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Chromosome-level genome assembly of the Chinese longsnout catfish Leiocassis longirostris

Wen-Ping He Jian Zhou Zhe Li Ting-Sen Jing Chun-Hua Li Yue-Jing Yang Meng-Bin Xiang Chao-Wei Zhou Guang-Jun Lv Hong-Yan Xu Hui Luo Hua Ye

Wen-Ping He, Jian Zhou, Zhe Li, Ting-Sen Jing, Chun-Hua Li, Yue-Jing Yang, Meng-Bin Xiang, Chao-Wei Zhou, Guang-Jun Lv, Hong-Yan Xu, Hui Luo, Hua Ye. Chromosome-level genome assembly of the Chinese longsnout catfish Leiocassis longirostris. Zoological Research, 2021, 42(4): 417-422. doi: 10.24272/j.issn.2095-8137.2020.327
Citation: Wen-Ping He, Jian Zhou, Zhe Li, Ting-Sen Jing, Chun-Hua Li, Yue-Jing Yang, Meng-Bin Xiang, Chao-Wei Zhou, Guang-Jun Lv, Hong-Yan Xu, Hui Luo, Hua Ye. Chromosome-level genome assembly of the Chinese longsnout catfish Leiocassis longirostris. Zoological Research, 2021, 42(4): 417-422. doi: 10.24272/j.issn.2095-8137.2020.327

基于染色体水平的长吻鮠参考基因组

doi: 10.24272/j.issn.2095-8137.2020.327

Chromosome-level genome assembly of the Chinese longsnout catfish Leiocassis longirostris

Funds: This study was supported by the China Agriculture Research System (CARS-46), Fundamental Research Funds for the Central Universities (XDJK2017B008, XDJK2017C035, XDJK2019C025, 5360300098), Natural Science Foundation of Chongqing (cstc2020jcyj-msxmX0438), and National Natural Science Foundation of China (32071651)
More Information
  • 摘要: 长吻鮠是中国重要的淡水经济鱼类之一,近年来,由于人工捕捞、水利工程修建等影响,野生长吻鮠资源衰减,数量急剧减少。作为进行性别二态性、比较生物学和保护生物学研究的有价值的模型,目前这一物种还缺乏用于比较基因组和进化分析的高质量染色体水平的参考基因组。因此,我们构建了首个长吻鮠高质量的染色体水平参考基因组。基因组大小为703.19 Mb,包含389个contigs,contig N50长度为4.29 Mb。利用高通量染色体构象捕获(Hi-C)数据,将685.53 Mb的基因组序列锚定到26条染色体上,长度为17.36~43.97 Mb,基因组的染色体锚定率为97.44%。长吻鮠基因组中共鉴定出23708个蛋白质编码基因、239.11 Mb重复序列(占全基因组的33.99%)和6303个非编码RNA。系统发育分析表明,长吻鮠和其亲缘关系最近的黄颡鱼大约在2660万年前开始分化。该研究获得的首个长吻鮠高质量参考基因组为今后的基因组比较和进化研究奠定了基础。
    #Authors contributed equally to this work
  • Figure  1.  Genome analysis of L. longirostris

    A: Image of L. longirostris used for genome sequencing. B: Hi-C contact map of L. longirostris genome, color bar shows contact density from red (high) to white (low). C: Phylogenetic tree of 11 fish genomes constructed using 3 585 single-copy orthologous genes. D: Genome comparisons between L. longirostris and I. punctatus.

    Table  1.   Summary of sequenced catfish genomes

    SpeciesFamilySequencing platformAssembly size (Mb)Identified genesScaffold N50 (Mb)Contig N50 (kb)References
    Longsnout catfish, Leiocassis longirostrisBagridaeBGISEQ-500, Nanopore, Hi-C703.1923 70828.033 090.00This study
    Yellow catfish, Pelteobagrus fulvidracoBagridaeIllumina, PacBio, Hi-C732.8024 55225.801 100.00Gong et al., 2018
    Illumina, PacBio714.0021 5623.65970.00Zhang et al., 2018
    Glyptosternon maculatumSisoridaePacBio, Illumina, 10X Genomics, BioNano662.3422 06620.90993.67Liu et al., 2018
    Channel catfish, Ictalurus punctatusIctaluridaeIllumina845.4021 5567.2548.50Chen et al., 2016
    Illumina, PacBio783.0026 6617.7377.20Liu et al., 2016
    Giant devil catfish, Bagarius yarrelliSisoridaeIllumina, PacBio571.0019 0273.101 600.00Jiang et al., 2019
    Walking catfish, Clarias batrachusClariidaeIllumina821.0022 9140.3619.00Li et al., 2018
    Striped catfish, Pangasianodon hypophthalmusPangasiidaeIllumina700.0028 60014.296.00Kim et al., 2018
    下载: 导出CSV
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出版历程
  • 收稿日期:  2021-03-04
  • 录用日期:  2021-04-09
  • 网络出版日期:  2021-05-08
  • 刊出日期:  2021-07-18

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