Liu Feng, Zhan Wei, Guo Dandan, Ye Ting, Lou Bao
Zhejiang Key Laboratory of Coastal Biological Germplasm Resources Conservation and Utilization, Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
State Key Laboratory for the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
Sci Data. 2025 Apr 30;12(1):721. doi: 10.1038/s41597-025-05072-y.
Small yellow croaker (Larimichthys polyactis) represents an important commercial fish species in China. A high-quality genome is essential for evaluating the fine-scale genetic structure, which has significant implications for the conservation of wild stocks, fishery management, and the utilization of germplasm in L. polyactis. This study presents a chromosome-level genome of L. polyactis generated by employing the PacBio high-fidelity (HiFi) and high-throughput chromosome conformation capture (Hi-C) technologies. The complete genome spans 677.35 Mb with a scaffold N50 size of 28.51 Mb. A substantial portion of the genome, totaling 663.13 Mb (97.90%), was anchored to 24 chromosomes. Based on Benchmarking Universal Single-Copy Ortholog (BUSCO) analysis, L. polyactis exhibits high genomic completeness (98.00%). A total of 28,640 annotated genes were identified, with 25,801 being functionally annotated. The comparisons of 24 chromosomes between L. polyactis and L. crocea proved high conservation of synteny between this pair of relatives. These findings provide valuable resources for the conservation, functional genomics, molecular breeding and evolutionary studies of L. polyactis.
小黄鱼（Larimichthys polyactis）是中国重要的商业鱼类品种。高质量的基因组对于评估精细尺度的遗传结构至关重要，这对小黄鱼野生种群的保护、渔业管理以及种质利用具有重要意义。本研究展示了一个利用PacBio高保真（HiFi）和高通量染色体构象捕获（Hi-C）技术生成的小黄鱼染色体水平基因组。完整基因组跨度为677.35 Mb，支架N50大小为28.51 Mb。基因组的大部分，总计663.13 Mb（97.90%），被锚定到24条染色体上。基于基准通用单拷贝直系同源基因（BUSCO）分析，小黄鱼表现出较高的基因组完整性（98.00%）。共鉴定出28,640个注释基因，其中25,801个具有功能注释。小黄鱼和大黄鱼（Larimichthys crocea）24条染色体的比较证明了这对亲属之间染色体同源性的高度保守性。这些发现为小黄鱼的保护、功能基因组学、分子育种和进化研究提供了宝贵资源。
