Genome Sequencing of the Japanese Eel () for Comparative Genomic Studies on and a Gene Cluster in Teleost Fishes.

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 () has been considered as one of the most essential factors in the regulation of the hindlimb development. We previously confirmed pelvic fin loss in -knockout zebrafish. Here, we report a high-quality genome assembly of the Japanese eel (), 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 sequences from 22 teleost fishes to explore the correlation between and pelvic fin evolution. However, we observed complete exon structures of in several pelvic-fin-loss species such as Ocean sunfish () and ricefield eel (). More interestingly, an inversion of a special gene cluster (--- ) 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 . 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 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 gene cluster and the evolutionary development of toxic fin spines. Because fin spines in teleosts are usually venoms, this gene cluster may facilitate the genetic engineering of toxin-related marine drugs.