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利用PacBio和Hi-C技术对乌鳢（Channa argus）进行染色体水平的基因组组装。

Chromosome-level genome assembly of the northern snakehead (Channa argus) using PacBio and Hi-C technologies.

作者信息

Sun Donglei, Wen Haishen, Qi Xin, Li Chao, Wang Lingyu, Li Jianlong, Zhu Mingxin, Zhang Xiaoyan, Li Yun

机构信息

Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Fisheries College, Ocean University of China, Qingdao, 266003, China.

School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.

出版信息

Sci Data. 2024 Dec 27;11(1):1437. doi: 10.1038/s41597-024-04314-9.

DOI:10.1038/s41597-024-04314-9
PMID:39730366
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11681256/
Abstract

The 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. 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. 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.

摘要

由于大多数此类器官在数百万年前就已进化，专门器官的进化起源对实证研究提出了重大挑战。北方黑鱼（乌鳢）是一种呼吸空气的鱼类，拥有鳃上器，这是攀鲈亚目鱼类的一个共同特征，为研究专门器官的功能和进化起源提供了独特的机会。在本研究中，利用PacBio HiFi测序和Hi-C技术构建了乌鳢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712.14 Mb，支架N50为28.08 Mb。组装的序列被锚定到24条假染色体上，并预测了21,643个蛋白质编码基因。该基因组包含27.70%的重复元件，包括3,588个（98.6%）完整的BUSCOs，与其他已发表的乌鳢组装序列相比，显示出更高的连续性和功能完整性。该基因组为探索水陆双模式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性策略。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/38b2/11681256/12845ae0f855/41597_2024_4314_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/38b2/11681256/4f80ba081f1c/41597_2024_4314_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/38b2/11681256/9329409e5ff5/41597_2024_4314_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/38b2/11681256/22e2846dbd2c/41597_2024_4314_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/38b2/11681256/12845ae0f855/41597_2024_4314_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/38b2/11681256/4f80ba081f1c/41597_2024_4314_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/38b2/11681256/9329409e5ff5/41597_2024_4314_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/38b2/11681256/22e2846dbd2c/41597_2024_4314_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/38b2/11681256/12845ae0f855/41597_2024_4314_Fig4_HTML.jpg

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