The southern house mosquito Culex quinquefasciatus is a major disease vector for multiple arboviruses, including West Nile virus and St. Louis Encephalitis virus. Given the threat to public health, preventative measures such as insecticide treatments are used to control populations. However, high levels of standing genetic variation in C. quinquefasciatus provide the genomic substrate for selection to act upon and enable these populations to rapidly evolve resistance to insecticides, which can sometimes develop in as little as 10 generations (approximately 10-20 weeks). As such, it is imperative that we understand the genomic basis for rapid adaptation to insecticides in this species. Previous work has mainly focused on single-nucleotide polymorphisms (SNPs), and this has left the contribution of structural variation to insecticide resistance relatively understudied in C. quinquefasciatus. Structural variants (insertions, deletions, and other genomic changes affecting > 50bp) occupy more of the genome than SNPs because of their size, and therefore can dramatically change phenotypes. They are also often more likely to impact organismal fitness because they can contain entire genes and/or other functional elements. Here, we used PacBio HiFi sequencing to examine structural variation in two populations of C. quinquefasciatus from Puerto Rico and Zambia. Using a combination of read-based and assembly-based approaches to detect structural variants, we identified a consensus set of variants containing or overlapping candidate insecticide resistance genes, including variants specific to each population, possibly reflecting local adaptation to insecticides. These findings suggest an important role of structural variation in rapid adaptation and will help elucidate the genomic basis of insecticide resistance in mosquitoes, which will be critical for informing vector control efforts.
Anna Trotter (Wed,) studied this question.