Li Ning, Zhang Xinhui, Liu Xin, Lin Xueqiang, Hu Cancan, Chen Jieming, Wang Shengchao, Zhang Dong, Wei Shuguang, Shi Qiong
College of Forensic Science, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China.
Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518057, China.
Sci Data. 2025 Jan 11;12(1):49. doi: 10.1038/s41597-024-04349-y.
Three-spotted seahorse (Hippocampi trimaculata) is a unique fish with important economic and medicinal values, and its total chromosome number is potentially quite different from other seahorse species. Herein, we constructed a chromosome-level genome assembly for this special seahorse by integration of MGI short-read, PacBio HiFi long-read and Hi-C sequencing techniques. A 416.57-Mb haplotypic genome assembly was obtained. Subsequently, 99.38% of its scaffold sequences were anchored onto 18 chromosomes, with identification of 29.1% repeat sequences in the assembled genome. Additional karyotype analysis validated the diploid chromosomes of 2n = 36, which are remarkably different from other seahorses' 2n = 42 or 44. The genome completeness (BUSCO score: 96.5%, CEGMA score: 97.87%) confirmed that this chromosome-scale assembly is indeed of high quality. Moreover, a total of 18,712 protein-coding genes were annotated, of which 96.36% could be predicted with functions. Based on construction of a phylogenetic tree, we estimated that Hippocampus and Syngnathoides diverged approximately 50.1 million years ago (Mya). Taken together, our genome data presented in this study provide a valuable genetic resource for numerical chromosome changes and in-depth evolutionary and functional investigations, as well as conservation and molecular breeding of this endangered teleost.
三斑海马（Hippocampi trimaculata）是一种具有重要经济和药用价值的独特鱼类，其染色体总数可能与其他海马物种有很大差异。在此，我们通过整合MGI短读长、PacBio HiFi长读长和Hi-C测序技术，为这种特殊的海马构建了染色体水平的基因组组装。获得了一个416.57 Mb的单倍型基因组组装。随后，其99.38%的支架序列被锚定到18条染色体上，在组装的基因组中鉴定出29.1%的重复序列。额外的核型分析验证了其二倍体染色体为2n = 36，这与其他海马的2n = 42或44明显不同。基因组完整性（BUSCO评分：96.5%，CEGMA评分：97.87%）证实了这种染色体水平的组装确实具有高质量。此外，总共注释了18,712个蛋白质编码基因，其中96.36%可以预测其功能。基于系统发育树的构建，我们估计海马属和管口鱼属大约在5010万年前（Mya）分化。综上所述，我们在本研究中呈现的基因组数据为这种濒危硬骨鱼的染色体数目变化、深入的进化和功能研究以及保护和分子育种提供了宝贵的遗传资源。
