| Summary: | <i>MIRNAs</i> are small non-coding RNAs that play important roles in a wide range of biological processes in plant growth and development. <i>MIR397</i> (involved in drought, low temperature, and nitrogen and copper (Cu) starvation) and <i>MIR408</i> (differentially expressed in response to environmental stresses such as copper, light, mechanical stress, dehydration, cold, reactive oxygen species, and drought) belong to conserved <i>MIRNA</i> families that either negatively or positively regulate their target genes. In the present study, we identified the homologs of <i>MIR397</i> and <i>MIR408</i> in <i>Oryza sativa</i> and its six wild progenitors, three non-<i>Oryza</i> species, and one dicot species. We analyzed the 100 kb segments harboring <i>MIRNA</i> homologs from 11 genomes to obtain a comprehensive view of their community evolution around these loci in the farthest (distant) relatives of rice. Our study showed that mature <i>MIR397</i> and <i>MIR408</i> were highly conserved among all <i>Oryza</i> species. Comparative genomics analyses also revealed that the microsynteny of the 100 kb region surrounding <i>MIRNAs</i> was only conserved in <i>Oryza</i> spp.; disrupted in <i>Sorghum,</i> maize, and wheat; and completely lost in <i>Arabidopsis</i>. There were deletions, rearrangements, and translocations within the 100 kb segments in <i>Oryza</i> spp., but the overall microsynteny of the region was maintained. The phylogenetic analyses of the precursor regions of all <i>MIRNAs</i> under study revealed a bimodal clade of common origin. This comparative analysis of miRNA involved in abiotic stress tolerance in plants provides a powerful tool for future <i>Oryza</i> research. Crop wild relatives (CWRs) offer multiple traits with potential to decrease the amount of yield loss owing to biotic and abiotic stresses. Using a comparative genomics approach, the exploration of CWRs as a source of tolerance to these stresses by understanding their evolution can be further used to leverage their yield potential.
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