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Whole-genome sequencing of leopard coral grouper (Plectropomus leopardus) and exploration of regulation mechanism of skin color and adaptive evolution

Yang Yang Li-Na Wu Jing-Fang Chen Xi Wu Jun-Hong Xia Zi-Ning Meng Xiao-Chun Liu Hao-Ran Lin

Yang Yang, Li-Na Wu, Jing-Fang Chen, Xi Wu, Jun-Hong Xia, Zi-Ning Meng, Xiao-Chun Liu, Hao-Ran Lin. Whole-genome sequencing of leopard coral grouper (Plectropomus leopardus) and exploration of regulation mechanism of skin color and adaptive evolution. Zoological Research, 2020, 41(3): 328-340. doi: 10.24272/j.issn.2095-8137.2020.038
Citation: Yang Yang, Li-Na Wu, Jing-Fang Chen, Xi Wu, Jun-Hong Xia, Zi-Ning Meng, Xiao-Chun Liu, Hao-Ran Lin. Whole-genome sequencing of leopard coral grouper (Plectropomus leopardus) and exploration of regulation mechanism of skin color and adaptive evolution. Zoological Research, 2020, 41(3): 328-340. doi: 10.24272/j.issn.2095-8137.2020.038

豹纹鳃棘鲈(Plectropomus leopardus)全基因组测序以及皮肤颜色调控机制与适应性进化探索

doi: 10.24272/j.issn.2095-8137.2020.038

Whole-genome sequencing of leopard coral grouper (Plectropomus leopardus) and exploration of regulation mechanism of skin color and adaptive evolution

Funds: This study was supported by the Agriculture Research System of China (ARS-47); Science and Technology Planning Project of Guangzhou (201804020013); National Natural Science Foundation of China (31872572; u1401213; 31802266); Yang Fan Innovative & Entrepreneurial Research Team Project (No.201312H10); and Program of the China-ASEAN Maritime Cooperation Fund of the Chinese Government (42000-41170002)
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  • 摘要:

    豹纹鳃棘鲈俗称东星斑,属于鲈形目,石斑鱼科,鳃棘鲈属,是一种重要的珊瑚礁鱼类,也是目前海水养殖石斑鱼类中市场价格昂贵的种类。我们使用PacBio三代测序和Hi-C技术对其基因组进行了测序与组装。豹纹鳃棘鲈染色体全长787.06 Mb,其中99.7% (784.57 Mb)的碱基可以锚定在24条染色体上,共检测到22 317个蛋白编码基因。豹纹鳃棘鲈的基因组小于其他石斑鱼的基因组,这可能与其在石斑鱼类中的原始地位有关。基于基因组数据的系统发育分析表明,13种鱼类中,棕点石斑鱼与豹纹鳃棘鲈具有较近的亲缘关系。豹纹鳃棘鲈基因组中的扩张基因主要与免疫反应和运动能力有关,这可能与该物种的适应性进化有关。此外,在对不同体色(红色和棕色)豹纹鳃棘鲈的转录组分析中,我们还发现了一些与类胡萝卜素代谢相关基因的差异表达。这些基因可能通过调节豹纹鳃棘鲈体内类胡萝卜素的含量,从而在皮肤颜色调节中发挥作用。

  • Figure  1.  Leopard coral grouper (Plectropomus leopardus)

    A: Bright red fish (used for genome assembly). B: Brown fish. Scale bars: 10 cm.

    Figure  2.  Statistics on genome assembly and annotation of leopard coral grouper (Plectropomus leopardus)

    A: Estimation of genome size, repeat content, and heterozygosity by survey using 19-mers. B: Genome contig contact matrix using Hi-C data, color bar indicates contact density from red (high) to white (low). C: Functional annotated protein-coding genes. D: Summary statistics of non-coding RNA. E: Statistics of leopard coral grouper genome assembly.

    Figure  3.  Prediction of gene families and analysis of genetic relationship

    A: Flower chart of gene family numbers in 13 fish species. Ple: P. leopardus, Efu: E. fuscoguttatus, Dre: D. rerio, Lcr: L. crocea, Ssa: S. Salar, Mal: M. albus, Gmo: G. morhua, Omy: O. mykiss, Lca: L. calcarifer Oni: O. niloticus, Lch: L. chalumnae, Ola: O. latipes, Bbe: B. belcheri. B: Gene family clustering for leopard coral grouper and other 12 fish species. C: Collinearity analysis of leopard coral grouper and brown-marbled grouper, orange arrows indicate genome of leopard coral grouper and blue arrows indicate genome of brown-marbled grouper. D: Phylogenetic tree of leopard coral grouper and other 12 fish species, with Branchiostoma belcheri set as outgroup.

    Figure  4.  Analysis of divergence time and gene family of leopard coral grouper with other fish species

    A: Phylogenetic tree with dynamic evolution of gene families and divergence time. MRCA: Most recent common ancestor. B: GO enrichment of expanded gene families in leopard coral grouper. C: Sketch map of expanded gene families related to immune response. Red font indicates expanded gene families.

    Table  1.   Differentially expressed genes (DEGs) between brown and red leopard coral grouper transcriptomes

    IDlog2 (Foldchange)q-valueDescriptionGene symbol
    Up-regulated candidate DEGs associated with skin color in brown fish
    Chr04.g04131.m1–2.642.12E–04Beta-carotene 9',10'-oxygenaseBCO2
    Chr12.g11897.m1–2.411.14E–03Eosinophil peroxidaseEPX
    Up-regulated candidate DEGs associated with skin color in red fish
    Chr16.g15722.m12.602.08E–04Low-density lipoprotein receptor-related protein 11LRP11
    Chr05.g04888.m12.137.79E–04Angiopoietin-related protein 4ANGPTL4
    Chr15.g14859.m13.808.48E–05High affinity cationic amino acid transporter 1SLC7A1
    Chr10.g09989.m12.687.40E–04Protein Wnt-2bWNT2B
    下载: 导出CSV
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  • 收稿日期:  2020-02-26
  • 录用日期:  2020-03-25
  • 网络出版日期:  2020-03-25
  • 刊出日期:  2020-05-18