Chromosome-level Genome Assembly of the Small Snakehead (Channa asiatica) Provides Insights into the Genetic Basis for its Pelvic Fin Loss.

Abstract

The paired appendages of vertebrates are a pivotal developmental innovation, of which the pelvic fins of teleosts are evolutionarily homologous to the hind limbs of tetrapods. The small snakehead (Channa asiatica), an important freshwater fish with significant commercial value, lacks the pelvic fins while some other fish species in the same genus have. To determine the genetic changes underlying the pelvic fin loss in the small snakehead, we assembled the chromosome-level genome of the species based on PacBio HiFi and Hi-C sequencing technology and performed comparative genomics analyses. The final genome assembly of the small snakehead has a total length of 714.57 Mb with 23 chromosomes (contig N50 of 27.93 Mb and scaffold N50 of 28.54 Mb), and 193.09 Mb (27.02%) interspersed repeats and 22,300 protein-coding genes were annotated. Phylogenetic and divergence analyses indicated that the small snakehead was the sister branch to the combination of the northern snakehead (C. argus) and the blotched snakehead (C. maculata) and diverged from the common ancestor approximately 24.7 Mya. Three small snakehead-specific missense mutations were identified in tbx4 gene whose loss could cause the pelvic fin loss. Significant chromosomal rearrangement and 214 small snakehead-specific structural variations (SSSVs) were detected between the small snakehead and other Channa species. Among these SSSVs, the deletion in pax7a was likely to play a role in the pelvic fin loss. Furthermore, the specific loss of conserved non-coding regulatory elements (CNEs) related to limb/fin development was detected in the small snakehead, which possibly led to the pelvic fin loss of the small snakehead. The present study generated the high-quality chromosome-scale reference genome of the small snakehead, which provided a valuable genomic resource for the follow-up studies, and our findings shed light on the important genetic clues regarding pelvic fin loss in the species.