title: Comprehensive analyses of microRNA gene evolution in paleopolyploid soybean genome.
abstract: miRNA genes are thought to undergo quick birth and death processes in genomes and the emergence of a MIRNA-like hairpin provides the base for functional miRNA gene formation. However, the factors affecting the formation of an active miRNA gene from a MIRNA-like hairpin within a genome remain unclear. We performed a genome-wide investigation of MIRNA-like hairpin accumulation, expression, structural changes and relationships with annotated genomic features in the paleopolyploid soybean genome. Our results showed that adjacent gene and transposable element content, rates of genetic recombination at location of emergence, along with its own gene structure divergence greatly affected miRNA gene evolution. Further investigation suggested that miRNA genes from different duplication sources followed distinct evolutionary trajectories and that the accumulation of MIRNA-like hairpins might be an important factor in causing long terminal repeat retrotransposons to lose activity during genome evolution.
authors.affiliation: State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
authors.forename: Zhengkui
authors.initials: Z
authors.lastname: Zhou
authors.forename: Zheng
authors.initials: Z
authors.lastname: Wang
authors.forename: Weiyu
authors.initials: W
authors.lastname: Li
authors.forename: Chao
authors.initials: C
authors.lastname: Fang
authors.forename: Yanting
authors.initials: Y
authors.lastname: Shen
authors.forename: Congcong
authors.initials: C
authors.lastname: Li
authors.forename: Yunshuai
authors.initials: Y
authors.lastname: Wu
authors.forename: Zhixi
authors.initials: Z
authors.lastname: Tian
mesh_terms: D017124:Conserved Sequence; D004251:DNA Transposable Elements; D019143:Evolution, Molecular; D020440:Gene Duplication; D018745:Genome, Plant; D035683:MicroRNAs / Q000235:genetics*; D011123:Polyploidy; D018749:RNA, Plant / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics; D011995:Recombination, Genetic; D017423:Sequence Analysis, RNA; D013025:Glycine max / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements; D035683:MicroRNAs; D018749:RNA, Plant; D034741:RNA, Small Interfering
keywords: MIRNA-like hairpin; evolution; microRNA; soybean; structure divergence