AbstractThe evolutionary origins of specialized organs pose significant challenges for empirical studies, as most such organs evolved millions of years ago. The Northern snakehead (Channa argus), an air-breathing fish, possesses a suprabranchial organ, a common feature of the Anabantoidei, offering a unique opportunity to investigate the function and evolutionary origins of specialized organs.

摘要专业器官的进化起源对实证研究提出了重大挑战，因为大多数此类器官是在数百万年前进化的。北蛇头（Channa argus）是一种呼吸空气的鱼，拥有鳃上器官，这是Anabantoidei的共同特征，为研究专门器官的功能和进化起源提供了独特的机会。

In this study, a high-quality chromosome-level reference genome of C. argus was constructed using PacBio HiFi sequencing and Hi-C technology. The final genome assembly size is 712.14 Mb, with a scaffold N50 of 28.08 Mb. The assembled sequences were anchored to 24 pseudo-chromosomes and predicted 21,643 protein-coding genes.

在这项研究中，使用PacBio HiFi测序和Hi-C技术构建了C.argus的高质量染色体水平参考基因组。最终的基因组组装大小为712.14Mb，支架N50为28.08Mb。组装的序列锚定在24条假染色体上，并预测了21643个蛋白质编码基因。

The genome comprises 27.70% repetitive elements and includes 3,588 (98.6%) complete BUSCOs, demonstrating superior contiguity and functional completeness compared to other published C. argus assemblies. This genome provides valuable genetic resources for exploring the evolution of the aquatic-aerial bimodal breathing system, including clarifying the evolutionary histories and adaptive strategies..

该基因组包含27.70%的重复元件，包括3588个（98.6%）完整的BUSCO，与其他已发表的C.argus装配体相比，表现出优越的连续性和功能完整性。该基因组为探索水生空中双峰呼吸系统的进化提供了宝贵的遗传资源，包括阐明进化历史和适应策略。。

Background & SummaryThe northern snakehead, Channa argus, belonging to the Anabantoidei, is an economically important freshwater species that is extensively cultivated in Asia and Africa1. Because of its strong growth capacity, high nutritive value, and significant hypoxia tolerance2, northern snakehead has become extremely popular in the Chinese aquaculture industry, with annual production exceeding 500,000 tons3.

背景与总结北方蛇头Channa argus属于Anabantoidei，是一种经济上重要的淡水物种，在亚洲和非洲广泛种植1。由于其强大的生长能力，高营养价值和显着的耐缺氧性2，北方蛇头在中国水产养殖业中非常受欢迎，年产量超过50万吨3。

In recent years, increasing market demands have promoted the development of genetic improvements in several economically important traits of the northern snakehead, such as body color3, growth4, and sex-related traits5. Additionally, the northern snakehead possesses a suprabranchial organ (SBO) for aerial respiration6,7, making it an excellent model for investigating the evolution and functional mechanism of the air-breathing organ (ABO) (Fig. 1).Fig.

近年来，不断增长的市场需求促进了北方蛇头几个经济重要性状的遗传改良的发展，如体色3，生长4和性别相关性状5。此外，北方蛇头拥有一个用于空中呼吸的鳃上器官（SBO）[6,7]，这使其成为研究空气呼吸器官（ABO）进化和功能机制的优秀模型（图1）。图。

1Morphological photograph of C. argus and suprabranchial organ. The suprabranchial organ are made up of areas 1, 2, and 3.Full size imageThe transformation from aquatic to aerial gas exchange in vertebrates has long been a hot topic of study for evolutionary biologists. Fish conduct aerial respiration, providing critical evidence for the evolution of life from the ocean to land8.

1乌鳢和鳃上器官的形态学照片。鳃上器官由区域1、2和3组成。全尺寸图像脊椎动物从水生到空中气体交换的转变一直是进化生物学家研究的热点。鱼类进行空中呼吸，为生命从海洋到陆地的进化提供了重要证据8。

Notably, some fish have evolved ABOs to adapt to anoxic environments9,10. More than 450 fish species across 50 families have been reported to possess ABOs11, but these organs vary significantly among different fishes. Several types of fish ABOs have been reported, including SBO, modified swim bladder, skin, stomach, oropharyngeal cavity, and intestine6,10,12.

。据报道，50个科的450多种鱼类具有ABOs11，但这些器官在不同鱼类中差异很大。已经报道了几种类型的鱼ABO，包括SBO，改良的游泳膀胱，皮肤，胃，口咽腔和肠6,10,12。

These organs share features similar to those of higher vertebrate lungs, such as being well-vascularized13 and having a short blood-gas diffusion distance14,15. Fish with bimodal r.

这些器官具有与高等脊椎动物肺相似的特征，例如血管化良好13，血气扩散距离短14,15。双峰r鱼。

De novo genome assembly and chromosome constructionThe genome size of C. argus was estimated based on the k-mer frequency distribution analysis using the clean data of short-read sequencing. The k-mer count frequencies were computed by GenomeScope (v 2.0)30 with a k-mer size of 27. The estimated genome size was 681.47 Mb, and the heterozygosity rate was 0.20% based on the k-mer frequency analysis (Table 2, Fig. 2a).Table 2 Statistical results of k-mer analysis.Full size tableFig.

从头基因组组装和染色体构建使用短读测序的干净数据，基于k-mer频率分布分析估计C.argus的基因组大小。k-mer计数频率由GenomeScope（v 2.0）30计算，k-mer大小为27。根据k-mer频率分析，估计的基因组大小为681.47Mb，杂合率为0.20%（表2，图2a）。表2 k-mer分析的统计结果。全尺寸表图。

2Chromosome-level genome assembly and annotation of the northern snakehead. (a) k-mer frequency distribution in the C. argus genome. The k-mer distributions showed that the genome size was calculated to be 681.47 Mb with a heterozygous rate of 0.20%. (b) Hi-C interaction heatmap for the northern snakehead genome.

2北蛇头的染色体水平基因组组装和注释。（a） C.argus基因组中的k-mer频率分布。k-mer分布显示，基因组大小计算为681.47Mb，杂合率为0.20%。（b） 北方蛇头基因组的Hi-C相互作用热图。

The map shows scaffolded and independently assembled chromosomes at high resolution. (c) Characterization of the assembled genome of C. argus. The tracks indicate a) gene density, b) GC density, c) DNA repeat, d) LINE repeat, e) LTR repeat, and f) SINE repeat. The densities of genes, GC, and TEs were calculated in 100 kb windows.

该图显示了高分辨率的支架和独立组装的染色体。（c） c.argus组装基因组的表征。轨迹表示a）基因密度，b）GC密度，c）DNA重复，d）线重复，e）LTR重复和f）正弦重复。在100kb的窗口中计算基因，GC和TE的密度。

(d) Distribution of divergence rate for TEs in the C. argus genome.Full size imageThe genome of C. argus was initially assembled by HiFiasm (v 0.13) using the HiFi reads from the long-read sequencing31. Duplicate contigs and redundant sequences in the primary assembly were removed using the Purge_dups program32.

（d） 乌鳢基因组中TE的发散率分布。全尺寸图像C.argus的基因组最初由HiFiasm（v 0.13）使用来自长读取序列的HiFi读数组装31。使用Purge\U dups程序删除了主组件中的重复重叠群和冗余序列32。

After de novo assembly and polishing, a 712.14 Mb reference genome of C. argus with a scaffold N50 length of 11.61 Mb was generated (Table 3). To further construct the chromosome-level genome, Hi-C clean reads were aligned with the primarily assembled genome by BWA (v 0.7.10)33 to construct inter-/intrachromosomal contact maps.

从头组装和抛光后，产生了支架N50长度为11.61 Mb的C.argus的712.14 Mb参考基因组（表3）。为了进一步构建染色体水平的基因组，通过BWA（v 0.7.10）33将Hi-C清洁读数与主要组装的基因组进行比对，以构建染色体间/染色体内接触图。

Open-source tools Juicer.

开源工具榨汁机。

Code availability

代码可用性

All software and pipelines used for data analyses were executed according to the manual and protocols of the published bioinformatic tools. The version and code/parameters of software have been described in Methods.

用于数据分析的所有软件和管道均根据已发布的生物信息学工具的手册和协议执行。软件的版本和代码/参数已在方法中描述。

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Seppey, M., Manni, M. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness. Methods Mol. Biol. 227-245 (2019).Download referencesAcknowledgementsThis work was supported by Shandong Technical System of Fish Industry (SDAIT-12-03). We acknowledge the support of the High-Performance Biological Supercomputing Center at the Ocean University of China for this research.Author informationAuthors and AffiliationsKey Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Fisheries College, Ocean University of China, Qingdao, 266003, ChinaDonglei Sun, Haishen Wen, Xin Qi, Lingyu Wang, Jianlong Li, Mingxin Zhu & Yun LiSchool of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, ChinaChao Li & Xiaoyan ZhangAuthorsDonglei SunView author publicationsYou can also search for this author in.

。方法分子生物学。227-245（2019）。下载参考文献致谢这项工作得到了山东省渔业技术系统（SDAIT-12-03）的支持。我们感谢中国海洋大学高性能生物超级计算中心对这项研究的支持。作者信息作者和附属机构中国海洋大学水产学院海水养殖实验室（中国海洋大学），教育部（KLMME），中国海洋大学，青岛，266003，中国孙东磊，温海深，齐欣，王凌宇，李建龙，朱明新和李云青岛农业大学海洋科学与工程学院，青岛，266109，李朝伟和张晓燕作者孙东磊作者出版物你也可以在中搜索这位作者。

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PubMed Google ScholarContributionsY.L. and H.W. conceived and supervised the study. Y.L. and H.W. coordinated and supervised the whole study. D.S. collected the sample and conducted the genome assembly and analysis. D.S. drafted the manuscript. Y.L. revised the manuscript. X.Q., C.L., L.W., J.L., M.Z.

PubMed谷歌学术贡献。五十、 H.W.构思并监督了这项研究。Y、 L.和H.W.协调并监督了整个研究。D、 美国收集了样本并进行了基因组组装和分析。D、 美国起草了手稿。Y、 L.修改了手稿。十、 Q.，C.L.，L.W.，J.L.，M.Z。

and X.Z. participated in discussions and provided suggestions for manuscript improvement. All authors have read and approved the final manuscript for publication.Corresponding authorCorrespondence to.

和X.Z.参加了讨论，并为稿件改进提供了建议。所有作者都阅读并批准了最终稿件的出版。对应作者对应。

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The authors declare no competing interests.

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Ethics statement

道德声明

This work was approved by the Animal Research and Ethics Committees of Ocean University of China (Permit Number: 20141201). All the methods used in this study were carried out following approved guidelines.

这项工作得到了中国海洋大学动物研究与伦理委员会的批准（许可证号：20141201）。本研究中使用的所有方法均按照批准的指南进行。

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Reprints and permissionsAbout this articleCite this articleSun, D., Wen, H., Qi, X. et al. Chromosome-level genome assembly of the northern snakehead (Channa argus) using PacBio and Hi-C technologies.

转载和许可本文引用本文Sun，D.，Wen，H.，Qi，X。等人使用PacBio和Hi-C技术对北蛇头（Channa argus）进行染色体水平的基因组组装。

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