title: Identification, evolution, and expression partitioning of miRNAs in allopolyploid Brassica napus.
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.
authors.affiliation: Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.
authors.forename: Enhui
authors.initials: E
authors.lastname: Shen
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China.
authors.forename: Jun
authors.initials: J
authors.lastname: Zou
authors.affiliation: Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts University of Kiel, Hermann Rodewald Str. 9, D-24118 Kiel, Germany.
authors.forename: Falk
authors.initials: F
authors.lastname: Hubertus Behrens
authors.affiliation: Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.
authors.forename: Li
authors.initials: L
authors.lastname: Chen
authors.affiliation: Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.
authors.forename: Chuyu
authors.initials: C
authors.lastname: Ye
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China.
authors.forename: Shutao
authors.initials: S
authors.lastname: Dai
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China.
authors.forename: Ruiyan
authors.initials: R
authors.lastname: Li
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China.
authors.forename: Meng
authors.initials: M
authors.lastname: Ni
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China.
authors.forename: Xiaoxue
authors.initials: X
authors.lastname: Jiang
authors.affiliation: Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.
authors.forename: Jie
authors.initials: J
authors.lastname: Qiu
authors.affiliation: Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.
authors.forename: Weidi
authors.initials: W
authors.lastname: Wang
authors.affiliation: CSIRO Agriculture Flagship, Canberra, ACT2601, Australia.
authors.forename: Qian-Hao
authors.initials: QH
authors.lastname: Zhu
authors.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.
authors.forename: Boulos
authors.initials: B
authors.lastname: Chalhoub
authors.affiliation: Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK.
authors.forename: Ian
authors.initials: I
authors.lastname: Bancroft
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China.
authors.forename: Jinling
authors.initials: J
authors.lastname: Meng
authors.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.
authors.forename: Daguang
authors.initials: D
authors.lastname: Cai
authors.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.
authors.forename: Longjiang
authors.initials: L
authors.lastname: Fan
mesh_terms: D029688:Brassica napus / Q000235:genetics*; D029741:Brassica rapa / Q000235:genetics; D002874:Chromosome Mapping; D019143:Evolution, Molecular; D018745:Genome, Plant; D035683:MicroRNAs / Q000096:biosynthesis*; D018749:RNA, Plant / Q000096:biosynthesis*; D013045:Species Specificity
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant
keywords: Brassica napus; allopolyploid evolution; expression partitioning; microRNA.