Comparative Mitogenome Analyses Uncover Mitogenome Features and Phylogenetic Implications of the Reef Fish Family Holocentridae (Holocentriformes)

SIMPLE SUMMARY: Mitochondria play a critical role in the energy metabolism of coral reef fish, providing ATP to fuel cellular processes. A mitogenome study has been employed to investigate the genetic diversity, population structure, and evolutionary relationships among coral reef fish taxa. Species of the Holocentridae family play important ecological roles in coral reef communities. Two subfamilies of this family, Holocentrinae and Myripristinae, exhibit similarities in morphology and distribution, with minor differences in habitation and feeding behavior. Here, we present full mitochondrial genome sequences of eight holocentrid species and report the results of a comparative analysis with six previously published species. The results indicate that these mitogenome structures are relatively conserved, except for the high variability in control regions. The whole genomes, except for nad6, exhibited positive AT-skews and negative GC-skews. Furthermore, we compared the two subfamilies to explore the reasons behind their varying inhabitation and behavior. Phylogenetic analysis indicated all species formed two subfamilies, the Holocentrinae and Myripristinae, with each subfamily comprising two genera. Positive selection analysis revealed that all protein-coding genes (PCGs) were subjected to purifying selection. The data obtained from our study could serve as a valuable resource for future investigations on the evolution and conservation of holocentrid fish. ABSTRACT: To understand the molecular mechanisms and adaptive strategies of holocentrid fish, we sequenced the mitogenome of eight species within the family Holocentridae and compared them with six other holocentrid species. The mitogenomes were found to be 16,507–16,639 bp in length and to encode 37 typical mitochondrial genes, including 13 PCGs, two ribosomal RNAs, and 22 transfer RNA genes. Structurally, the gene arrangement, base composition, codon usage, tRNA size, and putative secondary structures were comparable between species. Of the 13 PCGs, nad6 was the most specific gene that exhibited negative AT-skews and positive GC-skews. Most of the genes begin with the standard codon ATG, except cox1, which begins with the codon GTG. By examining their phylogeny, Sargocentron and Neoniphon were verified to be closely related and to belong to the same subfamily Holocentrinae, while Myripristis and Ostichthys belong to the other subfamily Myripristinae. The subfamilies were clearly distinguished by high-confidence-supported clades, which provide evidence to explain the differences in morphology and feeding habits between the two subfamilies. Selection pressure analysis indicated that all PCGs were subject to purifying selection. Overall, our study provides valuable insight into the habiting behavior, evolution, and ecological roles of these important marine fish.