High-throughput sequencing discovery of conserved and novel microRNAs in Chinese cabbage (Brassica rapa L. ssp. pekinensis).
Identifieur interne : 002A44 ( Main/Exploration ); précédent : 002A43; suivant : 002A45High-throughput sequencing discovery of conserved and novel microRNAs in Chinese cabbage (Brassica rapa L. ssp. pekinensis).
Auteurs : Fengde Wang [République populaire de Chine] ; Libin Li ; Lifeng Liu ; Huayin Li ; Yihui Zhang ; Yingyin Yao ; Zhongfu Ni ; Jianwei GaoSource :
- Molecular genetics and genomics : MGG [ 1617-4623 ] ; 2012.
Descripteurs français
- KwdFr :
- ADN complémentaire (composition chimique), ADN complémentaire (génétique), ARN des plantes (génétique), Analyse de séquence d'ADN (méthodes), Banque de gènes (MeSH), Brassica rapa (génétique), Données de séquences moléculaires (MeSH), RT-PCR (MeSH), Régulation de l'expression des gènes végétaux (MeSH), Séquence conservée (génétique), Séquence nucléotidique (MeSH), Séquençage nucléotidique à haut débit (méthodes), microARN (génétique).
- MESH :
- composition chimique : ADN complémentaire.
- génétique : ADN complémentaire, ARN des plantes, Brassica rapa, Séquence conservée, microARN.
- méthodes : Analyse de séquence d'ADN, Séquençage nucléotidique à haut débit.
- Banque de gènes, Données de séquences moléculaires, RT-PCR, Régulation de l'expression des gènes végétaux, Séquence nucléotidique.
English descriptors
- KwdEn :
- Base Sequence (MeSH), Brassica rapa (genetics), Conserved Sequence (genetics), DNA, Complementary (chemistry), DNA, Complementary (genetics), Gene Expression Regulation, Plant (MeSH), Gene Library (MeSH), High-Throughput Nucleotide Sequencing (methods), MicroRNAs (genetics), Molecular Sequence Data (MeSH), RNA, Plant (genetics), Reverse Transcriptase Polymerase Chain Reaction (MeSH), Sequence Analysis, DNA (methods).
- MESH :
- chemical , chemistry : DNA, Complementary.
- genetics : Brassica rapa, Conserved Sequence, DNA, Complementary, MicroRNAs, RNA, Plant.
- methods : High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA.
- Base Sequence, Gene Expression Regulation, Plant, Gene Library, Molecular Sequence Data, Reverse Transcriptase Polymerase Chain Reaction.
Abstract
MicroRNAs (miRNAs) are a class of 21-24 nucleotide non-coding RNAs that down-regulate gene expression by cleaving or inhibiting the translation of target gene transcripts. miRNAs have been extensively analyzed in a few model plant species such as Arabidopsis, rice and Populus, and partially investigated in other non-model plant species. However, only a few conserved miRNAs have been identified in Chinese cabbage, a common and economically important crop in Asia. To identify novel and conserved miRNAs in Chinese cabbage (Brassica rapa L. ssp. pekinensis) we constructed a small RNA library. Using high-throughput Solexa sequencing to identify microRNAs we found 11,210 unique sequences belonging to 321 conserved miRNA families and 228 novel miRNAs. We ran a Blast search with these sequences against the Chinese cabbage mRNA database and found 2,308 and 736 potential target genes for 221 conserved and 125 novel miRNAs, respectively. The BlastX search against the Arabidopsis genome and GO analysis suggested most of the targets were involved in plant growth, metabolism, development and stress response. This study provides the first large scale-cloning and characterization of Chinese cabbage miRNAs and their potential targets. These miRNAs add to the growing database of new miRNAs, prompt further study on Chinese cabbage miRNA regulation mechanisms, and help toward a greater understanding of the important roles of miRNAs in Chinese cabbage.
DOI: 10.1007/s00438-012-0699-3
PubMed: 22643909
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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sort="Ni, Zhongfu" uniqKey="Ni Z" first="Zhongfu" last="Ni">Zhongfu Ni</name></author><author><name sortKey="Gao, Jianwei" sort="Gao, Jianwei" uniqKey="Gao J" first="Jianwei" last="Gao">Jianwei Gao</name></author></analytic><series><title level="j">Molecular genetics and genomics : MGG</title><idno type="eISSN">1617-4623</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence (MeSH)</term><term>Brassica rapa (genetics)</term><term>Conserved Sequence (genetics)</term><term>DNA, Complementary (chemistry)</term><term>DNA, Complementary (genetics)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Gene Library (MeSH)</term><term>High-Throughput Nucleotide Sequencing (methods)</term><term>MicroRNAs (genetics)</term><term>Molecular Sequence Data (MeSH)</term><term>RNA, Plant (genetics)</term><term>Reverse Transcriptase Polymerase Chain 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However, only a few conserved miRNAs have been identified in Chinese cabbage, a common and economically important crop in Asia. To identify novel and conserved miRNAs in Chinese cabbage (Brassica rapa L. ssp. pekinensis) we constructed a small RNA library. Using high-throughput Solexa sequencing to identify microRNAs we found 11,210 unique sequences belonging to 321 conserved miRNA families and 228 novel miRNAs. We ran a Blast search with these sequences against the Chinese cabbage mRNA database and found 2,308 and 736 potential target genes for 221 conserved and 125 novel miRNAs, respectively. The BlastX search against the Arabidopsis genome and GO analysis suggested most of the targets were involved in plant growth, metabolism, development and stress response. This study provides the first large scale-cloning and characterization of Chinese cabbage miRNAs and their potential targets. These miRNAs add to the growing database of new miRNAs, prompt further study on Chinese cabbage miRNA regulation mechanisms, and help toward a greater understanding of the important roles of miRNAs in Chinese cabbage.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22643909</PMID><DateCompleted><Year>2012</Year><Month>09</Month><Day>07</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1617-4623</ISSN><JournalIssue CitedMedium="Internet"><Volume>287</Volume><Issue>7</Issue><PubDate><Year>2012</Year><Month>Jul</Month></PubDate></JournalIssue><Title>Molecular genetics and genomics : MGG</Title><ISOAbbreviation>Mol Genet Genomics</ISOAbbreviation></Journal><ArticleTitle>High-throughput sequencing discovery of conserved and novel microRNAs in Chinese cabbage (Brassica rapa L. ssp. pekinensis).</ArticleTitle><Pagination><MedlinePgn>555-63</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00438-012-0699-3</ELocationID><Abstract><AbstractText>MicroRNAs (miRNAs) are a class of 21-24 nucleotide non-coding RNAs that down-regulate gene expression by cleaving or inhibiting the translation of target gene transcripts. miRNAs have been extensively analyzed in a few model plant species such as Arabidopsis, rice and Populus, and partially investigated in other non-model plant species. However, only a few conserved miRNAs have been identified in Chinese cabbage, a common and economically important crop in Asia. To identify novel and conserved miRNAs in Chinese cabbage (Brassica rapa L. ssp. pekinensis) we constructed a small RNA library. Using high-throughput Solexa sequencing to identify microRNAs we found 11,210 unique sequences belonging to 321 conserved miRNA families and 228 novel miRNAs. We ran a Blast search with these sequences against the Chinese cabbage mRNA database and found 2,308 and 736 potential target genes for 221 conserved and 125 novel miRNAs, respectively. The BlastX search against the Arabidopsis genome and GO analysis suggested most of the targets were involved in plant growth, metabolism, development and stress response. This study provides the first large scale-cloning and characterization of Chinese cabbage miRNAs and their potential targets. These miRNAs add to the growing database of new miRNAs, prompt further study on Chinese cabbage miRNA regulation mechanisms, and help toward a greater understanding of the important roles of miRNAs in Chinese cabbage.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Fengde</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Institute of Vegetables, Shandong Academy of Agricultural Sciences Shandong, Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Jinan 250100, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Libin</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Lifeng</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Huayin</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Yihui</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Yao</LastName><ForeName>Yingyin</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Ni</LastName><ForeName>Zhongfu</ForeName><Initials>Z</Initials></Author><Author ValidYN="Y"><LastName>Gao</LastName><ForeName>Jianwei</ForeName><Initials>J</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2012</Year><Month>05</Month><Day>29</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Mol Genet Genomics</MedlineTA><NlmUniqueID>101093320</NlmUniqueID><ISSNLinking>1617-4623</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance 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uniqKey="Li H" first="Huayin" last="Li">Huayin Li</name><name sortKey="Li, Libin" sort="Li, Libin" uniqKey="Li L" first="Libin" last="Li">Libin Li</name><name sortKey="Liu, Lifeng" sort="Liu, Lifeng" uniqKey="Liu L" first="Lifeng" last="Liu">Lifeng Liu</name><name sortKey="Ni, Zhongfu" sort="Ni, Zhongfu" uniqKey="Ni Z" first="Zhongfu" last="Ni">Zhongfu Ni</name><name sortKey="Yao, Yingyin" sort="Yao, Yingyin" uniqKey="Yao Y" first="Yingyin" last="Yao">Yingyin Yao</name><name sortKey="Zhang, Yihui" sort="Zhang, Yihui" uniqKey="Zhang Y" first="Yihui" last="Zhang">Yihui Zhang</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Wang, Fengde" sort="Wang, Fengde" uniqKey="Wang F" first="Fengde" last="Wang">Fengde Wang</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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