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

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.

SUBMITTER: Wan F

PROVIDER: S-EPMC6748993 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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

Wan Fanghao F Yin Chuanlin C Tang Rui R Chen Maohua M Wu Qiang Q Huang Cong C Qian Wanqiang W Rota-Stabelli Omar O Yang Nianwan N Wang Shuping S Wang Guirong G Zhang Guifen G Guo Jianyang J Gu Liuqi Aloy LA Chen Longfei L Xing Longsheng L Xi Yu Y Liu Feiling F Lin Kejian K Guo Mengbo M Liu Wei W He Kang K Tian Ruizheng R Jacquin-Joly Emmanuelle E Franck Pierre P Siegwart Myriam M Ometto Lino L Anfora Gianfranco G Blaxter Mark M Meslin Camille C Nguyen Petr P Dalíková Martina M Marec František F Olivares Jérôme J Maugin Sandrine S Shen Jianru J Liu Jinding J Guo Jinmeng J Luo Jiapeng J Liu Bo B Fan Wei W Feng Likai L Zhao Xianxin X Peng Xiong X Wang Kang K Liu Lang L Zhan Haixia H Liu Wanxue W Shi Guoliang G Jiang Chunyan C Jin Jisu J Xian Xiaoqing X Lu Sha S Ye Mingli M Li Meizhen M Yang Minglu M Xiong Renci R Walters James R JR Li Fei F

Nature communications 20190917 1

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 insectici ...[more]

PMID: 31530873

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Project description:BackgroundSphaerophoria rueppellii, a European species of hoverfly, is a highly effective beneficial predator of hemipteran crop pests including aphids, thrips and coleopteran/lepidopteran larvae in integrated pest management (IPM) programmes. It is also a key pollinator of a wide variety of important agricultural crops. No genomic information is currently available for S. rueppellii. Without genomic information for such beneficial predator species, we are unable to perform comparative analyses of insecticide target-sites and genes encoding metabolic enzymes potentially responsible for insecticide resistance, between crop pests and their predators. These metabolic mechanisms include several gene families - cytochrome P450 monooxygenases (P450s), ATP binding cassette transporters (ABCs), glutathione-S-transferases (GSTs), UDP-glycosyltransferases (UGTs) and carboxyl/choline esterases (CCEs).Methods and findingsIn this study, a high-quality near-chromosome level de novo genome assembly (as well as a mitochondrial genome assembly) for S. rueppellii has been generated using a hybrid approach with PacBio long-read and Illumina short-read data, followed by super scaffolding using Hi-C data. The final assembly achieved a scaffold N50 of 87Mb, a total genome size of 537.6Mb and a level of completeness of 96% using a set of 1,658 core insect genes present as full-length genes. The assembly was annotated with 14,249 protein-coding genes. Comparative analysis revealed gene expansions of CYP6Zx P450s, epsilon-class GSTs, dietary CCEs and multiple UGT families (UGT37/302/308/430/431). Conversely, ABCs, delta-class GSTs and non-CYP6Zx P450s showed limited expansion. Differences were seen in the distributions of resistance-associated gene families across subfamilies between S. rueppellii and some hemipteran crop pests. Additionally, S. rueppellii had larger numbers of detoxification genes than other pollinator species.Conclusion and significanceThis assembly is the first published genome for a predatory member of the Syrphidae family and will serve as a useful resource for further research into selectivity and potential tolerance of insecticides by beneficial predators. Furthermore, the expansion of some gene families often linked to insecticide resistance and selectivity may be an indicator of the capacity of this predator to detoxify IPM selective insecticides. These findings could be exploited by targeted insecticide screens and functional studies to increase effectiveness of IPM strategies, which aim to increase crop yields by sustainably and effectively controlling pests without impacting beneficial predator populations.

Dataset Information

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

Publications

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

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