Haplotype-resolved genomics identifies cyp19a1a as a candidate master sex-determining gene in golden trevally (Gnathanodon speciosus)

Teleost fish exhibit diverse genetic sex determination systems, offering opportunities to understand its genetic basis and insights into sex chromosome evolution. The golden trevally (<i>Gnathanodon speciosus</i>), a commercially important Carangidae species, was studied to uncover its sex determination mechanism. We generated haplotype-resolved, chromosome-level genome assemblies for both sexes and identified a ZW system with a ∼90 kb sex-determining region (SDR) on Chr1. Within the SDR, <i>cyp19a1a</i> is uniquely expressed from the W allele prior to gonadal differentiation. A ∼1-kb upstream region of <i>cyp19a1a</i> harbors fixed variants between sexes. Reporter gene assays reveal that these variants reduce promoter activity in the Z allele, likely silencing <i>cyp19a1aZ</i>. This suggests that allelic diversification led to the emergence of <i>cyp19a1aW</i> as the master sex-determining gene. Minimal divergence in the SDR implies a recent origin of sex chromosomes. These findings provide key genomic resources and insights into sex determination evolution in teleosts.