Chromosome-scale genome assembly of three-spotted seahorse (Hippocampus trimaculatus) with a unique karyotype
文献类型： 外文期刊
作者： Li, Ning 1 ; Zhang, Xinhui 2 ; Liu, Xin 4 ; Lin, Xueqiang 5 ; Hu, Cancan 6 ; Chen, Jieming 3 ; Wang, Shengchao 5 ; Zhang, Dong 4 ; Wei, Shuguang 1 ; Shi, Qiong 2 ;
作者机构： 1.Xi An Jiao Tong Univ, Coll Forens Sci, Xian 710061, Shaanxi, Peoples R China
2.Shenzhen Univ, Coll Life Sci & Oceanog, Lab Aquat Genom, Shenzhen 518057, Peoples R China
3.BGI Acad Marine Sci, Shenzhen Key Lab Marine Genom, Guangdong Prov Key Lab Mol Breeding Marine Econ An, Shenzhen 518081, Peoples R China
4.Chinese Acad Fisheries Sci, East China Sea Fisheries Res Inst, Shanghai 200090, Peoples R China
5.Hainan BGI Marine Sci & Tech Co Ltd, Wenchang 571300, Peoples R China
6.Ocean Univ China, Shenzhen Inst, Shenzhen 518100, Peoples R China
7.Xi An Jiao Tong Univ, Key Lab Minist Publ Hlth Forens Sci, Xian 710061, Shaanxi, Peoples R China
8.Neijiang Normal Univ, Sch Life Sci, Key Lab Sichuan Prov Fishes Conservat & Utilizat U, Neijiang 641100, Peoples R China
期刊名称：SCIENTIFIC DATA （ 影响因子：6.9； 五年影响因子：8.7 ）
ISSN：
年卷期： 2025 年 12 卷 1 期
页码：
收录情况： SCI
摘要： 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.
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