Transposable element-mediated co-option drives the evolution of the miRNA regulatory system in Oryza AA-genome species

MicroRNAs (miRNAs) are key post-transcriptional regulators in plants, yet the evolutionary dynamics of the entire miRNA-mediated regulatory system remain poorly understood. We performed small RNA sequencing and comparative genomics analyses across all eight AA-genome species of Oryza within a well-resolved phylogenetic framework. We found that miRNA gene (MIRNA) families evolve with low birth-death rates, while individual paralogous MIRNAs turn over rapidly. We identified a novel mechanism in which transposable element (TE) insertions de novo generates functional miRNA target sites. miRNA target genes are characterized by distinct evolutionary signatures, including greater sequence length, lower GC content, moderately highly expression, reduced expression variability, and higher evolutionary conservation, which is consistent with their role as a conserved kernel regulatory subsystem. In contrast, the majority of recently evolved target genes that have acquired their miRNA binding sites through TE insertions tend to exhibit the opposite set of features. Furthermore, we uncovered co-evolutionary signatures between duplicated MIRNAs and their target genes, as well as between MIRNAs and phased siRNAs (phasiRNAs). Taken together, our study reveals multi-level evolutionary dynamics driven by TEs that rapidly generate new regulatory circuit and proposes a generalizable TE-MIRNA co-option model for regulatory network expansion in plants.