Genomic analysis of resistance in the yellow fever mosquito, Aedes aegypti

Aedes aegypti is the vector of four important human disease viruses: dengue, yellow fever, Zika and chikungunya. Because this mosquito has a wide global distribution and thrives in urban environments, it poses a serious risk to human health. For example, dengue is estimated to be a risk to over 50% of the world's population and Zika is a new emerging disease that has generated a great deal of human health concern since it reached the Americas in 2014.Finding strategies for delaying the development of resistance in mosquito vectors to the few available insecticides is critical. In order to design sensitive and precise monitoring programs, to understand the population genetics and evolution of resistance, and to design effective countermeasures to slow the development of resistance, it is essential to identify the mutations responsible for resistance. The ability to identify and track resistance alleles has led to an unprecedented leap in our knowledge of insecticide resistance (population genetics, fitness costs, resistance monitoring, etc.) in some species. However, in A. aegypti a great many questions remain. The current limitation in A. aegypti is that the mutation(s) responsible for pyrethroid resistance (other than kdr) are unknown. The Singapore strain (SP) characterized in 2015 was determined to have both CYP-mediated resistance and kdr alleles 989P+1016G conferring resistance. Our lab has created three strains congenic to the Rockefeller (ROCK) pesticide-susceptible strain with Singapore strain resistance introgressed in: KR (kdr alleles only), CR (CYP-mediated resistance only), and CKR (both CYP-mediated and kdr alleles). These five strains provide a unique opportunity to study the genomic basis of CYP-mediated resistance.This project uses a combination of three genomic approaches to map the resistance loci previously determined to be present on chromosome 1. Long-read whole-genome sequencing was performed for strains ROCK, CKR, and SP on the Oxford Nanopore PromethION platform on libraries composed of single-individual DNA extractions. Whole-genome shotgun sequencing was performed for strains ROCK, CKR, CR, and SP at 50x coverage on the Illumina NextSeq 500 platform on libraries composed of DNA extracted from 5 pooled females. Finally, target enrichment sequencing will be performed for loci of interest.