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

Fanghao Wan ,Yu X ,Wanqiang Qian ,Jiao Guo ,Lang Liü ,Hao Zhan ,Likai Feng ,Kang He ,Wanxue Liu ,Petr Nguyen ,G Anfora ,Mengbo Guo ,Liuqi Gu ,Renci Xiong ,Mark Blaxter ,Jin‐Meng Guo ,Lino Ometto ,Yang Ni ,Wei Liu ,Kang Wang ,Camille Meslin ,Chunyan Jiang ,Guifen Zhang ,Longfei Chen ,Maohua Chen ,Meizhen Li ,Sandrine Maugin ,Guo-Liang Shi ,Jérôme Olivares ,Chuanlin Yin ,Ruizheng Tian ,Jianru Shen ,Qiang Wu ,Rui Tang ,Jinding Liu ,Mingli Ye ,Sha Lu ,Xiaoqing Xian ,Shuping Wang ,Jisu Jin ,Longsheng Xing ,Xiong Peng ,Wei Fan ,Minglu Yang ,Pierre Franck ,Kejian Lin ,Myriam Siegwart ,Xianxin Zhao ,Martina Dalíková ,Guirong Wang ,Emmanuelle Jacquin‐Joly ,Cong Huang ,Bo Liu ,František Marec ,Jiapeng Luo ,Omar Rota‐Stabelli ,James R Walters ,Feiling Liu ,Fĕi Li

doi:10.1038/s41467-019-12175-9

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.

Highlights

The codling moth Cydia pomonella, a major invasive pest of pome fruit, has spread around the globe in the last half century
Using Quantitative PCR (qPCR), we estimated the expression of CYP6B2 in the three strains; the results showed that this gene is constitutively overexpressed in the two resistant strains (241.4-fold in Raz and 77.3fold in Rv) compared with the S strain (Student’s t test, Rv: P = 0.0102, Raz: P = 0.0002) (Fig. 6d), suggesting that these single nucleotide polymorphisms (SNPs) play a role in expression regulation of CYP6B2
To the best of our knowledge, this is the first assembly yielding chromosome-level scaffolds without linkage mapping for lepidopteran insects sequenced from whole organisms

Summary

Introduction

The codling moth Cydia pomonella, a major invasive pest of pome fruit, has spread around the globe in the last half century. The codling moth, Cydia pomonella (Lepidoptera, Tortricidae), is a wide-spread and highly impactful pest of pome fruit (apples and pears) and walnuts[1]. The larvae of this notorious pest bore into the fruit, causing damage making it unmarketable (Supplementary Fig. 1a). Pomonella can reach 80% for apples and 60% for pears in orchards without pest control treatment (Supplementary Fig. 1b)[2] Records of this species in Greece and Italy from over 2000 years ago suggest it has an origin in Mediterranean Europe[3]. Pomonella increasingly widened its distribution in Europe and North America while spreading to Africa and Western Asia[4]

Methods

Results

Conclusion