miRNAs genes are thought to undergo quick birth and death processes in genomes and the emergence of MIRNA-like hairpin provides the base for functional MIRNA gene formation. However, the factors affecting the formation of an active miRNA gene from an MIRNA-like hairpin within a genome remain unclear. We performed a genome-wide investigation of MIRNA-like hairpin accumulation, expression, structural changes and relationships with annotated genomic features in the paleopolyploid soybean genome. Our results showed that adjacent gene and transposable element content, rates of genetic recombination at location of emergence, along with its own gene structure divergence greatly affected miRNA gene evolution. Further investigation suggested that miRNA genes from different duplication sources followed distinct evolutionary trajectories and that the accumulation of MIRNA-like hairpins might be a major factor causing LTR-RTs to lose activity during genome evolution.

Keywords:
microRNA;MIRNA-like hairpin;Evolution;structure divergence;soybean