Li Xuemei, Wu Xingbing, Zhu Yongjiu, Li Xiaoli, Meng Zihao, Wei Nian, Xiang Miao, Yang Deguo, Zhu Tingbing
Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China.
Sci Data. 2025 Jan 15;12(1):76. doi: 10.1038/s41597-025-04416-y.
Coreius guichenoti, mainly distributed in upstream regions of the Yangtze River China, is currently on the brink of extinction and listed as national secondary protected animal. In this study, we aimed to obtain the chromosome-level genome of C. guichenoti using PacBio and Hi-C techniques. According to the PacBio sequencing, C. guichenoti genome was successfully assembled to 1100.1 Mb size, with a Contig N50 size of 25.0 Mb, and containing 731.0 Mb of repeats. Hi-C sequencing data was utilized for chromosome assembly and 25 chromosome sequences were ultimately yielded, with a total length of 1076.8 Mb. Moreover, a total of 22,506 protein-coding genes were predicted with average intron length of 2293 bp. Evolutionary analysis and divergence time prediction revealed that C. guichenoti was closely related to C. heterodon and they phylogenetically diverged from common ancestor ~20.7 million years ago (Mya), following the separation of Cyprinidae at 28.3 Mya. In the future, the utilization of comparative genomics research is important in elucidating the molecular mechanisms of Ichthyophthirius disease and ensuring the conservation of biological resources.
中华倒刺鲃主要分布于中国长江上游地区，目前已濒临灭绝，被列为国家二级保护动物。在本研究中，我们旨在利用PacBio和Hi-C技术获得中华倒刺鲃的染色体水平基因组。根据PacBio测序，中华倒刺鲃基因组成功组装至1100.1 Mb大小，Contig N50大小为25.0 Mb，包含731.0 Mb的重复序列。利用Hi-C测序数据进行染色体组装，最终获得25条染色体序列，总长1076.8 Mb。此外，共预测出22506个蛋白质编码基因，平均内含子长度为2293 bp。进化分析和分歧时间预测表明，中华倒刺鲃与高体倒刺鲃密切相关，它们在系统发育上于约2070万年前（Mya）从共同祖先分化而来，此前鲤科在2830万年前已分离。未来，比较基因组学研究的应用对于阐明小瓜虫病的分子机制和确保生物资源的保护具有重要意义。
