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

Fanghao Wan (), Chuanlin Yin, Rui Tang, Maohua Chen, Qiang Wu, Cong Huang, Wanqiang Qian, Omar Rota-Stabelli, Nianwan Yang (), Shuping Wang, Guirong Wang, Guifen Zhang, Jianyang Guo, Liuqi (Aloy) Gu, Longfei Chen, Longsheng Xing, Yu Xi, Feiling Liu, Kejian Lin, Mengbo Guo, Wei Liu, Kang He, Ruizheng Tian, Emmanuelle Jacquin-Joly, Pierre Franck, Myriam Siegwart, Lino Ometto, Gianfranco Anfora, Mark Blaxter, Camille Meslin, Petr Nguyen, Martina Dalíková, František Marec, Jérôme Olivares, Sandrine Maugin, Jianru Shen, Jinding Liu, Jinmeng Guo, Jiapeng Luo, Bo Liu, Wei Fan, Likai Feng, Xianxin Zhao, Xiong Peng, Kang Wang, Lang Liu, Haixia Zhan, Wanxue Liu, Guoliang Shi, Chunyan Jiang, Jisu Jin, Xiaoqing Xian, Sha Lu, Mingli Ye, Meizhen Li, Minglu Yang, Renci Xiong, James R. Walters () and Fei Li ()
Additional contact information
Fanghao Wan: Chinese Academy of Agricultural Sciences
Chuanlin Yin: Zhejiang University
Rui Tang: Chinese Academy of Agricultural Sciences
Maohua Chen: Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture
Qiang Wu: Chinese Academy of Agricultural Sciences
Cong Huang: Chinese Academy of Agricultural Sciences
Wanqiang Qian: Chinese Academy of Agricultural Sciences
Omar Rota-Stabelli: Fondazione Edmund Mach, Via Mach 1
Nianwan Yang: Chinese Academy of Agricultural Sciences
Shuping Wang: Shanghai Custom
Guirong Wang: Chinese Academy of Agricultural Sciences
Guifen Zhang: Chinese Academy of Agricultural Sciences
Jianyang Guo: Chinese Academy of Agricultural Sciences
Liuqi (Aloy) Gu: University of Kansas
Longfei Chen: Zhejiang University
Longsheng Xing: Chinese Academy of Agricultural Sciences
Yu Xi: Chinese Academy of Agricultural Sciences
Feiling Liu: Zhejiang University
Kejian Lin: Chinese Academy of Agricultural Sciences
Mengbo Guo: Chinese Academy of Agricultural Sciences
Wei Liu: Chinese Academy of Agricultural Sciences
Kang He: Zhejiang University
Ruizheng Tian: Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture
Emmanuelle Jacquin-Joly: INRA, Institute of Ecology and Environmental Sciences of Paris
Pierre Franck: INRA, Plantes et Systèmes de culture Horticole, 228 route de l’Aérodrome
Myriam Siegwart: INRA, Plantes et Systèmes de culture Horticole, 228 route de l’Aérodrome
Lino Ometto: Fondazione Edmund Mach, Via Mach 1
Gianfranco Anfora: Fondazione Edmund Mach, Via Mach 1
Mark Blaxter: The University of Edinburgh
Camille Meslin: INRA, Institute of Ecology and Environmental Sciences of Paris
Petr Nguyen: Institute of Entomology, Branišovská 31
Martina Dalíková: Institute of Entomology, Branišovská 31
František Marec: Institute of Entomology, Branišovská 31
Jérôme Olivares: INRA, Plantes et Systèmes de culture Horticole, 228 route de l’Aérodrome
Sandrine Maugin: INRA, Plantes et Systèmes de culture Horticole, 228 route de l’Aérodrome
Jianru Shen: Chinese Academy of Agricultural Sciences
Jinding Liu: Nanjing Agricultural University
Jinmeng Guo: Nanjing Agricultural University
Jiapeng Luo: Zhejiang University
Bo Liu: Chinese Academy of Agricultural Sciences
Wei Fan: Chinese Academy of Agricultural Sciences
Likai Feng: Xinjiang Academy of Agricultural and Reclamation Sciences
Xianxin Zhao: Zhejiang University
Xiong Peng: Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture
Kang Wang: Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture
Lang Liu: Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture
Haixia Zhan: Chinese Academy of Agricultural Sciences
Wanxue Liu: Chinese Academy of Agricultural Sciences
Guoliang Shi: Chinese Academy of Agricultural Sciences
Chunyan Jiang: Chinese Academy of Agricultural Sciences
Jisu Jin: Chinese Academy of Agricultural Sciences
Xiaoqing Xian: Chinese Academy of Agricultural Sciences
Sha Lu: Chinese Academy of Agricultural Sciences
Mingli Ye: Zhejiang Shuren University
Meizhen Li: Zhejiang University
Minglu Yang: Tarim University
Renci Xiong: Tarim University
James R. Walters: University of Kansas
Fei Li: Zhejiang University

Nature Communications, 2019, vol. 10, issue 1, 1-14

Abstract: 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.

Date: 2019
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DOI: 10.1038/s41467-019-12175-9

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