| Summary: | <i>Harbinger</i> elements are DNA transposons that are widespread from plants to vertebrates but absent from mammalian genomes. Among vertebrates, teleost fish are the clade presenting not only the largest number of species but also the highest diversity of transposable elements, both quantitatively and qualitatively, making them a very attractive group to investigate the evolution of mobile sequences. We studied <i>Harbinger</i> DNA transposons and the distantly related <i>ISL2EU</i> elements in fish, focusing on representative teleost species compared to the spotted gar, the coelacanth, the elephant shark and the amphioxus. We observed high variability in the genomic composition of <i>Harbinger</i>-like sequences in teleost fish, as they covered 0.002–0.14% of the genome, when present. While <i>Harbinger</i> transposons might have been present in a common ancestor of all the fish species studied here, with secondary loss in elephant shark, our results suggests that <i>ISL2EU</i> elements were gained by horizontal transfer at the base of teleost fish 200–300 million years ago, and that there was secondary loss in a common ancestor of pufferfishes and stickleback. <i>Harbinger</i> transposons code for a transposase and a <i>Myb</i>-like protein. We reconstructed and compared molecular phylogenies of both proteins to get insights into the evolution of <i>Harbinger</i> transposons in fish. Transposase and <i>Myb</i>-like protein phylogenies showed global congruent evolution, indicating unique origin of the association between both genes and suggesting rare recombination between transposon sublineages. Finally, we report one case of <i>Harbinger</i> horizontal transfer between divergent fish species and the transcriptional activity of both <i>Harbinger</i> and <i>ISL2EU</i> transposons in teleost fish. There was male-biased expression in the gonads of the medaka fish.
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