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赵娜, 郭浩冰, 贾磊, 邓秋霞, 朱春华, 张博. 2021: 高质量染色体水平基因组揭示了梭鱼对复杂生活环境的适应性. 动物学研究, 42(6): 796-799. DOI: 10.24272/j.issn.2095-8137.2021.255
引用本文: 赵娜, 郭浩冰, 贾磊, 邓秋霞, 朱春华, 张博. 2021: 高质量染色体水平基因组揭示了梭鱼对复杂生活环境的适应性. 动物学研究, 42(6): 796-799. DOI: 10.24272/j.issn.2095-8137.2021.255
Na Zhao, Hao-Bing Guo, Lei Jia, Qiu-Xia Deng, Chun-Hua Zhu, Bo Zhang. 2021. High-quality chromosome-level genome assembly of redlip mullet (Planiliza haematocheila). Zoological Research, 42(6): 796-799. DOI: 10.24272/j.issn.2095-8137.2021.255
Citation: Na Zhao, Hao-Bing Guo, Lei Jia, Qiu-Xia Deng, Chun-Hua Zhu, Bo Zhang. 2021. High-quality chromosome-level genome assembly of redlip mullet (Planiliza haematocheila). Zoological Research, 42(6): 796-799. DOI: 10.24272/j.issn.2095-8137.2021.255

高质量染色体水平基因组揭示了梭鱼对复杂生活环境的适应性

High-quality chromosome-level genome assembly of redlip mullet (Planiliza haematocheila)

  • 摘要: 梭鱼(Planiliza haematocheila)属于鲻形目(Mugiliformes),鲻科(Mugilidae),梭鱼属(Planiliza),主要分布于中国、日本和朝鲜半岛沿海,是温热带浅海区重要的经济鱼类之一,体纺锤形,身体像一个梭子,因此而得名。梭鱼为近岸半徊游性鱼类,梭鱼生活在沿海、江河的入海口或者咸水中,淡水也可生活,无长距离徊游现象。梭鱼适应能力强,是高纬度地区中的广盐、广温和抗病抗逆养殖品种。因此,梭鱼也是研究鱼类适应复杂环境的一个极好的模型。在该研究中,我们通过牛津纳米孔长读长技术(Oxford Nanopore long-read)、单管长片段序列读取技术 (single tube Long Fragment Read,stLFR)和高通量染色体构象捕获技术(High-throughput/resolution chromosome conformation capture,Hi-C)成功组装了一个高质量的梭鱼染色体水平基因组。该梭鱼基因组大小为652.91MB,基因组组装得到了超过93.8%的BUSCO基因,contigs 和 scaffolds和N50长度分别达到7.21MB和28.01MB,显示出较高的基因组完整性和序列连续性。共有21045个蛋白质编码基因被预测到,其中99.77%的基因进行了功能注释。比较基因组学和系统发育分析揭示了梭鱼在基因组水平上对复杂生活环境的适应性,突出了其作为一种重要经济鱼类对多种胁迫环境的抗性。这一高质量的参考基因组为进一步系统研究鲻科鱼类系统分化提供了重要的基因组资源。

     

    Abstract: In the present study, we successfully assembled a high-quality genome of Planiliza haematocheila (redlip mullet) based on Oxford Nanopore long read, single-tube long fragment read (stLFR), and Hi-C chromatin interaction sequencing. The size of the P. haematocheila genome was 652.91 Mb. More than 93.8% of BUSCO genes were detected, and the N50 lengths of contigs and scaffolds reached 7.21 Mb and 28.01 Mb, respectively, thus demonstrating outstanding genome completeness and sequence continuity. A total of 21 045 protein-coding genes were predicted in the assembled genome, and 99.77% of those genes were functionally annotated. Comparative genomic and phylogenetic analyses revealed the adaptability of P. haematocheila to complex living environments at the genomic level, highlighting its broad adaptability and resistance to multiple stresses as an important economic fish. The high-quality reference chromosome-level genome of P. haematocheila provides a powerful genomic resource for further systematic study of Mugilidae.

     

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