Identification and Characterization of MicroRNAs in the Leaf of Ma Bamboo (Dendrocalamus latiflorus) by Deep Sequencing
Identifieur interne : 000E24 ( Main/Merge ); précédent : 000E23; suivant : 000E25Identification and Characterization of MicroRNAs in the Leaf of Ma Bamboo (Dendrocalamus latiflorus) by Deep Sequencing
Auteurs : Hansheng Zhao [République populaire de Chine] ; Dongliang Chen [République populaire de Chine] ; Zhenhua Peng [République populaire de Chine] ; Lili Wang [République populaire de Chine] ; Zhimin Gao [République populaire de Chine]Source :
- PLoS ONE [ 1932-6203 ] ; 2013.
Abstract
MicroRNAs (miRNAs), a class of non-coding small endogenous RNAs of approximately 22 nucleotides, regulate gene expression at the post-transcriptional levels by targeting mRNAs for degradation or by inhibiting protein translation. Thousands of miRNAs have been identified in many species. However, there is no information available concerning miRNAs in ma bamboo (
Url:
DOI: 10.1371/journal.pone.0078755
PubMed: 24205306
PubMed Central: 3804618
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PMC:3804618Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Identification and Characterization of MicroRNAs in the Leaf of Ma Bamboo (<italic>Dendrocalamus latiflorus</italic>) by Deep Sequencing</title><author><name sortKey="Zhao, Hansheng" sort="Zhao, Hansheng" uniqKey="Zhao H" first="Hansheng" last="Zhao">Hansheng Zhao</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo, Rattan, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo, Rattan, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Chen, Dongliang" sort="Chen, Dongliang" uniqKey="Chen D" first="Dongliang" last="Chen">Dongliang Chen</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo, Rattan, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo, Rattan, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Peng, Zhenhua" sort="Peng, Zhenhua" uniqKey="Peng Z" first="Zhenhua" last="Peng">Zhenhua Peng</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo, Rattan, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo, Rattan, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Research Institute of Forestry, Chinese Academy of Forestry, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Wang, Lili" sort="Wang, Lili" uniqKey="Wang L" first="Lili" last="Wang">Lili Wang</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo, Rattan, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo, Rattan, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Gao, Zhimin" sort="Gao, Zhimin" uniqKey="Gao Z" first="Zhimin" last="Gao">Zhimin Gao</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo, Rattan, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo, Rattan, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24205306</idno><idno type="pmc">3804618</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3804618</idno><idno type="RBID">PMC:3804618</idno><idno type="doi">10.1371/journal.pone.0078755</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">001171</idno><idno type="wicri:Area/Pmc/Curation">001170</idno><idno type="wicri:Area/Pmc/Checkpoint">000A53</idno><idno type="wicri:Area/Ncbi/Merge">001481</idno><idno type="wicri:Area/Ncbi/Curation">001481</idno><idno type="wicri:Area/Ncbi/Checkpoint">001481</idno><idno type="wicri:Area/Main/Merge">000E24</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Identification and Characterization of MicroRNAs in the Leaf of Ma Bamboo (<italic>Dendrocalamus latiflorus</italic>) by Deep Sequencing</title><author><name sortKey="Zhao, Hansheng" sort="Zhao, Hansheng" uniqKey="Zhao H" first="Hansheng" last="Zhao">Hansheng Zhao</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo, Rattan, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo, Rattan, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Chen, Dongliang" sort="Chen, Dongliang" uniqKey="Chen D" first="Dongliang" last="Chen">Dongliang Chen</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo, Rattan, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo, Rattan, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Peng, Zhenhua" sort="Peng, Zhenhua" uniqKey="Peng Z" first="Zhenhua" last="Peng">Zhenhua Peng</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo, Rattan, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo, Rattan, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Research Institute of Forestry, Chinese Academy of Forestry, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Wang, Lili" sort="Wang, Lili" uniqKey="Wang L" first="Lili" last="Wang">Lili Wang</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo, Rattan, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo, Rattan, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Gao, Zhimin" sort="Gao, Zhimin" uniqKey="Gao Z" first="Zhimin" last="Gao">Zhimin Gao</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo, Rattan, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo, Rattan, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>MicroRNAs (miRNAs), a class of non-coding small endogenous RNAs of approximately 22 nucleotides, regulate gene expression at the post-transcriptional levels by targeting mRNAs for degradation or by inhibiting protein translation. Thousands of miRNAs have been identified in many species. However, there is no information available concerning miRNAs in ma bamboo (<italic>Dendrocalamus latiflorus</italic>), one of the most important non-timber forest products, which has essential ecological roles in forests. To identify miRNAs in <italic>D. latiflorus</italic>, a small RNA library was constructed from leaf tissues. Using next generation high-throughput sequencing technology and bioinformatics analysis, we obtained 11,513,607 raw sequence reads and identified 84 conserved miRNAs (54 mature miRNAs and 30 star miRNAs) belonging to 17 families, and 81 novel miRNAs (76 mature miRNAs and five star miRNAs) in <italic>D. latiflorus</italic>. One hundred and sixty-two potential targets were identified for the 81 novel bamboo miRNAs. Several targets for the novel miRNAs are transcription factors that play important roles in plant development. Among the novel miRNAs, 30 were selected and their expression profiles in response to different light conditions were validated by qRT-PCR. This study provides the first large-scale cloning and characterization of miRNAs in <italic>D. latiflorus</italic>. Eighty-four conserved and 81 novel miRNAs were identified in <italic>D. latiflorus</italic>. Our results present a broad survey of bamboo miRNAs based on experimental and bioinformatics analysis. Although it will be necessary to validate the functions of miRNAs by further experimental research, these results represent a starting point for future research on <italic>D. latiflorus</italic> and related species.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Lee, Rc" uniqKey="Lee R">RC Lee</name></author><author><name sortKey="Feinbaum, Rl" uniqKey="Feinbaum R">RL Feinbaum</name></author><author><name sortKey="Ambros, V" uniqKey="Ambros V">V Ambros</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bushati, N" uniqKey="Bushati N">N Bushati</name></author><author><name sortKey="Cohen, Sm" uniqKey="Cohen S">SM Cohen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, C" uniqKey="Chen C">C Chen</name></author><author><name sortKey="Ridzon, Da" uniqKey="Ridzon D">DA Ridzon</name></author><author><name sortKey="Broomer, Aj" uniqKey="Broomer A">AJ 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