Wang Yuanyuan, Yang Yexin, Wu Yuli, Liu Yi, Li Qingyong, Liu Chao, Jiang Zhiyong, Jiang Wanying, Chen Fangcan, Mu Xidong
Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
Agro-Tech Extension Center of Guangdong Province, Guangzhou, 510520, China.
Sci Data. 2024 Dec 26;11(1):1435. doi: 10.1038/s41597-024-04331-8.
The ratmouth barbel (Ptychidio jordani) is a critically endangered freshwater fish from the Cyprinidae family, primarily due to overfishing and habitat disruption. To address the challenges of its shrinking wild populations and the difficulties in artificial reproduction, we sequenced, assembled, and annotated a high-quality chromosome-level genome of P. jordani using next-generation short-read sequencing, third-generation long-read sequencing, and Hi-C sequencing. The final genome assembly was 1.14 Gb, consisting of 25 chromosomes with a contig N50 of 25.14 Mb and a scaffold N50 of 42.91 Mb. We identified 25,183 protein-coding genes, 751.75 Mb of repeats, and 19,373 ncRNAs. Methylation loci on most chromosomes ranged from 1,000 to 3,000 per 100 kb window. Gene expression levels across various tissues were analyzed, revealing 12,135 (caudal fin), 11,465 (liver), 14,438 (gill), 12,413 (heart), 8,301 (spleen), and 3,578 (kidney) differentially expressed genes compared to muscle. The comprehensive genomic and transcriptomic resources generated here will aid in understanding the ecology, adaptation, and environmental responses of P. jordani, supporting future research and conservation efforts.
鼠嘴鲃（Ptychidio jordani）是鲤科一种极度濒危的淡水鱼，主要原因是过度捕捞和栖息地破坏。为应对其野生种群数量减少的挑战以及人工繁殖的困难，我们使用二代短读长测序、三代长读长测序和Hi-C测序技术，对鼠嘴鲃的高质量染色体水平基因组进行了测序、组装和注释。最终的基因组组装大小为1.14 Gb，由25条染色体组成，重叠群N50为25.14 Mb，支架N50为42.91 Mb。我们鉴定出25,183个蛋白质编码基因、751.75 Mb的重复序列和19,373个非编码RNA。大多数染色体上每100 kb窗口的甲基化位点数量在1000到3000之间。分析了不同组织的基因表达水平，与肌肉相比，尾鳍中有12,135个差异表达基因，肝脏中有11,465个，鳃中有14,438个，心脏中有12,413个，脾脏中有8,301个，肾脏中有3,578个。这里生成的全面的基因组和转录组资源将有助于了解鼠嘴鲃的生态学、适应性和环境响应，为未来的研究和保护工作提供支持。
