A telomere-to-telomere reference genome assembly of the Hypomesus nipponensis

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.