Complete Mitochondrial Genome of Haemulon plumierii (Lacepède, 1801) Supports Its Use as a Sentinel Reef Fish

Background: Mitochondrial genomes provide valuable information on evolutionary relationships among organisms and on the selective pressures acting on energy metabolism, increasing their relevance in ecological and environmental genomics studies. Haemulon plumierii is a reef-associated fish distributed throughout the Gulf of Mexico and Caribbean Sea and has been proposed as a bioindicator species within the Mesoamerican Reef System. Methods: In this study, we present a high-quality mitochondrial genome of H. plumierii from the southeastern coast of Mexico generated using PacBio HiFi long-read sequencing. Results: The circular mitogenome is 16,823 bp long and contains the complete set of 37 canonical mitochondrial genes, including 13 protein-coding genes, 22 tRNAs, two rRNAs, and one control region (D-loop). The gene order, strand orientation, and tRNA secondary structures were consistent with the conserved vertebrate mitochondrial architecture. Comparative analyses with closely related haemulid species revealed conserved nucleotide composition patterns, negative GC skew values, strong AT enrichment within the D-loop, and highly conserved mitochondrial synteny. Phylogenetic reconstruction based on complete mitochondrial genomes placed H. plumierii firmly within the Haemulon clade. Selective pressure analyses revealed pervasive purifying selection acting on mitochondrial protein-coding genes, supported by low dN/dS ratios, high amino acid identity, constrained nucleotide diversity in cytochrome oxidase genes, and conserved codon usage patterns shaped primarily by AT-driven mutational bias. Pairwise genetic distance analyses further supported moderate interspecific divergence within Caribbean Haemulon species. Conclusions: Overall, the mitogenomic resource generated here provides an important evolutionary and functional framework for future phylogenetic, ecological, and environmental genomics studies in Caribbean reef fishes.