Selection fine-tunes the expression of microRNA target genes in Arabidopsis thaliana

MicroRNAs (miRNAs) are involved in posttranscriptional gene regulation by repressing the expression of their target genes through inhibition of translation and/or cleavage of mRNAs. In plants, the target genes of miRNAs usually belong to large gene families, and miRNA regulation is gained for individual genes throughout gene family evolution. To explore the selective effect of miRNA regulation on their target genes, we investigated the pattern of polymorphism and interspecific divergence in 11 multigene families that include target genes of ancient miRNAs in Arabidopsis thaliana. We found that the levels of polymorphism and divergence in target genes are significantly reduced, whereas those for nontarget genes are very similar to the genomic averages. This pattern is particularly clear at synonymous sites; we found that the reduction of synonymous variation is caused by selection for optimal codons, which increase the efficiency and accuracy of translation. Based on these results, we conclude that tuning via miRNA regulation has a strong impact on the evolution of target genes through which highly sophisticated regulation systems have been established.