Evolution and retention of oxidative phosphorylation paralogues in euteleosts: insights from gilthead seabream and European seabass

Abstract Background Oxidative phosphorylation (OXPHOS) is the primary source of cellular adenosine triphosphate (ATP), producing over 90% of cellular ATP through five multiprotein complexes in the inner mitochondrial membrane, encoded by both mitochondrial and nuclear genomes. Teleost fishes, which experienced two rounds of whole-genome duplication followed by a teleost-specific genome duplication, represent an excellent system to explore mechanisms of duplicate gene retention, divergence, and functional specialization, and to investigate how genome duplications shape core metabolic pathways. In this study, the evolution of OXPHOS genes in euteleosts was analyzed with a focus on two evolutionarily closely related but ecologically distinct teleosts of high commercial value with well-annotated genomes: the gilthead seabream ( Sparus aurata ) and the European seabass ( Dicentrarchus labrax ). Results Comparative genomics identified 23 multi-copy OXPHOS gene families in gilthead seabream and 21 in European seabass, most of which were traced back to the teleost-specific genome duplication. To test the hypothesis that retention of duplicated OXPHOS genes reflects a balance between dosage constraints and functional divergence, we focused on early larval development, a critical phase characterized by rapid growth and high energy demand. Transcriptomics analysis suggested differential expression patterns among the paralogues, with some exhibiting stable expression levels consistent with dosage balance, and others expressed only at specific developmental stages. Conclusions Together, our findings provide the first comprehensive view of OXPHOS paralogue evolution in the euteleostean lineages examined here and indicate how genome duplication shaped the nuclear-encoded OXPHOS repertoire and may have contributed to its developmental regulation. These findings highlight how gene duplication may support flexible mitochondrial energy regulation during development and suggest a conserved, functionally relevant diversification of core metabolic genes in the euteleostean lineages examined.