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日本方头甲(Serangium japonicum Chapin,1940)的染色体水平基因组组装(鞘翅目:瓢虫科)

A chromosome-level genome assembly of Serangium japonicum Chapin, 1940 (Coleoptera: Coccinellidae).

作者信息

Ye Maolin, Xie Yonghui, Jin Jianfeng, Huang Chuyang, Ning Kaide, Liu Zhengling, Li Hongming, Wang Xingmin

机构信息

College of Plant Protection, South China Agricultural University, Guangzhou, 510600, China.

Kunming Branch of Yunnan Provincial Tobacco Company, 650021, Kunming, China.

出版信息

Sci Data. 2024 Dec 23;11(1):1421. doi: 10.1038/s41597-024-04197-w.

Abstract

Serangium japonicum (Coleoptera; Coccinellidae) plays a crucial role as a predatory coccinellid in ecosystems, exhibiting adept predation on diverse whitefly species and effectively regulating their population dynamics. Nonetheless, the absence of high-quality genomic data has hindered our comprehension of the molecular mechanisms underlying this predatory beetle. This study performed genome sequencing of S. japonicum using the PacBio HiFi long reads and Hi-C data. The genome spans 433.74 Mb, which includes 104 contigs and 17 scaffolds, with a contig N50 size of 11.44 Mb and a scaffold N50 size of 42.67 Mb. A substantial portion of the genome, totaling 433.04 Mb (99.84%), was anchored to 10 chromosomes. BUSCO analysis demonstrates a high genomic completeness of 97.8% (n = 1,376), comprising 97.3% single-copy genes and 0.5% duplicated genes. The genome includes 54.66% (237.06 Mb) repetitive elements and 12,299 predicted protein-coding genes. The chromosome-level genome of S. japonicum offers important genomic insights that enhance our understanding of the evolution and ecology of the Coccinellidae family.

摘要

日本方头甲(鞘翅目;瓢虫科)作为一种捕食性瓢虫在生态系统中发挥着关键作用,对多种粉虱种类展现出娴熟的捕食能力,并能有效调节它们的种群动态。尽管如此,高质量基因组数据的缺乏阻碍了我们对这种捕食性甲虫潜在分子机制的理解。本研究利用PacBio HiFi长读长和Hi-C数据对日本方头甲进行了基因组测序。基因组大小为433.74 Mb,包含104个重叠群和17个支架,重叠群N50大小为11.44 Mb,支架N50大小为42.67 Mb。基因组的很大一部分,总计433.04 Mb(99.84%),被锚定到10条染色体上。BUSCO分析表明基因组完整性很高,为97.8%(n = 1,376),其中包括97.3%的单拷贝基因和0.5%的重复基因。基因组包含54.66%(237.06 Mb)的重复元件和12,299个预测的蛋白质编码基因。日本方头甲的染色体水平基因组提供了重要的基因组见解,增强了我们对瓢虫科进化和生态的理解。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2b03/11666535/defa0a717575/41597_2024_4197_Fig1_HTML.jpg

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