Liu Bingjian, Niu Xinyi, Zhang Chi, Zheng Sixu, Gao Luxiu, Han Mingzhe, Feng Taobo, Wu Jinghua, Jiang Chaoxuan, Kang Shuaishuo, Xu DongDong, Liu Yifan
College of Marine Science and Technology, Zhejiang Ocean University, 316022, Zhoushan, China.
National engineering research center for facilitated marine aquaculture, Zhejiang Ocean University, 316022, Zhoushan, China.
Sci Data. 2025 Apr 21;12(1):668. doi: 10.1038/s41597-025-04790-7.
The Chinese herring (Ilisha elongata) is a commercially and scientifically significant fish species. In this study, we conducted high-precision whole-genome sequencing using two high-throughput platforms: second-generation MGI and third-generation PacBio. Hi-C technology assisted in assembling the contig sequences onto 24 chromosomes, resulting in a high-quality chromosome-level genome map with excellent continuity and coverage. The completed genome size was approximately 815 Mb, with a contig N50 of 4.82 Mb, scaffold N50 of 32.61 Mb, and a chromosome mounting rate of 95.32%. SNP and InDel purity rates were 0.003% and 0.012%, respectively, and the genome assembly completeness was 96.68%, assessed by BUSCO. Repetitive sequences were annotated via ab initio and homology predictions, identifying 295.7 Mb of repetitive sequences, constituting 35.08% of the genome. A total of 26,381 protein-coding genes were predicted, with 24,596 functionally annotated.
中华鲥（Ilisha elongata）是一种具有商业和科学重要性的鱼类物种。在本研究中，我们使用了两个高通量平台进行高精度全基因组测序：第二代MGI和第三代PacBio。Hi-C技术协助将重叠群序列组装到24条染色体上，从而得到了具有出色连续性和覆盖度的高质量染色体水平基因组图谱。完成的基因组大小约为815 Mb，重叠群N50为4.82 Mb，支架N50为32.61 Mb，染色体挂载率为95.32%。SNP和InDel纯度率分别为0.003%和0.012%，通过BUSCO评估，基因组组装完整性为96.68%。通过从头预测和同源性预测对重复序列进行注释，鉴定出295.7 Mb的重复序列，占基因组的35.08%。总共预测了26,381个蛋白质编码基因，其中24,596个具有功能注释。
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