Multi-genome comparisons reveal gain-and-loss evolution of the gene, an old master sex determining gene, in Percidae.

The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in , and along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (), previously suggested to be the master sex determining (MSD) gene in . Phylogenetically related and structurally similar a duplications () were found in and , potentially dating this duplication event to their last common ancestor around 19-27 Mya. In and , this duplicate has been lost while it was subject to amplification in . Analyses of the locus in suggest that this duplication could be also male-specific as it is in . In , a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome-18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variants (SNVs) and no large duplication/insertion event, suggesting that has a male heterogametic sex determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (, , ) with higher expression in testis than ovary. Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known species.