High-quality reference genome assembly of the critically endangered blackchin guitarfish (Glaucostegus cemiculus)

Blackchin guitarfish (Glaucostegus cemiculus, family Glaucostegidae, order Rhinopristiformes), are among the most threatened marine fish globally. The inferred global population size of G. cemiculus has been significantly reduced over the past three generations (45 years), yet there are only few local protection measures in place, and knowledge to develop well-informed timely conservation or management actions is limited. Here, reference genomes can be a useful tool, however, despite their possible conservation applications, and the critically endangered status of all seven species in the family Glaucostegidae, there are currently no available reference genomes for any of the giant guitarfishes. In addition, the current taxonomy of the order Rhinopristiformes is uncertain, which provides challenges to understanding their demographic history and evolution of taxa- or population-specific traits. Therefore, this study utilized bioinformatic tools to provide the first high-quality reference genome for G. cemiculus. The reference genome was assembled utilizing PacBio long-read high-fidelity (HiFi) sequencing data, obtained from one male blackchin guitarfish originally sampled in the wild, and now held at the Nausicaá Centre National de la Mer in Boulogne-sur-Mer, France. In total, four different assemblers were used to create six different assemblies, with the Hifiasm assembler providing the highest quality assembly. The resulting assembled reference genome is one of the most contiguous of all elasmobranchs (sharks, skates, and rays) to date. At 2.85 Gigabases, this genome falls within the large genome size range typical for elasmobranchs, with only Pristis pectinata currently having a more contiguous assembly. Heterozygosity within the assembled genome indicates reduced fitness in the population from the here sampled specimen's wild origin, possibly the Mediterranean Sea, an area where blackchin guitarfish have now experienced local extirpation. Overall, this study provides a critical baseline resource for the genomic conservation and management of the critically endangered blackchin guitarfish.