The functional scope of plant microRNA-mediated silencing

•Deep sequencing has revealed a complex miRNome in plants.•Bioinformatics and molecular analyses suggest that plant miRNAs regulate many genes.•Evolutionary and genetic analyses argue that plant miRNAs regulate few genes.•Complexities in miRNA target recognition may explain the discrepancy.

Deep sequencing has identified a complex set of plant miRNAs that potentially regulates many target genes of high complementarity. Furthermore, the discovery that many plant miRNAs work through a translational repression mechanism, along with the identification of noncanonical targets, has encouraged bioinformatic searches with less stringent parameters, identifying an even wider range of potential targets. Together, these findings suggest that any given plant miRNA family may regulate a highly diverse set of mRNAs. Here we present evolutionary, genetic, and mechanistic evidence that opposes this idea but instead suggests that families of sequence-related miRNAs regulate very few functionally related targets. We propose that complexities beyond complementarity impact plant miRNA target recognition, possibly explaining the current disparity between bioinformatic prediction and functional evidence.