Identification and characterization of novel and conserved microRNAs in radish (Raphanus sativus L.) using high-throughput sequencing.
Identifieur interne : 002643 ( Main/Exploration ); précédent : 002642; suivant : 002644Identification and characterization of novel and conserved microRNAs in radish (Raphanus sativus L.) using high-throughput sequencing.
Auteurs : Liang Xu [République populaire de Chine] ; Yan Wang ; Yuanyuan Xu ; Liangju Wang ; Lulu Zhai ; Xianwen Zhu ; Yiqin Gong ; Shan Ye ; Liwang LiuSource :
- Plant science : an international journal of experimental plant biology [ 1873-2259 ] ; 2013.
Descripteurs français
- KwdFr :
- ARN des plantes (génétique), ARN des plantes (isolement et purification), Alignement de séquences (MeSH), Analyse de séquence d'ARN (MeSH), Banque de gènes (MeSH), Gènes de plante (MeSH), Racines de plante (génétique), Raphanus (génétique), Réaction de polymérisation en chaine en temps réel (MeSH), Spécificité d'espèce (MeSH), Séquence conservée (MeSH), Séquençage nucléotidique à haut débit (méthodes), Transcriptome (MeSH), microARN (génétique), microARN (isolement et purification).
- MESH :
- génétique : ARN des plantes, Racines de plante, Raphanus, microARN.
- isolement et purification : ARN des plantes, microARN.
- méthodes : Séquençage nucléotidique à haut débit.
- Alignement de séquences, Analyse de séquence d'ARN, Banque de gènes, Gènes de plante, Réaction de polymérisation en chaine en temps réel, Spécificité d'espèce, Séquence conservée, Transcriptome.
English descriptors
- KwdEn :
- Conserved Sequence (MeSH), Gene Library (MeSH), Genes, Plant (MeSH), High-Throughput Nucleotide Sequencing (methods), MicroRNAs (genetics), MicroRNAs (isolation & purification), Plant Roots (genetics), RNA, Plant (genetics), RNA, Plant (isolation & purification), Raphanus (genetics), Real-Time Polymerase Chain Reaction (MeSH), Sequence Alignment (MeSH), Sequence Analysis, RNA (MeSH), Species Specificity (MeSH), Transcriptome (MeSH).
- MESH :
- chemical , genetics : MicroRNAs, RNA, Plant.
- chemical , isolation & purification : MicroRNAs, RNA, Plant.
- genetics : Plant Roots, Raphanus.
- methods : High-Throughput Nucleotide Sequencing.
- Conserved Sequence, Gene Library, Genes, Plant, Real-Time Polymerase Chain Reaction, Sequence Alignment, Sequence Analysis, RNA, Species Specificity, Transcriptome.
Abstract
MicroRNAs (miRNAs) are endogenous, non-coding, small RNAs that play significant regulatory roles in plant growth, development, and biotic and abiotic stress responses. To date, a great number of conserved and species-specific miRNAs have been identified in many important plant species such as Arabidopsis, rice and poplar. However, little is known about identification of miRNAs and their target genes in radish (Raphanus sativus L.). In the present study, a small RNA library from radish root was constructed and sequenced using the high-throughput Solexa sequencing. Through sequence alignment and secondary structure prediction, a total of 545 conserved miRNA families as well as 15 novel (with their miRNA* strand) and 64 potentially novel miRNAs were identified. Quantitative real-time PCR (qRT-PCR) analysis confirmed that both conserved and novel miRNAs were expressed in radish, and some of them were preferentially expressed in certain tissues. A total of 196 potential target genes were predicted for 42 novel radish miRNAs. Gene ontology (GO) analysis showed that most of the targets were involved in plant growth, development, metabolism and stress responses. This study represents a first large-scale identification and characterization of radish miRNAs and their potential target genes. These results could lead to the further identification of radish miRNAs and enhance our understanding of radish miRNA regulatory mechanisms in diverse biological and metabolic processes.
DOI: 10.1016/j.plantsci.2012.11.010
PubMed: 23352408
Affiliations:
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College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture; College of Horticulture, Nanjing Agricultural University, Nanjing 210095</wicri:regionArea><wicri:noRegion>Nanjing 210095</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Yan" sort="Wang, Yan" uniqKey="Wang Y" first="Yan" last="Wang">Yan Wang</name></author><author><name sortKey="Xu, Yuanyuan" sort="Xu, Yuanyuan" uniqKey="Xu Y" first="Yuanyuan" last="Xu">Yuanyuan Xu</name></author><author><name sortKey="Wang, Liangju" sort="Wang, Liangju" uniqKey="Wang L" first="Liangju" last="Wang">Liangju Wang</name></author><author><name sortKey="Zhai, Lulu" sort="Zhai, Lulu" uniqKey="Zhai L" first="Lulu" last="Zhai">Lulu Zhai</name></author><author><name sortKey="Zhu, Xianwen" sort="Zhu, Xianwen" uniqKey="Zhu X" first="Xianwen" last="Zhu">Xianwen Zhu</name></author><author><name sortKey="Gong, Yiqin" sort="Gong, Yiqin" uniqKey="Gong Y" first="Yiqin" last="Gong">Yiqin Gong</name></author><author><name sortKey="Ye, Shan" sort="Ye, Shan" uniqKey="Ye S" first="Shan" last="Ye">Shan Ye</name></author><author><name sortKey="Liu, Liwang" sort="Liu, Liwang" uniqKey="Liu L" first="Liwang" last="Liu">Liwang Liu</name></author></analytic><series><title level="j">Plant science : an international journal of experimental plant biology</title><idno type="eISSN">1873-2259</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Conserved Sequence (MeSH)</term><term>Gene Library (MeSH)</term><term>Genes, Plant (MeSH)</term><term>High-Throughput Nucleotide Sequencing (methods)</term><term>MicroRNAs (genetics)</term><term>MicroRNAs (isolation & purification)</term><term>Plant Roots (genetics)</term><term>RNA, Plant (genetics)</term><term>RNA, Plant (isolation & purification)</term><term>Raphanus (genetics)</term><term>Real-Time Polymerase Chain Reaction (MeSH)</term><term>Sequence Alignment (MeSH)</term><term>Sequence Analysis, RNA (MeSH)</term><term>Species Specificity (MeSH)</term><term>Transcriptome (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN des plantes (génétique)</term><term>ARN des plantes (isolement et purification)</term><term>Alignement de séquences (MeSH)</term><term>Analyse de séquence d'ARN (MeSH)</term><term>Banque de gènes (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Racines de plante (génétique)</term><term>Raphanus (génétique)</term><term>Réaction de polymérisation en chaine en temps réel (MeSH)</term><term>Spécificité d'espèce (MeSH)</term><term>Séquence conservée (MeSH)</term><term>Séquençage nucléotidique à haut débit (méthodes)</term><term>Transcriptome (MeSH)</term><term>microARN (génétique)</term><term>microARN (isolement et purification)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>MicroRNAs</term><term>RNA, Plant</term></keywords><keywords scheme="MESH" type="chemical" qualifier="isolation & purification" xml:lang="en"><term>MicroRNAs</term><term>RNA, Plant</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Plant Roots</term><term>Raphanus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN des plantes</term><term>Racines de plante</term><term>Raphanus</term><term>microARN</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>ARN des plantes</term><term>microARN</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Séquençage nucléotidique à haut débit</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Conserved Sequence</term><term>Gene Library</term><term>Genes, Plant</term><term>Real-Time Polymerase Chain Reaction</term><term>Sequence Alignment</term><term>Sequence Analysis, RNA</term><term>Species Specificity</term><term>Transcriptome</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Analyse de séquence d'ARN</term><term>Banque de gènes</term><term>Gènes de plante</term><term>Réaction de polymérisation en chaine en temps réel</term><term>Spécificité d'espèce</term><term>Séquence conservée</term><term>Transcriptome</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">MicroRNAs (miRNAs) are endogenous, non-coding, small RNAs that play significant regulatory roles in plant growth, development, and biotic and abiotic stress responses. To date, a great number of conserved and species-specific miRNAs have been identified in many important plant species such as Arabidopsis, rice and poplar. However, little is known about identification of miRNAs and their target genes in radish (Raphanus sativus L.). In the present study, a small RNA library from radish root was constructed and sequenced using the high-throughput Solexa sequencing. Through sequence alignment and secondary structure prediction, a total of 545 conserved miRNA families as well as 15 novel (with their miRNA* strand) and 64 potentially novel miRNAs were identified. Quantitative real-time PCR (qRT-PCR) analysis confirmed that both conserved and novel miRNAs were expressed in radish, and some of them were preferentially expressed in certain tissues. A total of 196 potential target genes were predicted for 42 novel radish miRNAs. Gene ontology (GO) analysis showed that most of the targets were involved in plant growth, development, metabolism and stress responses. This study represents a first large-scale identification and characterization of radish miRNAs and their potential target genes. These results could lead to the further identification of radish miRNAs and enhance our understanding of radish miRNA regulatory mechanisms in diverse biological and metabolic processes.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23352408</PMID><DateCompleted><Year>2013</Year><Month>07</Month><Day>25</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1873-2259</ISSN><JournalIssue CitedMedium="Internet"><Volume>201-202</Volume><PubDate><Year>2013</Year><Month>Mar</Month></PubDate></JournalIssue><Title>Plant science : an international journal of experimental plant biology</Title><ISOAbbreviation>Plant Sci</ISOAbbreviation></Journal><ArticleTitle>Identification and characterization of novel and conserved microRNAs in radish (Raphanus sativus L.) using high-throughput sequencing.</ArticleTitle><Pagination><MedlinePgn>108-14</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.plantsci.2012.11.010</ELocationID><ELocationID EIdType="pii" ValidYN="Y">S0168-9452(12)00243-9</ELocationID><Abstract><AbstractText>MicroRNAs (miRNAs) are endogenous, non-coding, small RNAs that play significant regulatory roles in plant growth, development, and biotic and abiotic stress responses. To date, a great number of conserved and species-specific miRNAs have been identified in many important plant species such as Arabidopsis, rice and poplar. However, little is known about identification of miRNAs and their target genes in radish (Raphanus sativus L.). In the present study, a small RNA library from radish root was constructed and sequenced using the high-throughput Solexa sequencing. Through sequence alignment and secondary structure prediction, a total of 545 conserved miRNA families as well as 15 novel (with their miRNA* strand) and 64 potentially novel miRNAs were identified. Quantitative real-time PCR (qRT-PCR) analysis confirmed that both conserved and novel miRNAs were expressed in radish, and some of them were preferentially expressed in certain tissues. A total of 196 potential target genes were predicted for 42 novel radish miRNAs. Gene ontology (GO) analysis showed that most of the targets were involved in plant growth, development, metabolism and stress responses. This study represents a first large-scale identification and characterization of radish miRNAs and their potential target genes. These results could lead to the further identification of radish miRNAs and enhance our understanding of radish miRNA regulatory mechanisms in diverse biological and metabolic processes.</AbstractText><CopyrightInformation>Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Liang</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>National Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Yan</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Yuanyuan</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Liangju</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Zhai</LastName><ForeName>Lulu</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Zhu</LastName><ForeName>Xianwen</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Gong</LastName><ForeName>Yiqin</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Ye</LastName><ForeName>Shan</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Liwang</ForeName><Initials>L</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>12</Month><Day>03</Day></ArticleDate></Article><MedlineJournalInfo><Country>Ireland</Country><MedlineTA>Plant Sci</MedlineTA><NlmUniqueID>9882015</NlmUniqueID><ISSNLinking>0168-9452</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D035683">MicroRNAs</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018749">RNA, Plant</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D017124" MajorTopicYN="N">Conserved Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015723" MajorTopicYN="N">Gene Library</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D035683" MajorTopicYN="N">MicroRNAs</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="Y">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018517" MajorTopicYN="N">Plant Roots</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018749" MajorTopicYN="N">RNA, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="Y">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D031224" MajorTopicYN="N">Raphanus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D060888" MajorTopicYN="N">Real-Time Polymerase Chain Reaction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016415" MajorTopicYN="N">Sequence Alignment</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017423" MajorTopicYN="N">Sequence Analysis, RNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013045" MajorTopicYN="N">Species Specificity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059467" MajorTopicYN="N">Transcriptome</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2012</Year><Month>10</Month><Day>11</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2012</Year><Month>11</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2012</Year><Month>11</Month><Day>26</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2013</Year><Month>1</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2013</Year><Month>1</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2013</Year><Month>7</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">23352408</ArticleId><ArticleId IdType="pii">S0168-9452(12)00243-9</ArticleId><ArticleId IdType="doi">10.1016/j.plantsci.2012.11.010</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><noCountry><name sortKey="Gong, Yiqin" sort="Gong, Yiqin" uniqKey="Gong Y" first="Yiqin" last="Gong">Yiqin Gong</name><name sortKey="Liu, Liwang" sort="Liu, Liwang" uniqKey="Liu L" first="Liwang" last="Liu">Liwang Liu</name><name sortKey="Wang, Liangju" sort="Wang, Liangju" uniqKey="Wang L" first="Liangju" last="Wang">Liangju Wang</name><name sortKey="Wang, Yan" sort="Wang, Yan" uniqKey="Wang Y" first="Yan" last="Wang">Yan Wang</name><name sortKey="Xu, Yuanyuan" sort="Xu, Yuanyuan" uniqKey="Xu Y" first="Yuanyuan" last="Xu">Yuanyuan Xu</name><name sortKey="Ye, Shan" sort="Ye, Shan" uniqKey="Ye S" first="Shan" last="Ye">Shan Ye</name><name sortKey="Zhai, Lulu" sort="Zhai, Lulu" uniqKey="Zhai L" first="Lulu" last="Zhai">Lulu Zhai</name><name sortKey="Zhu, Xianwen" sort="Zhu, Xianwen" uniqKey="Zhu X" first="Xianwen" last="Zhu">Xianwen Zhu</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Xu, Liang" sort="Xu, Liang" uniqKey="Xu L" first="Liang" last="Xu">Liang Xu</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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