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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.

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