Identifying genomic changes associated with imidacloprid resistance in the dengue mosquito Aedes aegypti by deep targeted sequencing

Mosquitoes are vectors of major human diseases and their control is mainly based on the use of chemical insecticides. However, resistance to chemical insecticides including pyrethroids, the main insecticide class used against mosquitoes, led to a regain of interest for neonicotinoids. Though neonicotinoid resistance mechanisms have been investigated in agricultural pests, few data have been generated in mosquitoes. IThe present study aims at identifying DNA markers of imidacloprid resistance in the dengue vector mosquito Aedes aegypti using target enrichment technology followed by high-throughput DNA sequencing. Resistance mechanisms were studied by through genomic data obtained from a laboratory strain selected at the larval stage for 30 generations with imidacloprid (Imida-R line). An additional line showing a lower resistance level was also created by releasing the selection pressure after 10 generations in order to improve resistance allele detection and investigate fitness costs associated with resistance (Imida-S line). Genomic DNA was extracted from pools of 65 4th stage larvae from each line. The exon capture technology (Agilent Sureselect) was used to capture the coding sequence and the promoter sequence (1 kb upstream) of more than 760 genes belonging to protein families potentially involved in insecticide resistance. Capture libraries were sequenced on a genome analyzer II (illumine) as paired reads of 76 bp.