Genome-wide identification and evolutionary analysis of positively selected miRNA genes in domesticated rice

The next-generation sequencing of tens to hundreds of plant genotypes made the uncovering of miRNA genes evolution available at the genome-wide level. Using the combinations of population genetics and evolutionary biology approaches, we have identified 21 miRNA loci having significant negative Tajima's D and Fu and Li's D* and F* values, of which 14 miRNAs (ps-miRNAs) showing clear signatures of positive selection in domesticated rice. The average sequence diversity (π) of the 21 miRNAs in cultivated rice is only 13.8 % of that in their wild progenitors. Interestingly, protein-coding genes immediately flanking these ps-miRNAs are apparently under weaker selective constraints. Totally, the 21 miRNAs are predicted to target 68 mRNA genes, of which 12 targets are estimated to have endured positive selection during rice evolution. In addition, the expression pattern and potential biological functions of ps-miRNAs targets are further investigated by searching published micro-array data and different mutant databases, respectively. We conclude that miRNAs, like protein-coding genes, should be crucial for driving rice evolution. These analyses may deepen our understanding on the miRNA genes evolution and functions during rice domestication.