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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

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

  • 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。

     

    Abstract: Leopard coral groupers belong to the Plectropomus genus of the Epinephelidae family and are important fish for coral reef ecosystems and the marine aquaculture industry. To promote future research of this species, a high-quality chromosome-level genome was assembled using PacBio sequencing and Hi-C technology. A 787.06 Mb genome was assembled, with 99.7% (784.57 Mb) of bases anchored to 24 chromosomes. The leopard coral grouper genome size was smaller than that of other groupers, which may be related to its ancient status among grouper species. A total of 22 317 protein-coding genes were predicted. This high-quality genome of the leopard coral grouper is the first genomic resource for Plectropomus and should provide a pivotal genetic foundation for further research. Phylogenetic analysis of the leopard coral grouper and 12 other fish species showed that this fish is closely related to the brown-marbled grouper. Expanded genes in the leopard coral grouper genome were mainly associated with immune response and movement ability, which may be related to the adaptive evolution of this species to its habitat. In addition, we also identified differentially expressed genes (DEGs) associated with carotenoid metabolism between red and brown-colored leopard coral groupers. These genes may play roles in skin color decision by regulating carotenoid content in these groupers.

     

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