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Journal of Integrative Agriculture  2023, Vol. 22 Issue (3): 825-843    DOI: 10.1016/j.jia.2022.08.027
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Chromosome-level genome assembly of Cylas formicarius provides insights into its adaptation and invasion mechanisms

HUA Jin-feng1, 2#, ZHANG Lei1, HAN Yong-hua1, GOU Xiao-wan1, CHEN Tian-yuan2, HUANG Yong-mei2, LI Yan-qing2, MA Dai-fu1, 3#, LI Zong-yun1#

1 Institute of Integrative Plant Biology/Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics/School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, P.R.China

2 Sweet Potato Laboratory, Institute of Maize Research, Guangxi Academy of Agricultural Sciences, Nanning 530007, P.R.China

3 Xuzhou Academy of Agricultural Sciences/Institute of Sweet Potato Research, Chinese Academy of Agricultural Sciences, Xuzhou 221131, P.R.China

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甘薯小象甲是甘薯上危害最为严重的世界性害虫,对生态环境和社会经济遭受巨大损失。为提高甘薯小象甲综合防治的效果和深入理解其遗传进化机制,我们对甘薯小象甲功能基因组学进行了的深入研究。利用 Illumina  PacBio技术,对单对交配15代的甘薯小象甲进行测序。获得了甘薯小象甲成虫染色体水平的基因组,基因组大小为338.84MbContig N50  Scaffold N50 分别为 14.97 Mb34.23 Mb。预测重复序列为 157.51 Mb 11907 个编码蛋白质基因。共有 337.06 Mb长度的基因组序列被定位到 11 条染色体上,其中能够确定顺序和方向的序列长度为 333.79 Mb,占定位到染色体上总序列长度的 99.03 %。比较基因组学分析表明,甘薯小象甲和中欧山松大小蠹亲缘关系较近,约 1.38 亿年前从中欧山松大小蠹的祖先分化而来。许多重要的基因家族在甘薯小象甲基因组中得到了扩张,包括农药解毒、耐冷应激和化学感觉系统相关基因家族。为了进一步解析气味结合蛋白在甘薯小象甲嗅觉识别过程中的作用,竞争性结合分析结果表明,CforOBP4-6对性信息素其他配体具有很强的结合亲和力。高质量的甘薯小象甲基因组图谱为揭示其分子生态学基础、群体遗传和适应性进化机制及绿色有效防控的新方法和新技术提供了坚实的基础。


Cylas formicarius is one of the most important pests of sweet potato worldwide, causing considerable ecological and economic damage.  This study improved the effect of comprehensive management and understanding of genetic mechanisms by examining the functional genomics of Cformicarius.  Using Illumina and PacBio sequencing, this study obtained a chromosome-level genome assembly of adult weevils from lines inbred for 15 generations.  The high-quality assembly obtained was 338.84 Mb, with contig and scaffold N50 values of 14.97 and 34.23 Mb, respectively.  In total, 157.51 Mb of repeat sequences and 11 907 protein-coding genes were predicted.  A total of 337.06 Mb of genomic sequences was located on the 11 chromosomes, accounting for 99.03% of the total length of the associated chromosome.  Comparative genomic analysis showed that Cformicarius was sister to Dendroctonus ponderosae, and Cformicarius diverged from Dponderosae approximately 138.89 million years ago (Mya).  Many important gene families expanded in the Cformicarius genome were involved in the detoxification of pesticides, tolerance to cold stress and chemosensory system.  To further study the role of odorant-binding proteins (OBPs) in olfactory recognition of Cformicarius, the binding assay results indicated that CforOBP4–6 had strong binding affinities for sex pheromones and other ligands.  The high-quality Cformicarius genome provides a valuable resource to reveal the molecular ecological basis, genetic mechanism, and evolutionary process of major agricultural pests; it also offers new ideas and new technologies for ecologically sustainable pest control.

Keywords:  Cylas formicarius        PacBio sequencing        High-through chromosome conformation capture        chromosome-level genome        chemosensory genes        fluorescence competitive binding  
Received: 13 February 2022   Accepted: 31 May 2022

This research was supported by the Natural Science Foundation of Guangxi Autonomous Region, China (2022GXNSFAA035558), the Technology Development Foundation of Guangxi Academy of Agricultural Sciences (2021ZX09), the China Agriculture Research System of MOF and MARA (CARS-10-B3 and CARS-10-C19), the Guangxi Innovation Team Construction Project (nycytxgxcxtd-11-03), and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).


About author:  #Correspondence LI Zong-yun, Tel: +86-516-83500083, E-mail:; MA Dai-fu, Tel: +86-516-82189200, E-mail:; HUA Jin-feng, Tel: +86-771-3243101, E-mail:

Cite this article: 

HUA Jin-feng, ZHANG Lei, HAN Yong-hua, GOU Xiao-wan, CHEN Tian-yuan, HUANG Yong-mei, LI Yan-qing, MA Dai-fu, LI Zong-yun. 2023. Chromosome-level genome assembly of Cylas formicarius provides insights into its adaptation and invasion mechanisms. Journal of Integrative Agriculture, 22(3): 825-843.

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