Abstract
A small cold-water teleost endemic to Northeast Asia, Hypomesus nipponensis possesses a short lifecycle, high fecundity, and rapid population growth, with extensive introductions for aquacultural purposes across East Asia. In this study, we generated a gap-free, telomere-to-telomere (T2T) genome assembly of H. nipponensis using a combined sequencing strategy, incorporating MGI short reads, PacBio High-Fidelity (HiFi) reads, Oxford Nanopore Technologies (ONT) ultra-long reads, and Hi-C data. The final assembly spans 526.31 Mb with a contig N50 of 20.23 Mb, and all genomic sequences were successfully anchored to 28 pseudochromosomes. BUSCO assessment (Actinopterygii_odb10) confirms 98.19% completeness, including 3,548 single-copy and 26 duplicated orthologs out of 3,640 conserved genes. Repeat elements account for 39.17% (206.18 Mb) of the genome, and 31,310 protein-coding genes are annotated. This gap-free T2T assembly resolves previously uncharacterized genomic regions, providing a high-quality reference for molecular breeding, evolutionary analyses of the Hypomesus genus, and functional investigations into adaptive traits of cold-water fishes.
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Data availability
All data supporting this study have been publicly available. Raw sequencing data have been deposited in the NCBI Sequence Read Archive (SRA) database under the BioProject id PRJNA128279649, including RNA-seq data (SRR34259912 to SRR34259916), MGI genome survey data (SRR34259908), Hi-C reads (SRR34259911), Nanopore long-read data (SRR34259910) and PacBio long-read data (SRR34259909). The genome assembly has been deposited at the NCBl GenBank under the accession number of GCA_054491055.150. The genome assembly and gene structure annotation are also available on Figshare (https://doi.org/10.6084/m9.figshare.29672606.v1)51.
Code availability
All scripts and pipelines used for the genome assembly and gene annotation followed the standard manuals and protocols of the applied bioinformatics software. No specific code was developed for this study.
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Acknowledgements
This work was financially supported by the Earmarked Fund for the National Key R&D Program of China (Grant No. 2023YFD2400900) and the Modern Agricultural Technology System Grant (CARS-46).
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D. Xu designed and conceived the study. Y. Zhou, D. Fang, Y. You and X. Li collected the samples, conducted experiments. F. Tang, Y. Bai and M. Zhang performed bioinformatics analysis. Y. Zhou, G. Deng and D. Xu wrote and revised the manuscript. All authors have read and approved the final manuscript.
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Zhou, Y., Fang, D., You, Y. et al. A telomere-to-telomere reference genome assembly of the Hypomesus nipponensis. Sci Data (2026). https://doi.org/10.1038/s41597-026-07078-6
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DOI: https://doi.org/10.1038/s41597-026-07078-6
