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 nuciferaor 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 retainedMIRNAduplicates by imposing stronger purifying selection. However, these factors and selection influencing miRNA family evolution are not applicable to the putativeMIRNA-likes. Additionally, theMIRNAsparticipating in lotus pollen–pistil interaction, a conserved process in angiosperms, also have a strong signature of purifying selection. Functionally, sequence divergence inMIRNAsescalates 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 ofMIRNAsequence evolution.Significance statement
microRNAs are noncoding small RNAs known to regulate gene expression. Here we compared microRNAs from an early diverging eudicot (sacred lotus) with those of other eudicot families and concluded that copy number, target gene number and genome duplication all influence microRNA evolutionary trajectories, by imposing different levels of purifying selection.