Zhou Chuang, Wang Zhongyi, Wang Xiaodong, Qu Huantao, Song Zhaobin
Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China.
Integr Zool. 2025 Sep;20(5):1061-1073. doi: 10.1111/1749-4877.12926. Epub 2024 Dec 17.
The largemouth bronze gudgeon (Coreius guichenoti), an endemic fish species, is distributed in the upper Yangtze River drainage. Due to anthropogenetic factors such as water pollution, overfishing, and dam construction, the wild populations of C. guichenoti have dramatically declined in recent decades. In this study, we generated a reference chromosomal-level genome assembly of C. guichenoti on the basis of PacBio HiFi sequencing and Hi-C scaffolding technologies. The final genome assembly was 1.10 Gb in length (contig N50: 28.64 Mb; scaffold N50: 42.39 Mb) with 25 chromosomes. The completeness score of the C. guichenoti genome was 96.4%, and high synteny was detected compared with Danio rerio and Ictalurus punctatus genomes. A total of 24 325 PCGs were annotated for the C. guichenoti genome. Comparative genomics analysis identified 986 expanded gene families in C. guichenoti, which were significantly enriched in GO items associated with the development and interaction of sperm and egg as well as immunity. Furthermore, positively selected genes (PSGs) detected in C. guichenoti were mainly associated with DNA repair, ATP binding, mitochondrion, and lipid homeostasis. Based on the reference genome and resequencing data, the polymorphic microsatellite (SSR) loci were comprehensively analyzed for C. guichenoti, and the top 15 tetra-nucleotide SSR loci were selected for the construction of the genetic maker system after validation through PCR and genotyping. All of these 15 tetra-nucleotide SSR loci without Hardy-Weinberg equilibrium (HWE) deviation showed high polymorphism, good amplification stability, and selective neutrality. The PID (sibs) curves revealed that the subset of four tetra-nucleotide SSR loci (cgui1, cgui5, cgui3, cgui13) was sufficient for accurate identification of C. guichenoti individuals (PIDsib < 0.01). These 15 tetra-nucleotide SSR loci could also serve as genetic markers in subsequent parentage identification and genetic diversity analysis. The chromosome-level genome assembly and findings laid solid foundations for molecular breeding, genomic research, and biological conservation of C. guichenoti.
大口铜鱼（Coreius guichenoti）是一种长江上游特有的鱼类。由于水污染、过度捕捞和大坝建设等人为因素，近几十年来大口铜鱼的野生种群数量急剧下降。在本研究中，我们基于PacBio HiFi测序和Hi-C染色体挂载技术，构建了大口铜鱼的染色体水平参考基因组。最终的基因组组装长度为1.10 Gb（重叠群N50：28.64 Mb；支架N50：42.39 Mb），包含25条染色体。大口铜鱼基因组的完整性评分为96.4%，与斑马鱼（Danio rerio）和斑点叉尾鮰（Ictalurus punctatus）基因组相比，检测到高度的共线性。大口铜鱼基因组共注释了24325个蛋白质编码基因（PCG）。比较基因组学分析确定了大口铜鱼中986个扩张的基因家族，这些基因家族在与精子和卵子发育及相互作用以及免疫相关的基因本体（GO）条目中显著富集。此外，在大口铜鱼中检测到的正选择基因（PSG）主要与DNA修复、ATP结合、线粒体和脂质稳态相关。基于参考基因组和重测序数据，对大口铜鱼的多态性微卫星（SSR）位点进行了全面分析，并通过PCR验证和基因分型后，选择了前15个四核苷酸SSR位点构建遗传标记系统。这15个四核苷酸SSR位点均无哈迪-温伯格平衡（HWE）偏差，表现出高度多态性、良好的扩增稳定性和选择中性。亲权鉴定概率（PID，同胞）曲线显示，四个四核苷酸SSR位点（cgui1、cgui5、cgui3、cgui13）的子集足以准确鉴定大口铜鱼个体（PID同胞<0.01）。这15个四核苷酸SSR位点也可作为后续亲权鉴定和遗传多样性分析的遗传标记。染色体水平的基因组组装和研究结果为大口铜鱼的分子育种、基因组研究和生物保护奠定了坚实基础。
