Abstract
The giant pangasius (Pangasius sanitwongsei) is a critically endangered freshwater species with considerable ecological and economic significance in Southeast Asia and southern China. However, the lack of a high-quality reference genome has limited studies on its genetic adaptation and conservation strategies. Here, we present a chromosome-scale genome assembly of P. sanitwongsei, generated using PacBio HiFi long-read sequencing and Hi-C chromatin conformation capture. The final assembly spans 808.85 Mb, with a contig N50 of 18.70 Mb and a scaffold N50 of 28.10 Mb, achieving a BUSCO gene completeness of 99.15%. A total of 23,469 protein-coding genes were annotated, and 96.97% of the genes were functionally characterized. This high-quality genomic resource provides crucial insights into the adaptive evolution of Pangasiidae catfishes and offers a valuable foundation for conservation genomics, adaptive evolution, population genetics, and sustainable aquaculture development.
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Data availability
The raw sequencing datasets have been deposited in the NCBI Sequence Read Archive under accession SRP57947851. The assembled P. sanitwongsei genome is available in GenBank under accession GCA_051225755.152, and the corresponding genome annotation files has been archived on Figshare (https://doi.org/10.6084/m9.figshare.29715215)53.
Code availability
No special codes or scripts were used in this work, and data processing was carried out based on the protocols and manuals of the corresponding bioinformatics software.
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Acknowledgements
We acknowledge financial support from the Guangxi Key R&D Program Agriculture and Rural Areas (AB2506910048), National Modern Agriculture Industry Technology System Special Project (CARS-46), Central Public-interest Scientific Institution Basal Research Fund, CAFS (2025XK01, 2025SJHX1, 2023TD37), China-ASEAN Maritime Cooperation Fund (CAMC-2018F), Guangdong Province Rural Revitalization Strategy Special Fund (2023-SJS-00-001).
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Gan, B., Wei, L., Ma, Y. et al. A chromosome-level reference genome assembly of the giant pangasius (Pangasius sanitwongsei). Sci Data (2025). https://doi.org/10.1038/s41597-025-06445-z
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DOI: https://doi.org/10.1038/s41597-025-06445-z
