Abstract
The Scorpaeniformes order encompasses a diverse array of teleost fish, including commercially important and venomous species. Fish venoms offer significant pharmacological potential, but incomplete phylogenetic understanding has hindered research. Resolving relationships among venomous fish families is crucial for studying venom evolution and discovering novel bioactive compounds. To address these phylogenetic uncertainties, we generated and assembled the complete mitochondrial genomes of Paracentropogon rubripinnis (Tetrarogidae) and Inimicus japonicus (Synanceiidae), two representative venomous species. The circular mitogenomes, 16,465 bp and 16,676 bp in length, respectively, contain the typical vertebrate mitochondrial gene complement. Comparative analyses revealed a highly conserved gene order and orientation across Scorpaeniformes, with slight variations in the Notothenioidei outgroups. We identified three novel conserved sequence blocks in the control regions and characterized structural features of protein-coding genes, tRNAs, and non-coding elements. Phylogenetic analyses using 13 mitochondrial protein-coding genes from 71 Scorpaeniformes and three outgroup species provided a higher-resolution phylogeny of the order, including 12 families and 31 genera. Our results support the monophyly of Tetrarogidae and Synanceiidae, placing them in an early-diverging position within the Scorpaeniformes phylogeny. This study provides insights into the phylogenetic positions of venomous fish families and lays a foundation for future research on fish venom evolution and applications.