A chromosome-level assembly of the harlequin ladybird Harmonia axyridis as a genomic resource to study beetle and invasion biology
A chromosome-level assembly of the harlequin ladybird Harmonia axyridis as a genomic resource to study beetle and invasion biology
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DOI：
10.1111/1755-0998.13342
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发表时间：
2021-02-13
影响因子：
7.7
通讯作者：
Li, Fei
中科院分区：
文献类型：
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作者：
Chen, Mengyao;Mei, Yang;Li, Fei
异色瓢虫（Harmonia axyridis，Pallas）是一种著名的遗传学模式生物，也是一种被广泛研究的用于害虫防治的天敌。在被引入北美和欧洲作为害虫控制剂后，它成为一种入侵物种。虽然以前已经报道了这种昆虫的两个基因组组装，但在染色体水平上的高质量基因组组装仍然不可用。在此，我们获得了一个新的染色体水平的H。通过结合各种测序技术，即Illumina短读段、PacBio长读段、10 X Genomics和Hi-C，染色体水平的基因组组装为423 Mb，支架N50为45.92 Mb。使用Hi-C数据，将1，897个支架锚定到8条染色体上。共鉴定出730，068个重复序列，占组装基因组的51.2%。在掩蔽这些重复序列后，我们注释了22，810个蛋白质编码基因。还通过对雄性和雌性基因组重新测序并计算雄性与雌性的覆盖率来鉴定X染色体和Y-连锁支架。分析了与环境适应相关的两个基因家族，气味受体和细胞色素P450，结果表明在H.异色。我们成功地构建了一个假定的生物合成途径的harmonine，防御化合物在血淋巴的H。异染色质是H.异色性免疫力强。染色体水平的基因组组装。异色瓢虫是研究甲虫生物学和入侵生物学的有用资源。
The harlequin ladybird, Harmonia axyridis (Pallas), is a well-known model organism for genetic studies and is also a well-studied natural enemy used for pest control. It became an invasive species after being introduced to North America and Europe as a pest control agent. Though two genome assemblies for this insect have been previously reported, a high-quality genome assembly at the chromosome level is still not available. Here, we obtained a new chromosome-level genome assembly of H. axyridis by combining various sequencing technologies, namely Illumina short reads, PacBio long reads, 10X Genomics and Hi-C. The chromosome-level genome assembly is 423 Mb with a scaffold N50 of 45.92 Mb. Using Hi-C data 1,897 scaffolds were anchored to eight chromosomes. A total of 730,068 repeat sequences were identified, making up 51.2% of the assembled genome. After masking these repeat sequences, we annotated 22,810 protein-encoding genes. The X chromosome and Y-linked scaffolds were also identified by resequencing male and female genomes and calculating the male to female coverage ratios. Two gene families associated with environmental adaptation, odorant receptor and cytochrome P450, were analysed and showed no obvious expansion in H. axyridis. We successfully constructed a putative biosynthesis pathway of harmonine, a defence compound in the haemolymph of H. axyridis, which is a key factor for H. axyridis strong immunity. The chromosome-level genome assembly of H. axyridis is a helpful resource for studies of beetle biology and invasive biology.