First Chromosome-level Genome Assembly and Annotation of an Endangered Freshwater Stingray (Fontitrygon garouaensis) from Africa

Fontitrygon garouaensis (Smooth Freshwater Stingray) is an evolutionarily distinct and globally endangered species and is currently the only stingray known to be strictly adapted to African freshwater systems. Lack of a reference genome has limited studies of its adaptive evolution and genomic architecture. Here, we present the first chromosome-level genome assembly of F. garouaensis using a hybrid approach that integrates PacBio HiFi long reads, Illumina short reads, and Hi-C chromatin conformation capture. The assembly spans 4.19 Gb with 41 anchored chromosomes, a scaffold N50 of 86.49 Mb, and a contig N50 of 16.58 Mb. Overall, 84.07% of the genome was assigned to chromosomes, with 65.27% repetitive elements. BUSCO analysis showed 93.3% completeness, confirming a highly contiguous genome. We annotated 29,804 protein-coding genes, with 98.28% functionally annotated. Repetitive elements comprised 65.27% of the genome, including lineage-specific expansions of DNA transposons (7.13%) and LTRs (19.31%). This genomic resource establishes a foundation for systematic, evolutionary, and conservation research on this threatened species.