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Chromosome-Level Assembly and Annotation of the Grey Reef Shark (Carcharhinus amblyrhynchos) Genome.

Carolin Dahms·Laurent Vigliola·Leni Hiu Tong Cheung·Jerome Ho Lam Hui·Paolo Momigliano
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Abstract

To date less than 5% of shark species 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 pseudochromosomes; 2.9 Gbp) and high completeness (94% complete BUSCOs). BRAKER3 annotated 16,505 protein-coding genes after masking repetitive elements which accounted for 59% of the genome. We identified potential X and Y sex chromosomes on pseudochromosomes 36 and 57, respectively. The quality and completeness of the draft genome of C. amblyrhynchos will enable researchers to investigate genetic variations and adaptations specific to this species as well as across other Carcharhinus spp., opening new venues for comparative genomics and advancing conservation genetic applications.

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AnimalsSharksGenomeMolecular Sequence AnnotationCarcharhinidaeHiFireference genomesex chromosomeshark conservationJournal ArticleResearch Support, Non-U.S. Gov't

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Carolin Dahms, Laurent Vigliola, Leni Hiu Tong Cheung, Jerome Ho Lam Hui, Paolo Momigliano. 2025-09-30. Chromosome-Level Assembly and Annotation of the Grey Reef Shark (Carcharhinus amblyrhynchos) Genome.. https://doi.org/10.1093/gbe%2Fevaf176

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