :
- International journal of biological macromolecules [ 1879-0003 ] ; 2020.
Abstract
Regulation of gene expression related to chromatin modification at the transcriptional silencing and RNA interference (RNAi) at the post-transcriptional level. RNA-dependent RNA polymerase (RDR) and Argonaute (AGO), along with Dicer-like (DCL) from the core components of RNAi, play integral roles in these processes. Here, 14 PtAGOs, 5 PtDCLs, and 9 PtRDRs were identified in P. trichocarpa and compared them with those of another Salicaceae willow (Salix suchowensis Cheng). Maximum-likelihood trees revealed that each AGO, DCL, and RDR family members were divided into four subfamilies. Forty-three orthologous pairs were identified between the P. trichocarpa and S. suchowensis RNAi-toolbox genes. Sixteen collinear gene pairs were detected in highly microsynteny regions with containing more than ten pairs of conserved flanking-genes, indicated that they were considered to have evolved from the large-scale duplication events. Many of the RNAi-toolbox genes were up-regulated, suggesting P. trichocarpa should have evolved specialized regulatory mechanisms in response to cold, salt, drought and heat stresses. Some RNAi-toolbox genes were most highly expressed in stem, suggesting these genes may function in the regulation of small RNAs during P. trichocarpa stem development. Our results provided the integrative analysis and highlighted the function and duplication of the RNAi-toolbox genes in P. trichocarpa.
DOI: 10.1016/j.ijbiomac.2020.06.235
PubMed: 32599244
Affiliations:
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Electronic address: xfcypeng@126.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, Hunan, China; Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, Hunan</wicri:regionArea><wicri:noRegion>Hunan</wicri:noRegion></affiliation></author><author><name sortKey="Xu, Xiangqin" sort="Xu, Xiangqin" uniqKey="Xu X" first="Xiangqin" last="Xu">Xiangqin Xu</name><affiliation wicri:level="1"><nlm:affiliation>College of Chemistry and Biological Engineering, Hunan University of Science and Engineering, Yongzhou 425000, Hunan, China.. 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Electronic address: xfcypeng@126.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, Hunan, China; Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, Hunan</wicri:regionArea><wicri:noRegion>Hunan</wicri:noRegion></affiliation></author><author><name sortKey="Xu, Xiangqin" sort="Xu, Xiangqin" uniqKey="Xu X" first="Xiangqin" last="Xu">Xiangqin Xu</name><affiliation wicri:level="1"><nlm:affiliation>College of Chemistry and Biological Engineering, Hunan University of Science and Engineering, Yongzhou 425000, Hunan, China.. Electronic address: 5067093226@qq.com.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>College of Chemistry and Biological Engineering, Hunan University of Science and Engineering, Yongzhou 425000, Hunan</wicri:regionArea><wicri:noRegion>Hunan</wicri:noRegion></affiliation></author><author><name sortKey="Jiang, Lan" sort="Jiang, Lan" uniqKey="Jiang L" first="Lan" last="Jiang">Lan Jiang</name><affiliation wicri:level="1"><nlm:affiliation>Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu 241001, China. Electronic address: jianglanhi@163.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu 241001</wicri:regionArea><wicri:noRegion>Wuhu 241001</wicri:noRegion></affiliation></author></analytic><series><title level="j">International journal of biological macromolecules</title><idno type="eISSN">1879-0003</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">Regulation of gene expression related to chromatin modification at the transcriptional silencing and RNA interference (RNAi) at the post-transcriptional level. RNA-dependent RNA polymerase (RDR) and Argonaute (AGO), along with Dicer-like (DCL) from the core components of RNAi, play integral roles in these processes. Here, 14 PtAGOs, 5 PtDCLs, and 9 PtRDRs were identified in P. trichocarpa and compared them with those of another Salicaceae willow (Salix suchowensis Cheng). Maximum-likelihood trees revealed that each AGO, DCL, and RDR family members were divided into four subfamilies. Forty-three orthologous pairs were identified between the P. trichocarpa and S. suchowensis RNAi-toolbox genes. Sixteen collinear gene pairs were detected in highly microsynteny regions with containing more than ten pairs of conserved flanking-genes, indicated that they were considered to have evolved from the large-scale duplication events. Many of the RNAi-toolbox genes were up-regulated, suggesting P. trichocarpa should have evolved specialized regulatory mechanisms in response to cold, salt, drought and heat stresses. Some RNAi-toolbox genes were most highly expressed in stem, suggesting these genes may function in the regulation of small RNAs during P. trichocarpa stem development. Our results provided the integrative analysis and highlighted the function and duplication of the RNAi-toolbox genes in P. trichocarpa.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">32599244</PMID><DateRevised><Year>2020</Year><Month>10</Month><Day>06</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1879-0003</ISSN><JournalIssue CitedMedium="Internet"><Volume>162</Volume><PubDate><Year>2020</Year><Month>Nov</Month><Day>01</Day></PubDate></JournalIssue><Title>International journal of biological macromolecules</Title><ISOAbbreviation>Int J Biol Macromol</ISOAbbreviation></Journal><ArticleTitle>Integrative analysis of the RNA interference toolbox in two Salicaceae willow species, and their roles in stress response in poplar (Populus trichocarpa Torr. & Gray).</ArticleTitle><Pagination><MedlinePgn>1127-1139</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S0141-8130(20)33688-6</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.ijbiomac.2020.06.235</ELocationID><Abstract><AbstractText>Regulation of gene expression related to chromatin modification at the transcriptional silencing and RNA interference (RNAi) at the post-transcriptional level. RNA-dependent RNA polymerase (RDR) and Argonaute (AGO), along with Dicer-like (DCL) from the core components of RNAi, play integral roles in these processes. Here, 14 PtAGOs, 5 PtDCLs, and 9 PtRDRs were identified in P. trichocarpa and compared them with those of another Salicaceae willow (Salix suchowensis Cheng). Maximum-likelihood trees revealed that each AGO, DCL, and RDR family members were divided into four subfamilies. Forty-three orthologous pairs were identified between the P. trichocarpa and S. suchowensis RNAi-toolbox genes. Sixteen collinear gene pairs were detected in highly microsynteny regions with containing more than ten pairs of conserved flanking-genes, indicated that they were considered to have evolved from the large-scale duplication events. Many of the RNAi-toolbox genes were up-regulated, suggesting P. trichocarpa should have evolved specialized regulatory mechanisms in response to cold, salt, drought and heat stresses. Some RNAi-toolbox genes were most highly expressed in stem, suggesting these genes may function in the regulation of small RNAs during P. trichocarpa stem development. Our results provided the integrative analysis and highlighted the function and duplication of the RNAi-toolbox genes in P. trichocarpa.</AbstractText><CopyrightInformation>Copyright © 2020. Published by Elsevier B.V.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Cao</LastName><ForeName>Yunpeng</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, Hunan, China; Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, Hunan, China. Electronic address: xfcypeng@126.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Xiangqin</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>College of Chemistry and Biological Engineering, Hunan University of Science and Engineering, Yongzhou 425000, Hunan, China.. Electronic address: 5067093226@qq.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Lan</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu 241001, China. Electronic address: jianglanhi@163.com.</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>Netherlands</Country><MedlineTA>Int J Biol Macromol</MedlineTA><NlmUniqueID>7909578</NlmUniqueID><ISSNLinking>0141-8130</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Expression</Keyword><Keyword MajorTopicYN="N">Phylogenetic analysis</Keyword><Keyword MajorTopicYN="N">Populus trichocarpa</Keyword><Keyword MajorTopicYN="N">RNAi-toolbox genes</Keyword></KeywordList><CoiStatement>Declaration of competing interest The authors declare that they have no competing interests.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>04</Month><Day>28</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>05</Month><Day>31</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>06</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>7</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>7</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>6</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32599244</ArticleId><ArticleId IdType="pii">S0141-8130(20)33688-6</ArticleId><ArticleId IdType="doi">10.1016/j.ijbiomac.2020.06.235</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Cao, Yunpeng" sort="Cao, Yunpeng" uniqKey="Cao Y" first="Yunpeng" last="Cao">Yunpeng Cao</name></noRegion><name sortKey="Jiang, Lan" sort="Jiang, Lan" uniqKey="Jiang L" first="Lan" last="Jiang">Lan Jiang</name><name sortKey="Xu, Xiangqin" sort="Xu, Xiangqin" uniqKey="Xu X" first="Xiangqin" last="Xu">Xiangqin Xu</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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