Objective This study aims to characterize the mitochondrial genome of Plectropomus laevis and provide key molecular data for phylogenetic analysis, genetic diversity assessment, and germplasm conservation of this species.

Method The complete mitochondrial genome of P. laevis was sequenced and annotated for the first time. Illumina sequencing technology was employed to obtain the whole-genome sequence. After assembly and annotation, bioinformatics analyses were performed, including base composition, codon usage bias, tRNA secondary structure prediction, and phylogenetic reconstruction based on 13 protein-coding genes (PCGs).

Result The results showed that the complete mitochondrial genome of P. laevis is 16 771 bp in length, containing 13 PCGs, 2 rRNA genes, 22 tRNA genes, and a control region containing the heavy-strand origin (OH). No gene loss or rearrangement was detected, indicating a highly conserved structure. Base composition analysis revealed an overall AT content of 56.93%, with an AT-skew of 0.0120 and a GC-skew of -0.2318, which are typical characteristics of vertebrate mitochondrial bias. Except for cox1 (GTG) and atp6 (CTG), all other PCGs start with ATG. Among amino acids, leucine (Leu) showed the highest proportion (16.0%), while cysteine (Cys) had the lowest (1.6%). Relative synonymous codon usage (RSCU) analysis indicated that highly preferred codons predominantly end with A/U, and the codon usage pattern is highly similars to those of its congeneric species P. leopardus and P. areolatus, revealing conserved codon usage within the genus. Among the 22 tRNAs, all except trnS1 exhibited a complete typical cloverleaf secondary structure; the dihydrouridine arm stem of trnS1 retained only 2 base pairs, showing a highly reduced structure, a feature rarely reported in the family Epinephelidae. Phylogenetic trees constructed using neighbor-joining and maximum likelihood methods based on the 13 PCGs consistently supported the monophyly of the genus Plectropomus and suggested that Plectropomus may represent an early-diverging lineage within Epinephelidae.

Conclusion The mitochondrial genome of P. laevis is highly conserved in structure and exhibits typical vertebrate nucleotide bias. Its codon usage pattern is highly conserved within the genus. The DHU arm of trnS1 is highly reduced, a feature rarely documented in Epinephelidae. Phylogenetic analysis confirmed the monophyly of Plectropomus and its placement as an early-diverging lineage.