| Summary: | <i>Dada</i> is a unique superfamily of DNA transposons, inserted specifically in multicopy RNA genes. The zebrafish genome harbors five families of <i>Dada</i> transposons, whose targets are U6 and U1 snRNA genes, and tRNA-Ala and tRNA-Leu genes. <i>Dada-U6</i>, which is inserted specifically in U6 snRNA genes, is found in four animal phyla, but other target-specific lineages have been reported only from one or two species. Here, vertebrate genomes and transcriptomes were surveyed to characterize <i>Dada</i> families with new target specificities, and over 120 <i>Dada</i> families were characterized from the genomes of actinopterygian fish. They were classified into 12 groups with confirmed target specificities. Newly characterized <i>Dada</i> families target tRNA genes for Asp, Asn, Arg, Gly, Lys, Ser, Tyr, and Val, and 5S rRNA genes. Targeted positions inside of tRNA genes are concentrated in two regions: around the anticodon and the A box of RNA polymerase III promoter. Phylogenetic analysis revealed the relationships among actinopterygian <i>Dada</i> families, and one domestication event in the common ancestor of carps and minnows belonging to Cyprinoidei, Cypriniformes. Sequences targeted by phylogenetically related <i>Dada</i> families show sequence similarities, indicating that the target specificity of <i>Dada</i> is accomplished through the recognition of primary nucleotide sequences.
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