Identification, evolution, and expression partitioning of miRNAs in allopolyploid Brassica napus
Identifieur interne : 000F27 ( Pmc/Checkpoint ); précédent : 000F26; suivant : 000F28Identification, evolution, and expression partitioning of miRNAs in allopolyploid Brassica napus
Auteurs : Enhui Shen [République populaire de Chine] ; Jun Zou [République populaire de Chine] ; Falk Hubertus Behrens [Allemagne] ; Li Chen [République populaire de Chine] ; Chuyu Ye [République populaire de Chine] ; Shutao Dai [République populaire de Chine] ; Ruiyan Li [République populaire de Chine] ; Meng Ni [République populaire de Chine] ; Xiaoxue Jiang [République populaire de Chine] ; Jie Qiu [République populaire de Chine] ; Yang Liu [République populaire de Chine] ; Weidi Wang [République populaire de Chine] ; Qian-Hao Zhu [Australie] ; Boulos Chalhoub [France] ; Ian Bancroft [Royaume-Uni] ; Jinling Meng [République populaire de Chine] ; Daguang Cai [Allemagne] ; Longjiang Fan [République populaire de Chine]Source :
- Journal of Experimental Botany [ 0022-0957 ] ; 2015.
Abstract
The recently published genome of
Url:
DOI: 10.1093/jxb/erv420
PubMed: 26357884
PubMed Central: 4765792
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Identification, evolution, and expression partitioning of miRNAs in allopolyploid <italic>Brassica napus</italic></title><author><name sortKey="Shen, Enhui" sort="Shen, Enhui" uniqKey="Shen E" first="Enhui" last="Shen">Enhui Shen</name><affiliation wicri:level="1"><nlm:aff id="AF0001"><institution>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University</institution>,<addr-line>Hangzhou 310058</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Zou, Jun" sort="Zou, Jun" uniqKey="Zou J" first="Jun" last="Zou">Jun Zou</name><affiliation wicri:level="1"><nlm:aff id="AF0002"><institution>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University</institution>,<addr-line>Wuhan 430070</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Hubertus Behrens, Falk" sort="Hubertus Behrens, Falk" uniqKey="Hubertus Behrens F" first="Falk" last="Hubertus Behrens">Falk Hubertus Behrens</name><affiliation wicri:level="1"><nlm:aff id="AF0003"><institution>Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts University of Kiel</institution>,<addr-line>Hermann Rodewald Str. 9, D-24118 Kiel</addr-line>,<country>Germany</country></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Chen, Li" sort="Chen, Li" uniqKey="Chen L" first="Li" last="Chen">Li Chen</name><affiliation wicri:level="1"><nlm:aff id="AF0001"><institution>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University</institution>,<addr-line>Hangzhou 310058</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Ye, Chuyu" sort="Ye, Chuyu" uniqKey="Ye C" first="Chuyu" last="Ye">Chuyu Ye</name><affiliation wicri:level="1"><nlm:aff id="AF0001"><institution>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University</institution>,<addr-line>Hangzhou 310058</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Dai, Shutao" sort="Dai, Shutao" uniqKey="Dai S" first="Shutao" last="Dai">Shutao Dai</name><affiliation wicri:level="1"><nlm:aff id="AF0002"><institution>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University</institution>,<addr-line>Wuhan 430070</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Li, Ruiyan" sort="Li, Ruiyan" uniqKey="Li R" first="Ruiyan" last="Li">Ruiyan Li</name><affiliation wicri:level="1"><nlm:aff id="AF0002"><institution>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University</institution>,<addr-line>Wuhan 430070</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Ni, Meng" sort="Ni, Meng" uniqKey="Ni M" first="Meng" last="Ni">Meng Ni</name><affiliation wicri:level="1"><nlm:aff id="AF0002"><institution>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University</institution>,<addr-line>Wuhan 430070</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Jiang, Xiaoxue" sort="Jiang, Xiaoxue" uniqKey="Jiang X" first="Xiaoxue" last="Jiang">Xiaoxue Jiang</name><affiliation wicri:level="1"><nlm:aff id="AF0002"><institution>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University</institution>,<addr-line>Wuhan 430070</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Qiu, Jie" sort="Qiu, Jie" uniqKey="Qiu J" first="Jie" last="Qiu">Jie Qiu</name><affiliation wicri:level="1"><nlm:aff id="AF0001"><institution>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University</institution>,<addr-line>Hangzhou 310058</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Liu, Yang" sort="Liu, Yang" uniqKey="Liu Y" first="Yang" last="Liu">Yang Liu</name><affiliation wicri:level="1"><nlm:aff id="AF0001"><institution>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University</institution>,<addr-line>Hangzhou 310058</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Wang, Weidi" sort="Wang, Weidi" uniqKey="Wang W" first="Weidi" last="Wang">Weidi Wang</name><affiliation wicri:level="1"><nlm:aff id="AF0001"><institution>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University</institution>,<addr-line>Hangzhou 310058</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Zhu, Qian Hao" sort="Zhu, Qian Hao" uniqKey="Zhu Q" first="Qian-Hao" last="Zhu">Qian-Hao Zhu</name><affiliation wicri:level="1"><nlm:aff id="AF0004"><institution>CSIRO Agriculture Flagship</institution>,<addr-line>Canberra, ACT2601</addr-line>,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Chalhoub, Boulos" sort="Chalhoub, Boulos" uniqKey="Chalhoub B" first="Boulos" last="Chalhoub">Boulos Chalhoub</name><affiliation wicri:level="1"><nlm:aff id="AF0005"><institution>Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, Unité Mixte de Recherche 1165 (Institut National de Recherche Agronomique, Centre National de la Recherche Scientifique, Université Evry Val d’Essonne)</institution>,<addr-line>Evry 91057</addr-line>,<country>France</country></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Bancroft, Ian" sort="Bancroft, Ian" uniqKey="Bancroft I" first="Ian" last="Bancroft">Ian Bancroft</name><affiliation wicri:level="1"><nlm:aff id="AF0006"><institution>Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York</institution>,<addr-line>Wentworth Way, Heslington, York YO10 5DD</addr-line>,<country>UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Meng, Jinling" sort="Meng, Jinling" uniqKey="Meng J" first="Jinling" last="Meng">Jinling Meng</name><affiliation wicri:level="1"><nlm:aff id="AF0002"><institution>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University</institution>,<addr-line>Wuhan 430070</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Cai, Daguang" sort="Cai, Daguang" uniqKey="Cai D" first="Daguang" last="Cai">Daguang Cai</name><affiliation wicri:level="1"><nlm:aff id="AF0003"><institution>Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts University of Kiel</institution>,<addr-line>Hermann Rodewald Str. 9, D-24118 Kiel</addr-line>,<country>Germany</country></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Fan, Longjiang" sort="Fan, Longjiang" uniqKey="Fan L" first="Longjiang" last="Fan">Longjiang Fan</name><affiliation wicri:level="1"><nlm:aff id="AF0001"><institution>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University</institution>,<addr-line>Hangzhou 310058</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26357884</idno><idno type="pmc">4765792</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765792</idno><idno type="RBID">PMC:4765792</idno><idno type="doi">10.1093/jxb/erv420</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000552</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000552</idno><idno type="wicri:Area/Pmc/Curation">000552</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000552</idno><idno type="wicri:Area/Pmc/Checkpoint">000F27</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000F27</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Identification, evolution, and expression partitioning of miRNAs in allopolyploid <italic>Brassica napus</italic></title><author><name sortKey="Shen, Enhui" sort="Shen, Enhui" uniqKey="Shen E" first="Enhui" last="Shen">Enhui Shen</name><affiliation wicri:level="1"><nlm:aff id="AF0001"><institution>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University</institution>,<addr-line>Hangzhou 310058</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Zou, Jun" sort="Zou, Jun" uniqKey="Zou J" first="Jun" last="Zou">Jun Zou</name><affiliation wicri:level="1"><nlm:aff id="AF0002"><institution>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University</institution>,<addr-line>Wuhan 430070</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Hubertus Behrens, Falk" sort="Hubertus Behrens, Falk" uniqKey="Hubertus Behrens F" first="Falk" last="Hubertus Behrens">Falk Hubertus Behrens</name><affiliation wicri:level="1"><nlm:aff id="AF0003"><institution>Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts University of Kiel</institution>,<addr-line>Hermann Rodewald Str. 9, D-24118 Kiel</addr-line>,<country>Germany</country></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Chen, Li" sort="Chen, Li" uniqKey="Chen L" first="Li" last="Chen">Li Chen</name><affiliation wicri:level="1"><nlm:aff id="AF0001"><institution>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University</institution>,<addr-line>Hangzhou 310058</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Ye, Chuyu" sort="Ye, Chuyu" uniqKey="Ye C" first="Chuyu" last="Ye">Chuyu Ye</name><affiliation wicri:level="1"><nlm:aff id="AF0001"><institution>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University</institution>,<addr-line>Hangzhou 310058</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Dai, Shutao" sort="Dai, Shutao" uniqKey="Dai S" first="Shutao" last="Dai">Shutao Dai</name><affiliation wicri:level="1"><nlm:aff id="AF0002"><institution>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University</institution>,<addr-line>Wuhan 430070</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Li, Ruiyan" sort="Li, Ruiyan" uniqKey="Li R" first="Ruiyan" last="Li">Ruiyan Li</name><affiliation wicri:level="1"><nlm:aff id="AF0002"><institution>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University</institution>,<addr-line>Wuhan 430070</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Ni, Meng" sort="Ni, Meng" uniqKey="Ni M" first="Meng" last="Ni">Meng Ni</name><affiliation wicri:level="1"><nlm:aff id="AF0002"><institution>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University</institution>,<addr-line>Wuhan 430070</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Jiang, Xiaoxue" sort="Jiang, Xiaoxue" uniqKey="Jiang X" first="Xiaoxue" last="Jiang">Xiaoxue Jiang</name><affiliation wicri:level="1"><nlm:aff id="AF0002"><institution>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University</institution>,<addr-line>Wuhan 430070</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Qiu, Jie" sort="Qiu, Jie" uniqKey="Qiu J" first="Jie" last="Qiu">Jie Qiu</name><affiliation wicri:level="1"><nlm:aff id="AF0001"><institution>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University</institution>,<addr-line>Hangzhou 310058</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Liu, Yang" sort="Liu, Yang" uniqKey="Liu Y" first="Yang" last="Liu">Yang Liu</name><affiliation wicri:level="1"><nlm:aff id="AF0001"><institution>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University</institution>,<addr-line>Hangzhou 310058</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Wang, Weidi" sort="Wang, Weidi" uniqKey="Wang W" first="Weidi" last="Wang">Weidi Wang</name><affiliation wicri:level="1"><nlm:aff id="AF0001"><institution>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University</institution>,<addr-line>Hangzhou 310058</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Zhu, Qian Hao" sort="Zhu, Qian Hao" uniqKey="Zhu Q" first="Qian-Hao" last="Zhu">Qian-Hao Zhu</name><affiliation wicri:level="1"><nlm:aff id="AF0004"><institution>CSIRO Agriculture Flagship</institution>,<addr-line>Canberra, ACT2601</addr-line>,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Chalhoub, Boulos" sort="Chalhoub, Boulos" uniqKey="Chalhoub B" first="Boulos" last="Chalhoub">Boulos Chalhoub</name><affiliation wicri:level="1"><nlm:aff id="AF0005"><institution>Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, Unité Mixte de Recherche 1165 (Institut National de Recherche Agronomique, Centre National de la Recherche Scientifique, Université Evry Val d’Essonne)</institution>,<addr-line>Evry 91057</addr-line>,<country>France</country></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Bancroft, Ian" sort="Bancroft, Ian" uniqKey="Bancroft I" first="Ian" last="Bancroft">Ian Bancroft</name><affiliation wicri:level="1"><nlm:aff id="AF0006"><institution>Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York</institution>,<addr-line>Wentworth Way, Heslington, York YO10 5DD</addr-line>,<country>UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Meng, Jinling" sort="Meng, Jinling" uniqKey="Meng J" first="Jinling" last="Meng">Jinling Meng</name><affiliation wicri:level="1"><nlm:aff id="AF0002"><institution>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University</institution>,<addr-line>Wuhan 430070</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Cai, Daguang" sort="Cai, Daguang" uniqKey="Cai D" first="Daguang" last="Cai">Daguang Cai</name><affiliation wicri:level="1"><nlm:aff id="AF0003"><institution>Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts University of Kiel</institution>,<addr-line>Hermann Rodewald Str. 9, D-24118 Kiel</addr-line>,<country>Germany</country></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Fan, Longjiang" sort="Fan, Longjiang" uniqKey="Fan L" first="Longjiang" last="Fan">Longjiang Fan</name><affiliation wicri:level="1"><nlm:aff id="AF0001"><institution>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University</institution>,<addr-line>Hangzhou 310058</addr-line>,<country>PR China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Journal of Experimental Botany</title><idno type="ISSN">0022-0957</idno><idno type="eISSN">1460-2431</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The recently published genome of <italic>Brassica napus</italic> offers for the first time the opportunity to gain insights into the genomic organization and the evolution of miRNAs in oilseed rape. In this study, 12 small RNA libraries from two <italic>B. napus</italic> cultivars (Tapidor and Ningyou7) and their four double-haploid lines were sequenced, employing the newly sequenced <italic>B. napus</italic> genome, together with genomes of its progenitors <italic>Brassica rapa</italic> and <italic>Brassica oleracea</italic>. A total of 645 miRNAs including 280 conserved and 365 novel miRNAs were identified. Comparative analysis revealed a high level of genomic conservation of <italic>MIRNA</italic>s (75.9%) between the subgenomes of <italic>B. napus</italic> and its two progenitors’ genomes, and <italic>MIRNA</italic> lost/gain events (133) occurred in <italic>B. napus</italic> after its speciation. Furthermore, significant partitioning of miRNA expressions between the two subgenomes in <italic>B. napus</italic> was detected. The data of degradome sequencing, miRNA-mediated cleavage, and expression analyses support specific interactions between miRNAs and their targets in the modulation of diverse physiological processes in roots and leaves, as well as in biosynthesis of, for example, glucosinolates and lipids in oilseed rape. These data provide a first genome-wide view on the origin, evolution, and genomic organization of <italic>B. napus MIRNA</italic>s.</p></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="Allen, E" uniqKey="Allen E">E Allen</name></author><author><name sortKey="Xie, Z" uniqKey="Xie Z">Z Xie</name></author><author><name sortKey="Gustafson, Am" uniqKey="Gustafson A">AM Gustafson</name></author><author><name sortKey="Carrington, Jc" uniqKey="Carrington J">JC Carrington</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bancroft, I" uniqKey="Bancroft 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<front><journal-meta><journal-id journal-id-type="nlm-ta">J Exp Bot</journal-id><journal-id journal-id-type="iso-abbrev">J. Exp. Bot</journal-id><journal-id journal-id-type="hwp">jexbot</journal-id><journal-id journal-id-type="publisher-id">exbotj</journal-id><journal-title-group><journal-title>Journal of Experimental Botany</journal-title></journal-title-group><issn pub-type="ppub">0022-0957</issn><issn pub-type="epub">1460-2431</issn><publisher><publisher-name>Oxford University Press</publisher-name><publisher-loc>UK</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26357884</article-id><article-id pub-id-type="pmc">4765792</article-id><article-id pub-id-type="doi">10.1093/jxb/erv420</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Paper</subject></subj-group></article-categories><title-group><article-title>Identification, evolution, and expression partitioning of miRNAs in allopolyploid <italic>Brassica napus</italic></article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Shen</surname><given-names>Enhui</given-names></name><xref ref-type="aff" rid="AF0001"><sup>1</sup></xref><xref ref-type="corresp" rid="c2">*</xref></contrib><contrib contrib-type="author"><name><surname>Zou</surname><given-names>Jun</given-names></name><xref ref-type="aff" rid="AF0002"><sup>2</sup></xref><xref ref-type="corresp" rid="c2">*</xref></contrib><contrib contrib-type="author"><name><surname>Hubertus Behrens</surname><given-names>Falk</given-names></name><xref ref-type="aff" rid="AF0003"><sup>3</sup></xref><xref ref-type="corresp" rid="c2">*</xref></contrib><contrib contrib-type="author"><name><surname>Chen</surname><given-names>Li</given-names></name><xref ref-type="aff" rid="AF0001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ye</surname><given-names>Chuyu</given-names></name><xref ref-type="aff" rid="AF0001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Dai</surname><given-names>Shutao</given-names></name><xref ref-type="aff" rid="AF0002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Ruiyan</given-names></name><xref ref-type="aff" rid="AF0002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ni</surname><given-names>Meng</given-names></name><xref ref-type="aff" rid="AF0002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Jiang</surname><given-names>Xiaoxue</given-names></name><xref ref-type="aff" rid="AF0002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Qiu</surname><given-names>Jie</given-names></name><xref ref-type="aff" rid="AF0001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Yang</given-names></name><xref ref-type="aff" rid="AF0001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Weidi</given-names></name><xref ref-type="aff" rid="AF0001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhu</surname><given-names>Qian-Hao</given-names></name><xref ref-type="aff" rid="AF0004"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Chalhoub</surname><given-names>Boulos</given-names></name><xref ref-type="aff" rid="AF0005"><sup>5</sup></xref></contrib><contrib contrib-type="author"><name><surname>Bancroft</surname><given-names>Ian</given-names></name><xref ref-type="aff" rid="AF0006"><sup>6</sup></xref></contrib><contrib contrib-type="author"><name><surname>Meng</surname><given-names>Jinling</given-names></name><xref ref-type="aff" rid="AF0002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Cai</surname><given-names>Daguang</given-names></name><xref ref-type="aff" rid="AF0003"><sup>3</sup></xref><xref ref-type="corresp" rid="c1"><sup>†</sup></xref></contrib><contrib contrib-type="author"><name><surname>Fan</surname><given-names>Longjiang</given-names></name><xref ref-type="aff" rid="AF0001"><sup>1</sup></xref><xref ref-type="corresp" rid="c1"><sup>†</sup></xref></contrib><aff id="AF0001"><sup>1</sup><institution>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University</institution>,<addr-line>Hangzhou 310058</addr-line>,<country>PR China</country></aff><aff id="AF0002"><sup>2</sup><institution>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University</institution>,<addr-line>Wuhan 430070</addr-line>,<country>PR China</country></aff><aff id="AF0003"><sup>3</sup><institution>Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts University of Kiel</institution>,<addr-line>Hermann Rodewald Str. 9, D-24118 Kiel</addr-line>,<country>Germany</country></aff><aff id="AF0004"><sup>4</sup><institution>CSIRO Agriculture Flagship</institution>,<addr-line>Canberra, ACT2601</addr-line>,<country>Australia</country></aff><aff id="AF0005"><sup>5</sup><institution>Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, Unité Mixte de Recherche 1165 (Institut National de Recherche Agronomique, Centre National de la Recherche Scientifique, Université Evry Val d’Essonne)</institution>,<addr-line>Evry 91057</addr-line>,<country>France</country></aff><aff id="AF0006"><sup>6</sup><institution>Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York</institution>,<addr-line>Wentworth Way, Heslington, York YO10 5DD</addr-line>,<country>UK</country></aff></contrib-group><author-notes><corresp id="c2">* These authors contributed equally to this work.</corresp><corresp id="c1"><sup>†</sup> To whom correspondence should be addressed. E-mail: <email>fanlj@zju.edu.cn</email> or <email>dcai@phytomed.uni-kiel.de</email></corresp><fn id="fn01"><p>Editor: Ramanjulu Sunkar</p></fn></author-notes><pub-date pub-type="ppub"><month>12</month><year>2015</year></pub-date><pub-date pub-type="epub"><day>10</day><month>9</month><year>2015</year></pub-date><pub-date pub-type="pmc-release"><day>10</day><month>9</month><year>2015</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>66</volume><issue>22</issue><fpage>7241</fpage><lpage>7253</lpage><permissions><copyright-statement>© The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.</copyright-statement><copyright-year>2015</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by/3.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/3.0/">http://creativecommons.org/licenses/by/3.0/</ext-link>), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>The recently published genome of <italic>Brassica napus</italic> offers for the first time the opportunity to gain insights into the genomic organization and the evolution of miRNAs in oilseed rape. In this study, 12 small RNA libraries from two <italic>B. napus</italic> cultivars (Tapidor and Ningyou7) and their four double-haploid lines were sequenced, employing the newly sequenced <italic>B. napus</italic> genome, together with genomes of its progenitors <italic>Brassica rapa</italic> and <italic>Brassica oleracea</italic>. A total of 645 miRNAs including 280 conserved and 365 novel miRNAs were identified. Comparative analysis revealed a high level of genomic conservation of <italic>MIRNA</italic>s (75.9%) between the subgenomes of <italic>B. napus</italic> and its two progenitors’ genomes, and <italic>MIRNA</italic> lost/gain events (133) occurred in <italic>B. napus</italic> after its speciation. Furthermore, significant partitioning of miRNA expressions between the two subgenomes in <italic>B. napus</italic> was detected. The data of degradome sequencing, miRNA-mediated cleavage, and expression analyses support specific interactions between miRNAs and their targets in the modulation of diverse physiological processes in roots and leaves, as well as in biosynthesis of, for example, glucosinolates and lipids in oilseed rape. These data provide a first genome-wide view on the origin, evolution, and genomic organization of <italic>B. napus MIRNA</italic>s.</p></abstract><kwd-group><title>Key words:</title><kwd>allopolyploid evolution</kwd><kwd><italic>Brassica napus</italic></kwd><kwd>expression partitioning</kwd><kwd>microRNA.</kwd></kwd-group><counts><page-count count="13"></page-count></counts></article-meta></front></pmc><affiliations><list><country><li>Allemagne</li><li>Australie</li><li>France</li><li>Royaume-Uni</li><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Shen, Enhui" sort="Shen, Enhui" uniqKey="Shen E" first="Enhui" last="Shen">Enhui Shen</name></noRegion><name sortKey="Chen, Li" sort="Chen, Li" uniqKey="Chen L" first="Li" last="Chen">Li Chen</name><name sortKey="Dai, Shutao" sort="Dai, Shutao" uniqKey="Dai S" first="Shutao" last="Dai">Shutao Dai</name><name sortKey="Fan, Longjiang" sort="Fan, Longjiang" uniqKey="Fan L" first="Longjiang" last="Fan">Longjiang Fan</name><name sortKey="Jiang, Xiaoxue" sort="Jiang, Xiaoxue" uniqKey="Jiang X" first="Xiaoxue" last="Jiang">Xiaoxue Jiang</name><name sortKey="Li, Ruiyan" sort="Li, Ruiyan" uniqKey="Li R" first="Ruiyan" last="Li">Ruiyan Li</name><name sortKey="Liu, Yang" sort="Liu, Yang" uniqKey="Liu Y" first="Yang" last="Liu">Yang Liu</name><name sortKey="Meng, Jinling" sort="Meng, Jinling" uniqKey="Meng J" first="Jinling" last="Meng">Jinling Meng</name><name sortKey="Ni, Meng" sort="Ni, Meng" uniqKey="Ni M" first="Meng" last="Ni">Meng Ni</name><name sortKey="Qiu, Jie" sort="Qiu, Jie" uniqKey="Qiu J" first="Jie" last="Qiu">Jie Qiu</name><name sortKey="Wang, Weidi" sort="Wang, Weidi" uniqKey="Wang W" first="Weidi" last="Wang">Weidi Wang</name><name sortKey="Ye, Chuyu" sort="Ye, Chuyu" uniqKey="Ye C" first="Chuyu" last="Ye">Chuyu Ye</name><name sortKey="Zou, Jun" sort="Zou, Jun" uniqKey="Zou J" first="Jun" last="Zou">Jun Zou</name></country><country name="Allemagne"><noRegion><name sortKey="Hubertus Behrens, Falk" sort="Hubertus Behrens, Falk" uniqKey="Hubertus Behrens F" first="Falk" last="Hubertus Behrens">Falk Hubertus Behrens</name></noRegion><name sortKey="Cai, Daguang" sort="Cai, Daguang" uniqKey="Cai D" first="Daguang" last="Cai">Daguang Cai</name></country><country name="Australie"><noRegion><name sortKey="Zhu, Qian Hao" sort="Zhu, Qian Hao" uniqKey="Zhu Q" first="Qian-Hao" last="Zhu">Qian-Hao Zhu</name></noRegion></country><country name="France"><noRegion><name sortKey="Chalhoub, Boulos" sort="Chalhoub, Boulos" uniqKey="Chalhoub B" first="Boulos" last="Chalhoub">Boulos Chalhoub</name></noRegion></country><country name="Royaume-Uni"><noRegion><name sortKey="Bancroft, Ian" sort="Bancroft, Ian" uniqKey="Bancroft I" first="Ian" last="Bancroft">Ian Bancroft</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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