Abstract
The mandarin fish (Siniperca scherzeri), renowned as the “freshwater grouper”, has emerged as a commercially significant aquaculture species in China due to its superior flesh quality, disease resistance, and domestication adaptability. With the rapid development of bioinformatics, higher standards of genome analysis are now required compared to previous reference genomes. In this study, we integrated PacBio HiFi long-read sequencing, Oxford Nanopore Technologies ultralong-read sequencing, and Hi-C chromatin conformation capture to assemble a near-complete telomere-to-telomere genome. The gapless assembly spans 24 chromosomes, with telomeric repeats detected at both ends of 20 chromosomes and at only one end of the remaining four chromosomes. BUSCO evaluation against the Actinopterygii database (actinopterygii_odb10) revealed 98.7% genome completeness. Alignment analyses using minimap2 demonstrated >97% mapping rates for ONT ultralong reads, PacBio HiFi reads, and Hi-C data against the assembled genome. We annotated 23,296 protein-coding genes, establishing a crucial genomic resource for elucidating the species’ evolutionary biology and advancing molecular breeding strategies.
Data availability
The genome sequencing data generated in this study and the genome assembly as well as annotation data have been deposited into the China National GeneBank Sequence Archive (CNSA) under the project accession CNP000795142. The sequencing data have been also archived in the NCBI SRA under accession SRP65285743, and the assembled genome and annotation have been archived in the NCBI GenBank under accession JBVQOQ00000000044. The genome assembly data and annotations have also been deposited at Figshare45.
Code availability
No specific code was used in this study. The data analysis used standard bioinformatic tools specified in the methods.
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Acknowledgements
This work was financially supported by Fujian Province Seed Industry Innovation and Industrialization Engineering Fishery Project(2021MNZ05), and Agriculture Research System of China (CARS-46).
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D.Z. and Z.W. designed the study. Y.L. H.X. and Z.C. were involved in sample collection. Y.L., Z.C. and Y.W. performed the experiment and analyzed the data. Y.L. and Y.W. wrote the paper. M.W., X.Y. and M.L. revised the paper.
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Wu, Y., Cheng, Z., Li, Y. et al. Telomere-to-telomere gapless genome assembly of Siniperca scherzeri. Sci Data (2026). https://doi.org/10.1038/s41597-026-07113-6
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DOI: https://doi.org/10.1038/s41597-026-07113-6
