Insights into the Evolution of Ancient Shark and Ray Sex Chromosomes

While sex-determining mechanisms have been extensively characterized in many vertebrates, they have not been explored in chondrichthyan fishes until relatively recently. In the present study, we used high-quality whole genome reference assemblies to examine the putative sex chromosomes of 14 elasmobranch species spanning nine orders. We describe four newly assembled reference genomes belonging to the white shark Carcharodon carcharias, the Atlantic stingray Hypanus sabinus, the smalltooth sawfish Pristis pectinata, and the zebra shark Stegostoma tigrinum. We conducted sex chromosome identification and verification using short-read sequence data collected for multiple individuals for three of the species. This revealed putative pseudoautosomal regions (PARs) and, in one instance, a candidate sex chromosome reassignment. A synteny analysis revealed an ancient and shared origin of the chromosomes within elasmobranchs considerably older than any previously proposed scenario, and a potential candidate gene involved in sex determination shared across all examined species. The synteny analysis also revealed a historical fusion and the formation of neo-Y chromosomes between two myliobatiform species. Our results show that there has been strong conservation and homology of the X chromosomes among elasmobranchs in spite of their varied features and different evolutionary histories.