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SUMMARY

microRNAs (miRs) are small non-coding RNA molecules expressed in a tissue-specific manner in numerous organisms. Among them, miR-1, miR-206, and miR-133, which are encoded as bicistronic gene clusters in the genome, play major roles in the control of vertebrate myogenesis. To address how the gene organization and function of these miRs evolved, we identified their homologues in the cyclostomes, the chondrichthyans and the teleosts, and examined their patterns of expression during development. It was suggested that the chondrichthyans and the cyclostome lampreys possess fewer miR-1/miR-133 genes than the medaka. The medaka additionally possessed the miR-206 gene which was not found in the genomes of chondrichthyans and lampreys. In contrast, the number and genomic organization of medaka miR-1(206)/miR-133 were similar to those found in mammals. In the lamprey, shark and medaka, miR-1 and miR-133 were expressed in both skeletal and cardiac muscle cells in adults, a developmental feature traced back to chordate invertebrates such as ascidians. We further examined the expression of these miRs in different muscle tissues in medaka embryos. miR-206 was expressed in both the tail and pectoral fin muscles, whereas miR-1, which shares the similar nucleotide sequence with miR-206, was not detectable in the embryonic pectoral fins. Comparison of the relative positions with the neighboring protein-coding genes showed high conservation of synteny between the miR-1(206)/miR-133 clusters in a single species, as well as across the vertebrate taxa. Our results suggest that, after the gene duplications, these muscle-specific miRs acquired differential regulatory functions and have contributed to the establishment of diverse and complex musculature of vertebrates.