title: Impacts of Whole-Genome Triplication on MIRNA Evolution in Brassica rapa.
abstract: MicroRNAs (miRNAs) are a class of short non-coding, endogenous RNAs that play essential roles in eukaryotes. Although the influence of whole-genome triplication (WGT) on protein-coding genes has been well documented in Brassica rapa, little is known about its impacts on MIRNAs. In this study, through generating a comprehensive annotation of 680 MIRNAs for B. rapa, we analyzed the evolutionary characteristics of these MIRNAs from different aspects in B. rapa. First, while MIRNAs and genes show similar patterns of biased distribution among subgenomes of B. rapa, we found that MIRNAs are much more overretained than genes following fractionation after WGT. Second, multiple-copy MIRNAs show significant sequence conservation than that of single-copy MIRNAs, which is opposite to that of genes. This indicates that increased purifying selection is acting upon these highly retained multiple-copy MIRNAs and their functional importance over singleton MIRNAs. Furthermore, we found the extensive divergence between pairs of miRNAs and their target genes following the WGT in B. rapa. In summary, our study provides a valuable resource for exploring MIRNA in B. rapa and highlights the impacts of WGT on the evolution of MIRNA.
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie, Beijing, People's Republic of China Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, Yuanmingyuan Xilu, Beijing, People's Republic of China.
authors.forename: Chao
authors.initials: C
authors.lastname: Sun
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie, Beijing, People's Republic of China.
authors.forename: Jian
authors.initials: J
authors.lastname: Wu
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie, Beijing, People's Republic of China.
authors.forename: Jianli
authors.initials: J
authors.lastname: Liang
authors.affiliation: Department of Agronomy and Horticulture, University of Nebraska, Lincoln.
authors.forename: James C
authors.initials: JC
authors.lastname: Schnable
authors.affiliation: Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, Yuanmingyuan Xilu, Beijing, People's Republic of China.
authors.forename: Wencai
authors.initials: W
authors.lastname: Yang
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie, Beijing, People's Republic of China wangxiaowu@caas.cn chengfeng@caas.cn.
authors.forename: Feng
authors.initials: F
authors.lastname: Cheng
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie, Beijing, People's Republic of China wangxiaowu@caas.cn chengfeng@caas.cn.
authors.forename: Xiaowu
authors.initials: X
authors.lastname: Wang
mesh_terms: D029741:Brassica rapa / Q000235:genetics*; D017124:Conserved Sequence; D019143:Evolution, Molecular; D020440:Gene Duplication; D018745:Genome, Plant; D035683:MicroRNAs / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics*; D012641:Selection, Genetic; D057885:Triploidy
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant
keywords: Brassica rapa; MIRNA; coevolution; retention; whole-genome triplication