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A chromosome-level genome assembly of Cydia pomonella provides insights into chemical ecology and insecticide resistance

Fanghao Wan 1, 2 Chuanlin Yin 3 Rui Tang 2, 4 Maohua Chen 5 Qiang Wu 1 Cong Huang 1, 6 Wanqiang Qian 2 Omar Rota-Stabelli 7 Nianwan Yang 1 Shuping Wang 8 Guirong Wang 1 Guifen Zhang 1 Jianyang Guo 1 Liuqi (aloy) Gu 9 Longfei Chen 3 Longsheng Xing 2 Yu Xi 2 Feiling Liu 1 Kejian Lin 1 Mengbo Guo 1 Wei Liu 1 Kang He 3 Ruizheng Tian 5 Emmanuelle Joly 10 Pierre Franck 11 Myriam Siegwart 11 Lino Ometto 7, 12 Gianfranco Anfora 7, 13 Mark Blaxter 14 Camille Meslin 10 Petr Nguyen 15, 16 Martina Dalíková 15, 16 František Marec 15 Jerome Olivares 11 Sandrine Maugin 11 Jianru Shen 1 Jinding Liu 1 Jinmeng Guo 1 Jiapeng Luo 3 Bo Liu 2 Wei Fan 2 Likai Feng 17 Xianxin Zhao 3 Xiong Peng 5 Kang Wang 5 Lang Liu 5 Haixia Zhan 2 Wanxue Liu 1 Guoliang Shi 1, 18 Chunyan Jiang 1, 18 Jisu Jin 1, 6 Xiaoqing Xian 1 Sha Lu 1, 18 Mingli Ye 19 Meizhen Li 3 Minglu Yang 20 Renci Xiong 20 James R. Walters 9 Fei Li 3
Abstract : The codling moth Cydia pomonella, a major invasive pest of pome fruit, has spread around the globe in the last half century. We generated a chromosome-level scaffold assembly including the Z chromosome and a portion of the W chromosome. This assembly reveals the duplication of an olfactory receptor gene (OR3), which we demonstrate enhances the ability of C. pomonella to exploit kairomones and pheromones in locating both host plants and mates. Genome-wide association studies contrasting insecticide-resistant and susceptible strains identify hundreds of single nucleotide polymorphisms (SNPs) potentially associated with insecticide resistance, including three SNPs found in the promoter of CYP6B2. RNAi knockdown of CYP6B2 increases C. pomonella sensitivity to two insecticides, deltamethrin and azinphos methyl. The high-quality genome assembly of C. pomonella informs the genetic basis of its invasiveness, suggesting the codling moth has distinctive capabilities and adaptive potential that may explain its worldwide expansion.
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Fanghao Wan, Chuanlin Yin, Rui Tang, Maohua Chen, Qiang Wu, et al.. A chromosome-level genome assembly of Cydia pomonella provides insights into chemical ecology and insecticide resistance. Nature Communications, Nature Publishing Group, 2019, 10 (1), ⟨10.1038/s41467-019-12175-9⟩. ⟨hal-02622730⟩

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