Multi-genome comparisons reveal gain-and-loss evolution of theanti-Mullerian hormone receptor type 2gene, an old master sex determining gene, in Percidae

Abstract

ABSTRACTThe Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies inPerca fluviatilis,Perca schrenkiiandSander vitreusalong 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 (amhr2bY), previously suggested to be the master sex determining (MSD) gene inP. flavescens. Phylogenetically related and structurally similar amhr2duplications (amhr2b) were found inP. schrenkiiandSander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. InP. fluviatilisandS. vitreus, thisamhr2bduplicate has been lost while it was subject to amplification inS. lucioperca. Analyses of theamhr2blocus inP. schrenkiisuggest that this duplication could be also male-specific as it is inP. flavescens. InP. fluviatilis, 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 thatP. fluviatilishas a male heterogametic sex determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198,hsdl1,tbc1d32) 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 knownPercaspecies.