Abstract
Siniperca obscura is an economically valuable and ecologically significant species in China, yet the lack of comprehensive genomic resources has hindered genetic studies and breeding efforts. In this study, we present a high-quality, chromosome-level genome assembly for S. obscura, generated by integrating PacBio HiFi long-read sequencing with Hi-C scaffolding. The final assembly spans 734.12 Mb, with 99.85% of the assembled bases anchored and oriented onto 24 chromosomes. It achieves a contig N50 of 24.59 Mb and a scaffold N50 of 30.62 Mb, with high genome completeness further demonstrated by a BUSCO score of 99.37%. We predicted 23,225 protein-coding genes, with a 99.12% BUSCO completeness, and 98.50% of the genes were functionally annotated. Approximately 30.54% of the genome sequences were classified as repeat elements. This high-quality reference genome provides a valuable resource for advancing molecular breeding, comparative genomics, and evolutionary studies of S. obscura and closely related species.
Data availability
All data generated in this study have been deposited in public repositories and are freely available. Raw sequencing data, including PacBio HiFi, Hi-C, MGI short-read, and transcriptome datasets, are available in the NCBI Sequence Read Archive under accession number PRJNA124564946. The chromosome-level genome assembly of Siniperca obscura has been deposited in NCBI GenBank under accession GCA_049996615.147. The corresponding genome annotation files have been deposited in the Figshare repository48.
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 National Modern Agriculture Industry Technology System Special Project (CARS-46), Monitoring of Aquatic Resources in Key Waters of Anhui Province (2024BFAFZ02936), Special Fund for Anhui Agriculture Research System (2021-711), 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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Liu, H., Liu, H., Cui, K. et al. Chromosome-level genome assembly of the Siniperca obscura. Sci Data (2026). https://doi.org/10.1038/s41597-026-06678-6
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DOI: https://doi.org/10.1038/s41597-026-06678-6
