In silico identification and computational characterization of endogenous small interfering RNAs from diverse grapevine tissues and stages.
Identifieur interne : 000242 ( Main/Corpus ); précédent : 000241; suivant : 000243In silico identification and computational characterization of endogenous small interfering RNAs from diverse grapevine tissues and stages.
Auteurs : Xudong Zhu ; Songtao Jiu ; Xiaopeng Li ; Kekun Zhang ; Mengqi Wang ; Chen Wang ; Jinggui FangSource :
- Genes & genomics [ 2092-9293 ] ; 2018.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : MicroRNAs, Plant Proteins, RNA, Plant, RNA, Small Interfering.
- genetics : Vitis.
- growth & development : Vitis.
- Computational Biology, Computer Simulation, Gene Expression Regulation, Plant.
Abstract
Small interfering RNAs (siRNAs) are effectors of regulatory pathways underlying plant development, metabolism, and stress- and nutrient-signaling regulatory networks. The endogenous siRNAs are generally not conserved between plants; consequently, it is necessary and important to identify and characterize siRNAs from various plants. To address the nature and functions of siRNAs, and understand the biological roles of the huge siRNA population in grapevine (Vitis vinifera L.). The high-throughput sequencing technology was used to identify a large set of putative endogenous siRNAs from six grapevine tissues/organs. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed to classify the target genes of siRNA. In total, 520,519 candidate siRNAs were identified and their expression profiles exhibited typical temporal characters during grapevine development. In addition, we identified two grapevine trans-acting siRNA (TAS) gene homologs (VvTAS3 and VvTAS4) and the derived trans-acting siRNAs (tasiRNAs) that could target grapevine auxin response factor (ARF) and myeloblastosis (MYB) genes. Furthermore, the GO and KEGG analysis of target genes showed that most of them covered a broad range of functional categories, especially involving in disease-resistance process. The large-scale and completely genome-wide level identification and characterization of grapevine endogenous siRNAs from the diverse tissues by high throughput technology revealed the nature and functions of siRNAs in grapevine.
DOI: 10.1007/s13258-018-0679-z
PubMed: 30047108
Links to Exploration step
pubmed:30047108Le document en format XML
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Nanjing, 210095, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Kekun" sort="Zhang, Kekun" uniqKey="Zhang K" first="Kekun" last="Zhang">Kekun Zhang</name><affiliation><nlm:affiliation>College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Mengqi" sort="Wang, Mengqi" uniqKey="Wang M" first="Mengqi" last="Wang">Mengqi Wang</name><affiliation><nlm:affiliation>College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Chen" sort="Wang, Chen" uniqKey="Wang C" first="Chen" last="Wang">Chen Wang</name><affiliation><nlm:affiliation>College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China.</nlm:affiliation></affiliation></author><author><name sortKey="Fang, Jinggui" sort="Fang, Jinggui" uniqKey="Fang J" first="Jinggui" last="Fang">Jinggui Fang</name><affiliation><nlm:affiliation>College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China. fanggg@njau.edu.cn.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2018">2018</date><idno type="RBID">pubmed:30047108</idno><idno type="pmid">30047108</idno><idno type="doi">10.1007/s13258-018-0679-z</idno><idno type="wicri:Area/Main/Corpus">000242</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000242</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">In silico identification and computational characterization of endogenous small interfering RNAs from diverse grapevine tissues and stages.</title><author><name sortKey="Zhu, Xudong" sort="Zhu, Xudong" uniqKey="Zhu X" first="Xudong" last="Zhu">Xudong Zhu</name><affiliation><nlm:affiliation>College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China.</nlm:affiliation></affiliation></author><author><name sortKey="Jiu, Songtao" sort="Jiu, Songtao" uniqKey="Jiu S" first="Songtao" last="Jiu">Songtao Jiu</name><affiliation><nlm:affiliation>College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China.</nlm:affiliation></affiliation></author><author><name sortKey="Li, Xiaopeng" sort="Li, Xiaopeng" uniqKey="Li X" first="Xiaopeng" last="Li">Xiaopeng Li</name><affiliation><nlm:affiliation>College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Kekun" sort="Zhang, Kekun" uniqKey="Zhang K" first="Kekun" last="Zhang">Kekun Zhang</name><affiliation><nlm:affiliation>College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Mengqi" sort="Wang, Mengqi" uniqKey="Wang M" first="Mengqi" last="Wang">Mengqi Wang</name><affiliation><nlm:affiliation>College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Chen" sort="Wang, Chen" uniqKey="Wang C" first="Chen" last="Wang">Chen Wang</name><affiliation><nlm:affiliation>College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China.</nlm:affiliation></affiliation></author><author><name sortKey="Fang, Jinggui" sort="Fang, Jinggui" uniqKey="Fang J" first="Jinggui" last="Fang">Jinggui Fang</name><affiliation><nlm:affiliation>College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China. fanggg@njau.edu.cn.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Genes & genomics</title><idno type="eISSN">2092-9293</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology (MeSH)</term><term>Computer Simulation (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>MicroRNAs (genetics)</term><term>Plant Proteins (genetics)</term><term>RNA, Plant (genetics)</term><term>RNA, Small Interfering (genetics)</term><term>Vitis (genetics)</term><term>Vitis (growth & development)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>MicroRNAs</term><term>Plant Proteins</term><term>RNA, Plant</term><term>RNA, Small Interfering</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Vitis</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Vitis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computational Biology</term><term>Computer Simulation</term><term>Gene Expression Regulation, Plant</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Small interfering RNAs (siRNAs) are effectors of regulatory pathways underlying plant development, metabolism, and stress- and nutrient-signaling regulatory networks. The endogenous siRNAs are generally not conserved between plants; consequently, it is necessary and important to identify and characterize siRNAs from various plants. To address the nature and functions of siRNAs, and understand the biological roles of the huge siRNA population in grapevine (Vitis vinifera L.). The high-throughput sequencing technology was used to identify a large set of putative endogenous siRNAs from six grapevine tissues/organs. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed to classify the target genes of siRNA. In total, 520,519 candidate siRNAs were identified and their expression profiles exhibited typical temporal characters during grapevine development. In addition, we identified two grapevine trans-acting siRNA (TAS) gene homologs (VvTAS3 and VvTAS4) and the derived trans-acting siRNAs (tasiRNAs) that could target grapevine auxin response factor (ARF) and myeloblastosis (MYB) genes. Furthermore, the GO and KEGG analysis of target genes showed that most of them covered a broad range of functional categories, especially involving in disease-resistance process. The large-scale and completely genome-wide level identification and characterization of grapevine endogenous siRNAs from the diverse tissues by high throughput technology revealed the nature and functions of siRNAs in grapevine.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30047108</PMID><DateCompleted><Year>2018</Year><Month>10</Month><Day>24</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>14</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">2092-9293</ISSN><JournalIssue CitedMedium="Internet"><Volume>40</Volume><Issue>8</Issue><PubDate><Year>2018</Year><Month>08</Month></PubDate></JournalIssue><Title>Genes & genomics</Title><ISOAbbreviation>Genes Genomics</ISOAbbreviation></Journal><ArticleTitle>In silico identification and computational characterization of endogenous small interfering RNAs from diverse grapevine tissues and stages.</ArticleTitle><Pagination><MedlinePgn>801-817</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s13258-018-0679-z</ELocationID><Abstract><AbstractText>Small interfering RNAs (siRNAs) are effectors of regulatory pathways underlying plant development, metabolism, and stress- and nutrient-signaling regulatory networks. The endogenous siRNAs are generally not conserved between plants; consequently, it is necessary and important to identify and characterize siRNAs from various plants. To address the nature and functions of siRNAs, and understand the biological roles of the huge siRNA population in grapevine (Vitis vinifera L.). The high-throughput sequencing technology was used to identify a large set of putative endogenous siRNAs from six grapevine tissues/organs. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed to classify the target genes of siRNA. In total, 520,519 candidate siRNAs were identified and their expression profiles exhibited typical temporal characters during grapevine development. In addition, we identified two grapevine trans-acting siRNA (TAS) gene homologs (VvTAS3 and VvTAS4) and the derived trans-acting siRNAs (tasiRNAs) that could target grapevine auxin response factor (ARF) and myeloblastosis (MYB) genes. Furthermore, the GO and KEGG analysis of target genes showed that most of them covered a broad range of functional categories, especially involving in disease-resistance process. The large-scale and completely genome-wide level identification and characterization of grapevine endogenous siRNAs from the diverse tissues by high throughput technology revealed the nature and functions of siRNAs in grapevine.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhu</LastName><ForeName>Xudong</ForeName><Initials>X</Initials><Identifier Source="ORCID">0000-0003-0110-2423</Identifier><AffiliationInfo><Affiliation>College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jiu</LastName><ForeName>Songtao</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Xiaopeng</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Kekun</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Mengqi</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Chen</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fang</LastName><ForeName>Jinggui</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China. fanggg@njau.edu.cn.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>31672131</GrantID><Agency>National Natural Science Foundation of China</Agency><Country>International</Country></Grant><Grant><GrantID>31401846</GrantID><Agency>National Natural Science Foundation of China</Agency><Country>International</Country></Grant><Grant><GrantID>31301759</GrantID><Agency>Natural Science Foundation of China</Agency><Country>International</Country></Grant><Grant><GrantID>2016M590465</GrantID><Agency>China Postdoctoral Science Foundation Funded Project</Agency><Country>International</Country></Grant><Grant><GrantID>ZW2014009</GrantID><Agency>Opening Project of State Key Laboratory of Crop Genetics and Germplasm Enhancement</Agency><Country>International</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>04</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>Korea (South)</Country><MedlineTA>Genes Genomics</MedlineTA><NlmUniqueID>101481027</NlmUniqueID><ISSNLinking>1976-9571</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D035683">MicroRNAs</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018749">RNA, Plant</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D034741">RNA, Small 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|area= GrapevineDiseaseV1
|flux= Main
|étape= Corpus
|type= RBID
|clé= pubmed:30047108
|texte= In silico identification and computational characterization of endogenous small interfering RNAs from diverse grapevine tissues and stages.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Corpus/RBID.i -Sk "pubmed:30047108" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Corpus/biblio.hfd \
| NlmPubMed2Wicri -a GrapevineDiseaseV1
| This area was generated with Dilib version V0.6.37. |  |