Mitogenomic Characterization, Genetic Diversity, and Matrilineal Phylogenetic Insights of the Marbled Goby (Oxyeleotris marmorata) from Its Native Range in Indonesia

Butidae is a family of teleost fishes with diverse morphological and ecological adaptations, including the marbled goby (<i>Oxyeleotris marmorata</i>), a large species of high economic value in Southeast and East Asia. The previous mitogenomic studies on cultured populations of <i>O. marmorata</i> from non-native habitats have provided limited insights into genetic divergence, structural variation, and evolutionary relationships. Hence, this study presented the complete mitochondrial genome of <i>O. marmorata</i> from its native habitat in Indonesia, providing structural characterization, assessment of genetic diversity, and matrilineal phylogenetic analysis. The circular mitogenome was 16,525 bp, comprising 37 genes and a non-coding control region (CR). The gene organization and strand distribution were conserved among <i>Oxyeleotris</i> species, with 28 genes on the heavy strand and nine on the light strand, and a pronounced A+T compositional bias. The comparative analyses of <i>O. marmorata</i> (from both native and cultured habitats) and <i>Oxyeleotris lineolata</i> mitogenomes revealed minor variations in intergenic spacers, gene overlaps, protein-coding gene (PCGs) lengths, and codon usage patterns. Conversely, the nonsynonymous and synonymous substitution ratios observed in species of the family Butidae and its closest related family (Eleotridae) indicate strong purifying selection in the present dataset. Notably, the ATG was the predominant start codon, whereas the COI gene utilized GTG, and amino acid composition analysis demonstrated high frequencies of arginine, leucine, and serine. Most transfer RNAs retained the canonical cloverleaf secondary structure except for trnS1, which lacked a functional dihydrouridine arm, whereas the CR contained four conserved sequence blocks with variable nucleotide motifs and no detectable tandem repeats. The haplotype analysis of native (Indonesia) and introduced populations (China) highlighted three haplotypes with high diversity (Hd = 1.0000) and substantial nucleotide variation (π = 0.6667). The genetic divergence across 13 PCGs was gene-specific, with COI and ND5 showing the highest variation, while ND4L and ATP8 were highly conserved. The phylogenetic analyses based on concatenated 13 PCGs using both Bayesian Inference and Maximum Likelihood methods revealed that <i>Oxyeleotris</i> forms a monophyletic clade and is closely related to <i>Bostrychus sinensis</i>. In addition, the broader phylogenetic framework inferred the matrilineal relationships within the family Butidae and its closest related family, Eleotridae. This study also recommends expanding analyses to include the mitogenomes of the remaining 17 <i>Oxyeleotris</i> species, together with comprehensive genomic data, to further elucidate their genetic architecture, evolutionary history, and ecological adaptability across diverse aquatic ecosystems.