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.

Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen 518120 China

Biology Centre of the Czech Academy of Sciences Institute of Entomology Branišovská 31 37005 České Budějovice Czech Republic

Centre Agriculture Food Environment Italy

College of Biological and Environmental Engineering Zhejiang Shuren University Hangzhou 310015 China

College of Plant Health and Medicine Qingdao Agricultural University Qingdao 266109 China

College of Plant Protection Hunan Agricultural University Changsha 410128 China

College of Plant Protection Nanjing Agricultural University Nanjing 210095 China

Department of Biology and Biotechnology University of Pavia 27100 Pavia Italy

Department of Sustainable Agro ecosystems and Bioresources IASMA Research and Innovation Centre Fondazione Edmund Mach Via Mach 1 38010 San Michele all'Adige Italy

Ecology and Evolutionary Biology University of Kansas Lawrence KS 66046 USA

Edinburgh Genomics and Institute of Evolutionary Biology School of Biological Sciences The King's Buildings The University of Edinburgh Edinburgh EH9 3JT UK

Faculty of Science University of South Bohemia Branišovská 1760 37005 České Budějovice Czech Republic

INRA Institute of Ecology and Environmental Sciences of Paris 78000 Versailles France

INRA Plantes et Systèmes de culture Horticole 228 route de l'Aérodrome 84914 Avignon Cedex 09 France

Institute of Plant Protection Xinjiang Academy of Agricultural and Reclamation Sciences Shihezi 832000 China

MARA CABI Joint Laboratory for Bio safety Institute of Plant Protection Chinese Academy of Agricultural Sciences Beijing 100193 China

Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests Institute of Insect Science College of Agriculture and Biotechnology Zhejiang University Hangzhou 310058 China

Northwest A and F University State Key Laboratory of Crop Stress Biology for Arid Areas Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture Yangling 712100 China

State Key Laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant Protection Chinese Academy of Agricultural Sciences Beijing 100193 China

State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing 100101 China

Technical Centre for Animal Plant and Food Inspection and Quarantine Shanghai Custom Shanghai 200135 China

Xinjiang Production and Construction Corps Key Laboratory of Integrated Pest Management on Agriculture in South Xinjiang Tarim University Alar 843300 China

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Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths

Odorant receptor phylogeny confirms conserved channels for sex pheromone and host plant signals in tortricid moths