title: The evolution of plant microRNAs: insights from a basal eudicot sacred lotus.
abstract: microRNAs (miRNAs) are important noncoding small RNAs that regulate mRNAs in eukaryotes. However, under which circumstances different miRNAs/miRNA families exhibit different evolutionary trajectories in plants remains unclear. In this study, we sequenced the small RNAs and degradome from a basal eudicot, sacred lotus (Nelumbo nucifera or lotus), to identify miRNAs and their targets. Combining with public miRNAs, we predicted 57 pre-eudicot miRNA families from different evolutionary stages. We found that miRNA families featuring older age, higher copy and target number tend to show lower propensity for miRNA family loss (PGL) and stronger signature of purifying selection during divergence of temperate and tropical lotus. Further analyses of lotus genome revealed that there is an association between loss of miRNA families in descendent plants and in duplicated genomes. Gene dosage balance is crucial in maintaining those preferentially retained MIRNA duplicates by imposing stronger purifying selection. However, these factors and selection influencing miRNA family evolution are not applicable to the putative MIRNA-likes. Additionally, the MIRNAs participating in lotus pollen-pistil interaction, a conserved process in angiosperms, also have a strong signature of purifying selection. Functionally, sequence divergence in MIRNAs escalates expression divergence of their target genes between temperate and tropical lotus during rhizome and leaf growth. Overall, our study unravels several important factors and selection that determine the miRNA family distribution in plants and duplicated genomes, and provides evidence for functional impact of MIRNA sequence evolution.
authors.affiliation: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Shi
authors.affiliation: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan, China.|School of Life Sciences, Wuhan University, Wuhan, China.
authors.forename: Kun
authors.initials: K
authors.lastname: Wang
authors.affiliation: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan, China.|Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, China.
authors.forename: Pingfang
authors.initials: P
authors.lastname: Yang
mesh_terms: D019143:Evolution, Molecular; D035264:Flowers / Q000235:genetics; D020440:Gene Duplication; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics; D035683:MicroRNAs / Q000145:classification / Q000235:genetics*; D031653:Nelumbo / Q000235:genetics*; D010802:Phylogeny; D018515:Plant Leaves / Q000235:genetics; D011058:Pollen / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics*; D012641:Selection, Genetic
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant
keywords: basal eudicot; evolution; genome duplication; microRNA; sacred lotus (Nelumbo nucifera)