Identification and characterization of the microRNA transcriptome of a moth orchid Phalaenopsis aphrodite
Identifieur interne : 000E21 ( Main/Merge ); précédent : 000E20; suivant : 000E22Identification and characterization of the microRNA transcriptome of a moth orchid Phalaenopsis aphrodite
Auteurs : Ya-Ting Chao [Taïwan] ; Chun-Lin Su [Taïwan] ; Wen-Han Jean [Taïwan] ; Wan-Chieh Chen [Taïwan] ; Yao-Chien Alex Chang [Taïwan] ; Ming-Che Shih [Taïwan]Source :
- Plant Molecular Biology [ 0167-4412 ] ; 2013.
Abstract
Orchids display unique phenotypes, functional characteristics and ecological adaptations that are not found in model plants. In this study, we aimed to characterize the microRNA (miRNA) transcriptome and identify species- and tissue-specific miRNAs in
The online version of this article (doi:10.1007/s11103-013-0150-0) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1007/s11103-013-0150-0
PubMed: 24173913
PubMed Central: 3920020
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Identification and characterization of the microRNA transcriptome of a moth orchid <italic>Phalaenopsis aphrodite</italic></title><author><name sortKey="Chao, Ya Ting" sort="Chao, Ya Ting" uniqKey="Chao Y" first="Ya-Ting" last="Chao">Ya-Ting Chao</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Agricultural Biotechnology Research Center, Academia Sinica, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Su, Chun Lin" sort="Su, Chun Lin" uniqKey="Su C" first="Chun-Lin" last="Su">Chun-Lin Su</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Agricultural Biotechnology Research Center, Academia Sinica, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Jean, Wen Han" sort="Jean, Wen Han" uniqKey="Jean W" first="Wen-Han" last="Jean">Wen-Han Jean</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Agricultural Biotechnology Research Center, Academia Sinica, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Wan Chieh" sort="Chen, Wan Chieh" uniqKey="Chen W" first="Wan-Chieh" last="Chen">Wan-Chieh Chen</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Agricultural Biotechnology Research Center, Academia Sinica, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Chang, Yao Chien Alex" sort="Chang, Yao Chien Alex" uniqKey="Chang Y" first="Yao-Chien Alex" last="Chang">Yao-Chien Alex Chang</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, 10617 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Shih, Ming Che" sort="Shih, Ming Che" uniqKey="Shih M" first="Ming-Che" last="Shih">Ming-Che Shih</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Agricultural Biotechnology Research Center, Academia Sinica, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24173913</idno><idno type="pmc">3920020</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3920020</idno><idno type="RBID">PMC:3920020</idno><idno type="doi">10.1007/s11103-013-0150-0</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000691</idno><idno type="wicri:Area/Pmc/Curation">000690</idno><idno type="wicri:Area/Pmc/Checkpoint">000A50</idno><idno type="wicri:Area/Ncbi/Merge">001469</idno><idno type="wicri:Area/Ncbi/Curation">001469</idno><idno type="wicri:Area/Ncbi/Checkpoint">001469</idno><idno type="wicri:doubleKey">0167-4412:2013:Chao Y:identification:and:characterization</idno><idno type="wicri:Area/Main/Merge">000E21</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Identification and characterization of the microRNA transcriptome of a moth orchid <italic>Phalaenopsis aphrodite</italic></title><author><name sortKey="Chao, Ya Ting" sort="Chao, Ya Ting" uniqKey="Chao Y" first="Ya-Ting" last="Chao">Ya-Ting Chao</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Agricultural Biotechnology Research Center, Academia Sinica, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Su, Chun Lin" sort="Su, Chun Lin" uniqKey="Su C" first="Chun-Lin" last="Su">Chun-Lin Su</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Agricultural Biotechnology Research Center, Academia Sinica, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Jean, Wen Han" sort="Jean, Wen Han" uniqKey="Jean W" first="Wen-Han" last="Jean">Wen-Han Jean</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Agricultural Biotechnology Research Center, Academia Sinica, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Wan Chieh" sort="Chen, Wan Chieh" uniqKey="Chen W" first="Wan-Chieh" last="Chen">Wan-Chieh Chen</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Agricultural Biotechnology Research Center, Academia Sinica, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Chang, Yao Chien Alex" sort="Chang, Yao Chien Alex" uniqKey="Chang Y" first="Yao-Chien Alex" last="Chang">Yao-Chien Alex Chang</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, 10617 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Shih, Ming Che" sort="Shih, Ming Che" uniqKey="Shih M" first="Ming-Che" last="Shih">Ming-Che Shih</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Agricultural Biotechnology Research Center, Academia Sinica, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author></analytic><series><title level="j">Plant Molecular Biology</title><idno type="ISSN">0167-4412</idno><idno type="eISSN">1573-5028</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>Orchids display unique phenotypes, functional characteristics and ecological adaptations that are not found in model plants. In this study, we aimed to characterize the microRNA (miRNA) transcriptome and identify species- and tissue-specific miRNAs in <italic>Phalaenopsis aphrodite</italic>. After data filtering and cleanup, a total of 59,387,374 reads, representing 1,649,996 unique reads, were obtained from four <italic>P. aphrodite</italic> small RNA libraries. A systematic bioinformatics analysis pipeline was developed that can be used for miRNA and precursor mining, and target gene prediction in non-model plants. A total of 3,251 unique reads for 181 known plant miRNAs (belonging to 88 miRNA families), 23 new miRNAs and 91 precursors were identified. All the miRNA star sequences (miRNA*), the complementary strands of miRNA that from miRNA/miRNA* duplexes, of the predicted new miRNAs were detected in our small RNA libraries, providing additional evidence for their existence as new miRNAs in <italic>P. aphrodite</italic>. Furthermore, 240 potential miRNA-targets that appear to be involved in many different biological activities and molecular functions, especially transcription factors, were identified, suggesting that miRNAs can impact multiple processes in <italic>P. aphrodite</italic>. We also verified the cleavage sites for six targets using RNA ligase-mediated rapid amplification of 5′ ends assay. The results provide valuable information about the composition, expression and function of miRNA in <italic>P. aphrodite</italic>, and will aid functional genomics studies of orchids.</p><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1007/s11103-013-0150-0) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Achard, P" uniqKey="Achard P">P Achard</name></author><author><name sortKey="Herr, A" uniqKey="Herr A">A Herr</name></author><author><name sortKey="Baulcombe, Dc" uniqKey="Baulcombe D">DC Baulcombe</name></author><author><name sortKey="Harberd, Np" uniqKey="Harberd N">NP Harberd</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Adai, A" uniqKey="Adai A">A Adai</name></author><author><name sortKey="Johnson, C" uniqKey="Johnson C">C Johnson</name></author><author><name 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uniqKey="Zhang J">J Zhang</name></author><author><name sortKey="Xu, Y" uniqKey="Xu Y">Y Xu</name></author><author><name sortKey="Huan, Q" uniqKey="Huan Q">Q Huan</name></author><author><name sortKey="Chong, K" uniqKey="Chong K">K Chong</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, L" uniqKey="Zhang L">L Zhang</name></author><author><name sortKey="Chia, Jm" uniqKey="Chia J">JM Chia</name></author><author><name sortKey="Kumari, S" uniqKey="Kumari S">S Kumari</name></author><author><name sortKey="Stein, Jc" uniqKey="Stein J">JC Stein</name></author><author><name sortKey="Liu, Z" uniqKey="Liu Z">Z Liu</name></author><author><name sortKey="Narechania, A" uniqKey="Narechania A">A Narechania</name></author><author><name sortKey="Maher, Ca" uniqKey="Maher C">CA Maher</name></author><author><name sortKey="Guill, K" uniqKey="Guill K">K Guill</name></author><author><name sortKey="Mcmullen, Md" uniqKey="Mcmullen M">MD McMullen</name></author><author><name sortKey="Ware, D" uniqKey="Ware D">D Ware</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zuker, M" uniqKey="Zuker M">M Zuker</name></author></analytic></biblStruct></listBibl></div1></back></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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