Telomere-to-telomere genome assembly of Hypomesus nipponensis

Hypomesus nipponensis is a small, cold-water fish species characterized by a short life cycle, high fecundity, and rapid population growth. It is naturally found in northeastern Asia and has been extensively introduced for commercial purposes across eastern 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 assembled genome has a total length of approximately 526.31 Mb, with an N50 of 20.23 Mb, and all genomic sequences were successfully anchored to 28 pseudo-chromosomes.

日本公鱼（Hypomesus nipponensis）是一种小型冷水性鱼类，具有生命周期短、繁殖力旺盛、种群增长迅速的特征。该物种自然分布于亚洲东北部，且为商业目的被广泛引种至东亚地区。本研究采用联合测序策略，整合MGI短读长测序数据、PacBio高保真（HiFi）读长数据、牛津纳米孔技术（ONT）超长长读长测序数据及Hi-C染色质构象捕获数据，完成了日本公鱼的无间隙、端粒到端粒（T2T）基因组组装。组装所得基因组总长度约为526.31 Mb，N50值为20.23 Mb，所有基因组序列均成功锚定至28条伪染色体。