title: Identifying genomic changes associated with insecticide resistance in the dengue mosquito Aedes aegypti by deep targeted sequencing.
abstract: The capacity of mosquitoes to resist insecticides threatens the control of diseases such as dengue and malaria. Until alternative control tools are implemented, characterizing resistance mechanisms is crucial for managing resistance in natural populations. Insecticide biodegradation by detoxification enzymes is a common resistance mechanism; however, the genomic changes underlying this mechanism have rarely been identified, precluding individual resistance genotyping. In particular, the role of copy number variations (CNVs) and polymorphisms of detoxification enzymes have never been investigated at the genome level, although they can represent robust markers of metabolic resistance. In this context, we combined target enrichment with high-throughput sequencing for conducting the first comprehensive screening of gene amplifications and polymorphisms associated with insecticide resistance in mosquitoes. More than 760 candidate genes were captured and deep sequenced in several populations of the dengue mosquito Ae. aegypti displaying distinct genetic backgrounds and contrasted resistance levels to the insecticide deltamethrin. CNV analysis identified 41 gene amplifications associated with resistance, most affecting cytochrome P450s overtranscribed in resistant populations. Polymorphism analysis detected more than 30,000 variants and strong selection footprints in specific genomic regions. Combining Bayesian and allele frequency filtering approaches identified 55 nonsynonymous variants strongly associated with resistance. Both CNVs and polymorphisms were conserved within regions but differed across continents, confirming that genomic changes underlying metabolic resistance to insecticides are not universal. By identifying novel DNA markers of insecticide resistance, this study opens the way for tracking down metabolic changes developed by mosquitoes to resist insecticides within and among populations.
authors.affiliation: Laboratoire d'Ecologie Alpine (LECA), CNRS, UMR 5553, 38041 Grenoble Cedex 9, France; Université Grenoble-Alpes, 38041 Grenoble Cedex 9, France; Environmental and Systems Biology (BEeSy), Université Grenoble-Alpes, 38041 Grenoble Cedex 9, France;
authors.forename: Frederic
authors.initials: F
authors.lastname: Faucon
authors.affiliation: Unité d'Entomologie Médicale, Institut Pasteur de la Guyane, 97306 Cayenne Cedex, France;
authors.forename: Isabelle
authors.initials: I
authors.lastname: Dusfour
authors.affiliation: Laboratoire d'Ecologie Alpine (LECA), CNRS, UMR 5553, 38041 Grenoble Cedex 9, France; Université Grenoble-Alpes, 38041 Grenoble Cedex 9, France; Environmental and Systems Biology (BEeSy), Université Grenoble-Alpes, 38041 Grenoble Cedex 9, France;
authors.forename: Thierry
authors.initials: T
authors.lastname: Gaude
authors.affiliation: Pôle Rhône Alpes de Bioinformatique, Université Lyon 1, 69100 Villeurbanne, France;
authors.forename: Vincent
authors.initials: V
authors.lastname: Navratil
authors.affiliation: Laboratoire d'Ecologie Alpine (LECA), CNRS, UMR 5553, 38041 Grenoble Cedex 9, France; Université Grenoble-Alpes, 38041 Grenoble Cedex 9, France; Environmental and Systems Biology (BEeSy), Université Grenoble-Alpes, 38041 Grenoble Cedex 9, France;
authors.forename: Frederic
authors.initials: F
authors.lastname: Boyer
authors.affiliation: Institut de Recherche pour le Développement (IRD), Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle (IRD 224-CNRS 5290 UM1-UM2), 34394 Montpellier Cedex 5, France;
authors.forename: Fabrice
authors.initials: F
authors.lastname: Chandre
authors.affiliation: Department of Entomology, Faculty of Agriculture, Kasetsart University, Lat Yao Chatuchak Bangkok 10900, Thailand; Center for Advanced Studies for Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand (CASAF, NRU-KU, Thailand);
authors.forename: Patcharawan
authors.initials: P
authors.lastname: Sirisopa
authors.affiliation: Bureau of Vector Borne Diseases, Department of Disease Control, Ministry of Public Health, Mueang, Nonthaburi 11000, Thailand;
authors.forename: Kanutcharee
authors.initials: K
authors.lastname: Thanispong
authors.affiliation: Department of Entomology, Faculty of Agriculture, Kasetsart University, Lat Yao Chatuchak Bangkok 10900, Thailand; Center for Advanced Studies for Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand (CASAF, NRU-KU, Thailand);
authors.forename: Waraporn
authors.initials: W
authors.lastname: Juntarajumnong
authors.affiliation: Vector Biology Group, Liverpool School of Tropical Medicine, L35QA Liverpool, United Kingdom.
authors.forename: Rodolphe
authors.initials: R
authors.lastname: Poupardin
authors.affiliation: Department of Entomology, Faculty of Agriculture, Kasetsart University, Lat Yao Chatuchak Bangkok 10900, Thailand; Center for Advanced Studies for Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand (CASAF, NRU-KU, Thailand);
authors.forename: Theeraphap
authors.initials: T
authors.lastname: Chareonviriyaphap
authors.affiliation: Unité d'Entomologie Médicale, Institut Pasteur de la Guyane, 97306 Cayenne Cedex, France;
authors.forename: Romain
authors.initials: R
authors.lastname: Girod
authors.affiliation: Institut de Recherche pour le Développement (IRD), Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle (IRD 224-CNRS 5290 UM1-UM2), 34394 Montpellier Cedex 5, France; Department of Entomology, Faculty of Agriculture, Kasetsart University, Lat Yao Chatuchak Bangkok 10900, Thailand; Center for Advanced Studies for Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand (CASAF, NRU-KU, Thailand);
authors.forename: Vincent
authors.initials: V
authors.lastname: Corbel
authors.affiliation: Laboratoire d'Ecologie Alpine (LECA), CNRS, UMR 5553, 38041 Grenoble Cedex 9, France; Université Grenoble-Alpes, 38041 Grenoble Cedex 9, France; Environmental and Systems Biology (BEeSy), Université Grenoble-Alpes, 38041 Grenoble Cedex 9, France;
authors.forename: Stephane
authors.initials: S
authors.lastname: Reynaud
authors.affiliation: Laboratoire d'Ecologie Alpine (LECA), CNRS, UMR 5553, 38041 Grenoble Cedex 9, France; Université Grenoble-Alpes, 38041 Grenoble Cedex 9, France; Environmental and Systems Biology (BEeSy), Université Grenoble-Alpes, 38041 Grenoble Cedex 9, France;
authors.forename: Jean-Philippe
authors.initials: JP
authors.lastname: David
mesh_terms: D000330:Aedes / Q000187:drug effects* / Q000235:genetics*; D000818:Animals; D016000:Cluster Analysis; D005784:Gene Amplification; D049750:Genome, Insect; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D007305:Insecticide Resistance; D007306:Insecticides / Q000494:pharmacology; D007928:Lethal Dose 50; D005810:Multigene Family; D009154:Mutation; D009570:Nitriles / Q000494:pharmacology; D011110:Polymorphism, Genetic; D011722:Pyrethrins / Q000494:pharmacology; D015203:Reproducibility of Results; D014158:Transcription, Genetic
chemical_list: D007306:Insecticides; D009570:Nitriles; D011722:Pyrethrins; C017180:decamethrin