Lian Kaiqi, Shan Jinyan, Ma Jun, Liu Yuling, Li Xiaolong, Lu Meng, Ding Miao, Wei Jie, Zhou Li, Kuang Youyi, Gui Jianfang, Peng Renhai
School of Biotechnology and Food Science, Anyang Institute of Technology, Anyang, 455000, China.
Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
Sci Data. 2025 Jul 24;12(1):1290. doi: 10.1038/s41597-025-05636-y.
Qihe gibel carp (Carassius gibelio var. Qihe) is a local population of natural gynogenetic amphitriploid (AAABBB) Carassius gibelio, and has high nutritional and economic value. In this study, we assemble a high-quality chromosome-level genome of Qihe gibel carp through DNBSEQ, PacBio HiFi, and Hi-C sequencing data. The resulting assembly consisted of 350 contigs with the full length of 1.607 Gb and 96.21% (1.515 Gb) of the assembled genome was successfully anchored to 50 chromosomes, with a contig N50 of 28.97 Mb and a scaffold N50 of 29.84 Mb. Repeated sequences accounting for 43.72% (732.494 Mb) of the total were also identified, and gene prediction revealed 46,131 protein-coding genes with an annotation ratio of 96.48%. Furthermore, Benchmarking Universal Single-Copy Orthologue (BUSCO) analysis demonstrated that the genome assembly achieved high completeness, with a score of 97.66%. This high-quality chromosome-level genome lays the foundation for molecular biology research as well as molecular breeding and evolutionary studies of Qihe gibel carp in the future.
淇河鲫（Carassius gibelio var. Qihe）是天然雌核发育三倍体（AAABBB）鲫鱼的一个地方种群，具有较高的营养和经济价值。在本研究中，我们通过DNBSEQ、PacBio HiFi和Hi-C测序数据组装了高质量的淇河鲫染色体水平基因组。所得组装结果由350个重叠群组成，全长1.607 Gb，96.21%（1.515 Gb）的组装基因组成功锚定到50条染色体上，重叠群N50为28.97 Mb，支架N50为29.84 Mb。还鉴定出占总数43.72%（732.494 Mb）的重复序列，并通过基因预测发现了46131个蛋白质编码基因，注释率为96.48%。此外，基准通用单拷贝直系同源基因（BUSCO）分析表明，基因组组装具有较高的完整性，得分97.66%。这种高质量的染色体水平基因组为淇河鲫未来的分子生物学研究以及分子育种和进化研究奠定了基础。
