| Summary: | Limbs originated from paired fish fins are an important innovation in Gnathostomata. Many studies have focused on limb development-related genes, of which the T-box transcription factor 4 gene (<i>tbx4</i>) has been considered as one of the most essential factors in the regulation of the hindlimb development. We previously confirmed pelvic fin loss in <i>tbx4</i>-knockout zebrafish. Here, we report a high-quality genome assembly of the Japanese eel (<i>Anguilla japonica</i>), which is an economically important fish without pelvic fins. The assembled genome is 1.13 Gb in size, with a scaffold N50 of 1.03 Mb. In addition, we collected 24 <i>tbx4</i> sequences from 22 teleost fishes to explore the correlation between <i>tbx4</i> and pelvic fin evolution. However, we observed complete exon structures of <i>tbx4</i> in several pelvic-fin-loss species such as Ocean sunfish (<i>Mola mola</i>) and ricefield eel (<i>Monopterus albus</i>). More interestingly, an inversion of a special <i>tbx4</i> gene cluster (<i>brip1</i>-<i>tbx4</i>-<i>tbx2b</i>- <i>bcas3</i>) occurred twice independently, which coincides with the presence of fin spines. A nonsynonymous mutation (M82L) was identified in the nuclear localization sequence (NLS) of the Japanese eel <i>tbx4</i>. We also examined variation and loss of hindlimb enhancer B (HLEB), which may account for pelvic fin loss in Tetraodontidae and Diodontidae. In summary, we generated a genome assembly of the Japanese eel, which provides a valuable genomic resource to study the evolution of fish <i>tbx4</i> and helps elucidate the mechanism of pelvic fin loss in teleost fishes. Our comparative genomic studies, revealed for the first time a potential correlation between the <i>tbx4</i> gene cluster and the evolutionary development of toxic fin spines. Because fin spines in teleosts are usually venoms, this <i>tbx4</i> gene cluster may facilitate the genetic engineering of toxin-related marine drugs.
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