Identification, evolution, and expression partitioning of miRNAs in allopolyploid Brassica napus.
Identifieur interne : 002A80 ( PubMed/Checkpoint ); précédent : 002A79; suivant : 002A81Identification, 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 [République populaire de Chine] ; Longjiang Fan [République populaire de Chine]Source :
- Journal of experimental botany [ 1460-2431 ] ; 2015.
Descripteurs français
- KwdFr :
- MESH :
- biosynthèse : ARN des plantes, microARN.
- génétique : Brassica napus, Brassica rapa.
- Cartographie chromosomique, Génome végétal, Spécificité d'espèce, Évolution moléculaire.
English descriptors
- KwdEn :
- MESH :
- chemical , biosynthesis : MicroRNAs, RNA, Plant.
- genetics : Brassica napus, Brassica rapa.
- Chromosome Mapping, Evolution, Molecular, Genome, Plant, Species Specificity.
Abstract
The recently published genome of Brassica napus 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 B. napus cultivars (Tapidor and Ningyou7) and their four double-haploid lines were sequenced, employing the newly sequenced B. napus genome, together with genomes of its progenitors Brassica rapa and Brassica oleracea. A total of 645 miRNAs including 280 conserved and 365 novel miRNAs were identified. Comparative analysis revealed a high level of genomic conservation of MIRNAs (75.9%) between the subgenomes of B. napus and its two progenitors' genomes, and MIRNA lost/gain events (133) occurred in B. napus after its speciation. Furthermore, significant partitioning of miRNA expressions between the two subgenomes in B. napus 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 B. napus MIRNAs.
DOI: 10.1093/jxb/erv420
PubMed: 26357884
Affiliations:
- Allemagne, Australie, France, Royaume-Uni, République populaire de Chine
- Schleswig-Holstein, Zhejiang
- Hangzhou, Kiel
- Université de Zhejiang
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Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070</wicri:regionArea><wicri:noRegion>Wuhan 430070</wicri:noRegion></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:affiliation>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070</wicri:regionArea><wicri:noRegion>Wuhan 430070</wicri:noRegion></affiliation></author><author><name sortKey="Ni, Meng" sort="Ni, Meng" uniqKey="Ni M" 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430070</wicri:noRegion></affiliation></author><author><name sortKey="Qiu, Jie" sort="Qiu, Jie" uniqKey="Qiu J" first="Jie" last="Qiu">Jie Qiu</name><affiliation wicri:level="4"><nlm:affiliation>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region><settlement type="city">Hangzhou</settlement></placeName><orgName type="university">Université de Zhejiang</orgName></affiliation></author><author><name sortKey="Liu, Yang" sort="Liu, Yang" uniqKey="Liu Y" first="Yang" last="Liu">Yang Liu</name><affiliation wicri:level="4"><nlm:affiliation>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region><settlement type="city">Hangzhou</settlement></placeName><orgName type="university">Université de Zhejiang</orgName></affiliation></author><author><name sortKey="Wang, Weidi" sort="Wang, Weidi" uniqKey="Wang W" first="Weidi" last="Wang">Weidi Wang</name><affiliation wicri:level="4"><nlm:affiliation>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region><settlement type="city">Hangzhou</settlement></placeName><orgName type="university">Université de Zhejiang</orgName></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:affiliation>CSIRO Agriculture Flagship, Canberra, ACT2601, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Agriculture Flagship, Canberra, ACT2601</wicri:regionArea><wicri:noRegion>ACT2601</wicri:noRegion></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:affiliation>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), Evry 91057, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>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), Evry 91057</wicri:regionArea><wicri:noRegion>91057</wicri:noRegion><wicri:noRegion>91057</wicri:noRegion></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:affiliation>Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD</wicri:regionArea><wicri:noRegion>York YO10 5DD</wicri:noRegion></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:affiliation>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070</wicri:regionArea><wicri:noRegion>Wuhan 430070</wicri:noRegion></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:affiliation>Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts University of Kiel, Hermann Rodewald Str. 9, D-24118 Kiel, Germany fanlj@zju.edu.cn dcai@phytomed.uni-kiel.de.</nlm:affiliation><country wicri:rule="url">République populaire de Chine</country><wicri:regionArea>Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts University of Kiel, Hermann Rodewald Str. 9, D-24118 Kiel</wicri:regionArea><wicri:noRegion>D-24118 Kiel</wicri:noRegion></affiliation></author><author><name sortKey="Fan, Longjiang" sort="Fan, Longjiang" uniqKey="Fan L" first="Longjiang" last="Fan">Longjiang Fan</name><affiliation wicri:level="4"><nlm:affiliation>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China fanlj@zju.edu.cn 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type="province">Zhejiang</region><settlement type="city">Hangzhou</settlement></placeName><orgName type="university">Université de Zhejiang</orgName></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:affiliation>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070</wicri:regionArea><wicri:noRegion>Wuhan 430070</wicri:noRegion></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="3"><nlm:affiliation>Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts University of Kiel, Hermann Rodewald Str. 9, D-24118 Kiel, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts University of Kiel, Hermann Rodewald Str. 9, D-24118 Kiel</wicri:regionArea><placeName><region type="land" nuts="2">Schleswig-Holstein</region><settlement type="city">Kiel</settlement></placeName></affiliation></author><author><name sortKey="Chen, Li" sort="Chen, Li" uniqKey="Chen L" first="Li" last="Chen">Li Chen</name><affiliation wicri:level="4"><nlm:affiliation>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region><settlement type="city">Hangzhou</settlement></placeName><orgName type="university">Université de Zhejiang</orgName></affiliation></author><author><name sortKey="Ye, Chuyu" sort="Ye, Chuyu" uniqKey="Ye C" first="Chuyu" last="Ye">Chuyu Ye</name><affiliation wicri:level="4"><nlm:affiliation>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region><settlement type="city">Hangzhou</settlement></placeName><orgName type="university">Université de Zhejiang</orgName></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:affiliation>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070</wicri:regionArea><wicri:noRegion>Wuhan 430070</wicri:noRegion></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:affiliation>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070</wicri:regionArea><wicri:noRegion>Wuhan 430070</wicri:noRegion></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:affiliation>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070</wicri:regionArea><wicri:noRegion>Wuhan 430070</wicri:noRegion></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:affiliation>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070</wicri:regionArea><wicri:noRegion>Wuhan 430070</wicri:noRegion></affiliation></author><author><name sortKey="Qiu, Jie" sort="Qiu, Jie" uniqKey="Qiu J" first="Jie" last="Qiu">Jie Qiu</name><affiliation wicri:level="4"><nlm:affiliation>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region><settlement type="city">Hangzhou</settlement></placeName><orgName type="university">Université de Zhejiang</orgName></affiliation></author><author><name sortKey="Liu, Yang" sort="Liu, Yang" uniqKey="Liu Y" first="Yang" last="Liu">Yang Liu</name><affiliation wicri:level="4"><nlm:affiliation>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region><settlement type="city">Hangzhou</settlement></placeName><orgName type="university">Université de Zhejiang</orgName></affiliation></author><author><name sortKey="Wang, Weidi" sort="Wang, Weidi" uniqKey="Wang W" first="Weidi" last="Wang">Weidi Wang</name><affiliation wicri:level="4"><nlm:affiliation>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region><settlement type="city">Hangzhou</settlement></placeName><orgName type="university">Université de Zhejiang</orgName></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:affiliation>CSIRO Agriculture Flagship, Canberra, ACT2601, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Agriculture Flagship, Canberra, ACT2601</wicri:regionArea><wicri:noRegion>ACT2601</wicri:noRegion></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:affiliation>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), Evry 91057, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>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), Evry 91057</wicri:regionArea><wicri:noRegion>91057</wicri:noRegion><wicri:noRegion>91057</wicri:noRegion></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:affiliation>Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD</wicri:regionArea><wicri:noRegion>York YO10 5DD</wicri:noRegion></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:affiliation>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070</wicri:regionArea><wicri:noRegion>Wuhan 430070</wicri:noRegion></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:affiliation>Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts University of Kiel, Hermann Rodewald Str. 9, D-24118 Kiel, Germany fanlj@zju.edu.cn dcai@phytomed.uni-kiel.de.</nlm:affiliation><country wicri:rule="url">République populaire de Chine</country><wicri:regionArea>Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts University of Kiel, Hermann Rodewald Str. 9, D-24118 Kiel</wicri:regionArea><wicri:noRegion>D-24118 Kiel</wicri:noRegion></affiliation></author><author><name sortKey="Fan, Longjiang" sort="Fan, Longjiang" uniqKey="Fan L" first="Longjiang" last="Fan">Longjiang Fan</name><affiliation wicri:level="4"><nlm:affiliation>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China fanlj@zju.edu.cn dcai@phytomed.uni-kiel.de.</nlm:affiliation><country wicri:rule="url">République populaire de Chine</country><wicri:regionArea>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region><settlement type="city">Hangzhou</settlement></placeName><orgName type="university">Université de Zhejiang</orgName></affiliation></author></analytic><series><title level="j">Journal of experimental botany</title><idno type="eISSN">1460-2431</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Brassica napus (genetics)</term><term>Brassica rapa (genetics)</term><term>Chromosome Mapping</term><term>Evolution, Molecular</term><term>Genome, Plant</term><term>MicroRNAs (biosynthesis)</term><term>RNA, Plant (biosynthesis)</term><term>Species Specificity</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN des plantes (biosynthèse)</term><term>Brassica napus (génétique)</term><term>Brassica rapa (génétique)</term><term>Cartographie chromosomique</term><term>Génome végétal</term><term>Spécificité d'espèce</term><term>microARN (biosynthèse)</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en"><term>MicroRNAs</term><term>RNA, Plant</term></keywords><keywords scheme="MESH" qualifier="biosynthèse" xml:lang="fr"><term>ARN des plantes</term><term>microARN</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Brassica napus</term><term>Brassica rapa</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Brassica napus</term><term>Brassica rapa</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosome Mapping</term><term>Evolution, Molecular</term><term>Genome, Plant</term><term>Species Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Cartographie chromosomique</term><term>Génome végétal</term><term>Spécificité d'espèce</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The recently published genome of Brassica napus 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 B. napus cultivars (Tapidor and Ningyou7) and their four double-haploid lines were sequenced, employing the newly sequenced B. napus genome, together with genomes of its progenitors Brassica rapa and Brassica oleracea. A total of 645 miRNAs including 280 conserved and 365 novel miRNAs were identified. Comparative analysis revealed a high level of genomic conservation of MIRNAs (75.9%) between the subgenomes of B. napus and its two progenitors' genomes, and MIRNA lost/gain events (133) occurred in B. napus after its speciation. Furthermore, significant partitioning of miRNA expressions between the two subgenomes in B. napus 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 B. napus MIRNAs.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26357884</PMID><DateCreated><Year>2016</Year><Month>02</Month><Day>25</Day></DateCreated><DateCompleted><Year>2016</Year><Month>10</Month><Day>12</Day></DateCompleted><DateRevised><Year>2017</Year><Month>02</Month><Day>20</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1460-2431</ISSN><JournalIssue CitedMedium="Internet"><Volume>66</Volume><Issue>22</Issue><PubDate><Year>2015</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Journal of experimental botany</Title><ISOAbbreviation>J. Exp. Bot.</ISOAbbreviation></Journal><ArticleTitle>Identification, evolution, and expression partitioning of miRNAs in allopolyploid Brassica napus.</ArticleTitle><Pagination><MedlinePgn>7241-53</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/jxb/erv420</ELocationID><Abstract><AbstractText>The recently published genome of Brassica napus 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 B. napus cultivars (Tapidor and Ningyou7) and their four double-haploid lines were sequenced, employing the newly sequenced B. napus genome, together with genomes of its progenitors Brassica rapa and Brassica oleracea. A total of 645 miRNAs including 280 conserved and 365 novel miRNAs were identified. Comparative analysis revealed a high level of genomic conservation of MIRNAs (75.9%) between the subgenomes of B. napus and its two progenitors' genomes, and MIRNA lost/gain events (133) occurred in B. napus after its speciation. Furthermore, significant partitioning of miRNA expressions between the two subgenomes in B. napus 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 B. napus MIRNAs.</AbstractText><CopyrightInformation>© The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Shen</LastName><ForeName>Enhui</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zou</LastName><ForeName>Jun</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hubertus Behrens</LastName><ForeName>Falk</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts University of Kiel, Hermann Rodewald Str. 9, D-24118 Kiel, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Li</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ye</LastName><ForeName>Chuyu</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dai</LastName><ForeName>Shutao</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Ruiyan</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ni</LastName><ForeName>Meng</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Xiaoxue</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Qiu</LastName><ForeName>Jie</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Yang</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Weidi</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhu</LastName><ForeName>Qian-Hao</ForeName><Initials>QH</Initials><AffiliationInfo><Affiliation>CSIRO Agriculture Flagship, Canberra, ACT2601, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chalhoub</LastName><ForeName>Boulos</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>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), Evry 91057, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bancroft</LastName><ForeName>Ian</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Meng</LastName><ForeName>Jinling</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cai</LastName><ForeName>Daguang</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts University of Kiel, Hermann Rodewald Str. 9, D-24118 Kiel, Germany fanlj@zju.edu.cn dcai@phytomed.uni-kiel.de.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fan</LastName><ForeName>Longjiang</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China fanlj@zju.edu.cn dcai@phytomed.uni-kiel.de.</Affiliation></AffiliationInfo></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 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Mapping</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D035683" MajorTopicYN="N">MicroRNAs</DescriptorName><QualifierName UI="Q000096" MajorTopicYN="Y">biosynthesis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018749" MajorTopicYN="N">RNA, Plant</DescriptorName><QualifierName UI="Q000096" MajorTopicYN="Y">biosynthesis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013045" MajorTopicYN="N">Species Specificity</DescriptorName></MeshHeading></MeshHeadingList><OtherID Source="NLM">PMC4765792</OtherID><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Brassica napus</Keyword><Keyword MajorTopicYN="N">allopolyploid evolution</Keyword><Keyword MajorTopicYN="N">expression partitioning</Keyword><Keyword MajorTopicYN="N">microRNA.</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>9</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>9</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>10</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26357884</ArticleId><ArticleId IdType="pii">erv420</ArticleId><ArticleId IdType="doi">10.1093/jxb/erv420</ArticleId><ArticleId IdType="pmc">PMC4765792</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Allemagne</li><li>Australie</li><li>France</li><li>Royaume-Uni</li><li>République populaire de Chine</li></country><region><li>Schleswig-Holstein</li><li>Zhejiang</li></region><settlement><li>Hangzhou</li><li>Kiel</li></settlement><orgName><li>Université de Zhejiang</li></orgName></list><tree><country name="République populaire de Chine"><region name="Zhejiang"><name sortKey="Shen, Enhui" sort="Shen, Enhui" uniqKey="Shen E" first="Enhui" last="Shen">Enhui Shen</name></region><name sortKey="Cai, Daguang" sort="Cai, Daguang" uniqKey="Cai D" first="Daguang" last="Cai">Daguang Cai</name><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"><region name="Schleswig-Holstein"><name sortKey="Hubertus Behrens, Falk" sort="Hubertus Behrens, Falk" uniqKey="Hubertus Behrens F" first="Falk" last="Hubertus Behrens">Falk Hubertus Behrens</name></region></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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