The pangenome of Acanthopagrus provides genomic variation evidence for genetic diversity

Acanthopagrus species are ecologically and economically important sparid fishes with strong environmental adaptability. To characterize genomic architecture underlying their adaptation and phenotypic diversity, a population-scale survey of intraspecific variation in yellowfin seabream (A. latus) was conducted using whole-genome resequencing data from 80 wild individuals. Among the genomic variations identified, structural variations (SVs) contribute disproportionately high to genomic diversity, defining 11,463 variable genes associated with immunity, ion transport, and environmental adaptation. Compared to the core genes with conserved functions in basic metabolism, these variable genes exhibit lower expression levels but higher transcriptional variance. Furthermore, a pangenome graph for Acanthopagrus species identifies a 24-bp deletion in the gch2 promoter of blackhead seabream (A. schlegelii) as a candidate variant for the loss of xanthophore pigmentation. This deletion disrupts a conserved motif, potentially impairing Pax7a-mediated regulation. These findings uncover genetic mechanisms driving adaptation and phenotypic divergence in Acanthopagrus species with high aquaculture values.