Chromosome-level assembly and annotation of the grey reef shark (Carcharhinus amblyrhynchos) genome

Abstract

To date only four of nine shark orders have nuclear reference genomes, despite next-generation sequencing advances. Particularly for threatened shark species, there is a lack of reliable genomes which are crucial in facilitating research and conservation applications. We assembled the first nuclear reference genome of the endangered grey reef shark (Carcharhinus amblyrhynchos) using long-read PacBio HiFi and Omni-C sequencing to reach chromosome-level contiguity (36 pseudo chromosomes; 2.9 Gbp) and high completeness (94% complete BUSCOs). BRAKER3 annotated 16,522 protein-coding genes after masking repetitive elements which accounted for 59% of the genome. We identified potential X and Y sex chromosomes on pseudo chromosomes 36 and 57, respectively. The quality and completeness of the draft genome of C. amblyrhynchos suggest that it has the potential to facilitate comprehensive comparative genomics, enabling researchers to investigate genetic variations and adaptations specific to this population and will help advance conservation genetic applications. Significance StatementStemming from an ancient vertebrate lineage, sharks present an interesting evolutionary study system. A third of shark species face extinction, yet critical genomic resources necessary for research and conservation remain scarce. To address this gap, we assembled and annotated the first chromosome-level nuclear reference genome of the threatened grey reef shark (Carcharhinus amblyrhynchos) at high completeness. This genome will help advance studies in evolution, phylogenetics, adaptation, and conservation, offering insights not only for this species but for wider elasmobranch and vertebrate research.