Whole-genome sequencing of leopard coral grouper (Plectropomus leopardus) and exploration of regulation mechanism of skin color and adaptive evolution
Whole-genome sequencing of leopard coral grouper (Plectropomus leopardus) and exploration of regulation mechanism of skin color and adaptive evolution
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豹纹珊瑚石斑鱼（Plectropomus leopardus）全基因组测序及肤色调控机制及适应性进化探索
DOI：
10.24272/j.issn.2095-8137.2020.038
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发表时间：
2020-03
影响因子：
4.9
通讯作者：
Haoran Lin
中科院分区：
文献类型：
--
作者：
Yang Yang;Lina Wu;Jingfang Chen;Xi Wu;Junhong Xia;Zining Meng;Xiaochun Liu;Haoran Lin
豹斑鱼属于石斑鱼科的棘头鱼属，是珊瑚礁生态系统和海水养殖业的重要鱼类。为了促进该物种的未来研究，使用PacBio测序和Hi-C技术组装了高质量的染色体水平基因组。基因组全长787.06 Mb，其中99.7%（784.57 Mb）的碱基锚定在24条染色体上。豹斑石斑鱼基因组的大小比其他石斑鱼小，这可能与其在石斑鱼物种中的古老地位有关。共预测出22317个蛋白质编码基因。这种高质量的豹珊瑚石斑鱼基因组是第一个基因组资源，为进一步研究提供了关键的遗传基础。对豹斑石斑鱼和其他12种鱼类的系统发育分析表明，这种鱼与棕色大理石石斑鱼关系密切。豹斑石斑鱼基因组中扩增的基因主要与免疫反应和运动能力相关，这可能与该物种对栖息地的适应性进化有关。此外，我们还确定了红色和棕色豹珊瑚石斑鱼之间与类胡萝卜素代谢相关的差异表达基因（DEG）。这些基因可能通过调节类胡萝卜素的含量在石斑鱼的肤色决定中发挥作用。
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 proteincoding 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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DOI：
10.1016/j.jaci.2018.06.017
发表时间：
2018-08
期刊：
The Journal of allergy and clinical immunology
影响因子：
--
作者：
Van Dyken SJ;Locksley RM
通讯作者：
Locksley RM
影响因子：
5.8
作者：
Tong, Mark Y.;Cassa, Christopher A.;Kohane, Isaac S.
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Kohane, Isaac S.
影响因子：
9.1
作者：
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Dela Cruz CS
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
14.9
作者：
Ritchie ME;Phipson B;Wu D;Hu Y;Law CW;Shi W;Smyth GK
通讯作者：
Smyth GK