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

• Published in: Biology (Basel, Switzerland) Switzerland), 2023-09, Vol.12 (10), p.1273
• Main Authors: Tang, Qin, Liu, Yong, Li, Chun-Hou, Zhao, Jin-Fa, Wang, Teng
• Format: Article
• Language: English
• Subjects: Animal behavior; Base composition; Codon; codon usage; Comparative analysis; Coral reefs; Coral reefs and islands; Energy metabolism; Evolution & development; Evolutionary biology; Evolutionary conservation; Feeding behavior; Fish; Fishes; Fishing; gene rearrangement; Genes; Genetic diversity; Genetic testing; Genomes; Genomics; Holocentridae; Holocentrinae; Mitochondria; Mitochondrial DNA; mitogenome; Molecular modelling; Morphology; Myripristinae; Phylogenetics; Phylogeny; Population genetics; Population structure; Positive selection; Proteins; selection pressure; Species; Transfer RNA; tRNA
• ISSN: 2079-7737; 2079-7737
• DOI: 10.3390/biology12101273

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.