Chromosome-Level Genome Assembly and Genetic Maker System of the Endangered Largemouth Bronze Gudgeon (Coreius guichenoti) with Focus on Conservation Applications.

IF 3.5 1区 生物学 Q1 ZOOLOGY
Chuang Zhou, Zhongyi Wang, Xiaodong Wang, Huantao Qu, Zhaobin Song
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引用次数: 0

Abstract

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.

濒危大嘴青铜鲟染色体水平基因组组装与基因制造系统及其保护应用
大嘴铜鳉(Coreius guichenoti)是长江上游地区的一种特有鱼类。由于水污染、过度捕捞和大坝建设等人为因素,近几十年来,古切诺蒂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脚手架技术,生成了guichenoti的参考染色体水平基因组组装。最终基因组组装全长1.10 Gb (contig N50: 28.64 Mb;支架N50: 42.39 Mb),有25条染色体。该基因组的完整性评分为96.4%,与斑马鱼和褐家鼠基因组具有较高的一致性。共注释了24 325个PCGs。比较基因组学分析鉴定出986个扩增基因家族,这些基因家族显著富集与精子和卵子发育、相互作用以及免疫相关的氧化石墨烯。此外,正选择基因(PSGs)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,综合分析吉氏假体的多态性微卫星(SSR)位点,通过PCR和基因分型验证,筛选出排名前15位的四核苷酸SSR位点构建遗传maker系统。这15个无Hardy-Weinberg平衡(HWE)偏差的四核苷酸SSR位点多态性高,扩增稳定性好,具有选择性中性。PID (sibs)曲线显示,4个四核苷酸SSR位点(cgui1、cgui5、cgui3、cgui13)的亚群足以准确鉴定贵氏恙虫个体(PIDsib < 0.01)。这15个四核苷酸SSR位点也可作为后续亲本鉴定和遗传多样性分析的遗传标记。染色体水平上的基因组组装和研究结果为桂衣虫的分子育种、基因组研究和生物保护奠定了坚实的基础。
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来源期刊
CiteScore
6.40
自引率
12.10%
发文量
81
审稿时长
>12 weeks
期刊介绍: The official journal of the International Society of Zoological Sciences focuses on zoology as an integrative discipline encompassing all aspects of animal life. It presents a broader perspective of many levels of zoological inquiry, both spatial and temporal, and encourages cooperation between zoology and other disciplines including, but not limited to, physics, computer science, social science, ethics, teaching, paleontology, molecular biology, physiology, behavior, ecology and the built environment. It also looks at the animal-human interaction through exploring animal-plant interactions, microbe/pathogen effects and global changes on the environment and human society. Integrative topics of greatest interest to INZ include: (1) Animals & climate change (2) Animals & pollution (3) Animals & infectious diseases (4) Animals & biological invasions (5) Animal-plant interactions (6) Zoogeography & paleontology (7) Neurons, genes & behavior (8) Molecular ecology & evolution (9) Physiological adaptations
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