A targeted amplicon sequencing panel for cost-effective high-throughput genotyping of Aedes aegypti

Background: The mosquito Aedes aegypti is the primary vector of several medically important arboviruses, including dengue, Zika, chikungunya, and yellow fever. Characterizing genetic diversity in Ae. aegypti is essential to understand its evolutionary history and population dynamics and to evaluate vector control strategies, but large-scale whole-genome sequencing (WGS) remains cost-prohibitive due to the species' large genome. Reduced-representation approaches offer a cost-effective alternative, yet a standardized genome-wide marker set for population genetic studies of Ae. aegypti is lacking. Methods: We designed a targeted amplicon sequencing panel for cost-effective, high-throughput genotyping across 291 loci distributed throughout the Ae. aegypti genome. We evaluated the panel in silico by comparing population structure and admixture inference obtained from the panel to results typically derived from WGS data. Results: In silico analyses indicate that the amplicon panel recapitulates population structure patterns commonly obtained from WGS. The panel accurately discriminates among diverse laboratory colonies of Ae. aegypti and yields consistent estimates of individual genetic admixture comparable to WGS-based analyses. Conclusions: This targeted amplicon sequencing panel enables high-throughput genotyping at reduced cost and provides a practical alternative to WGS for population structure and surveillance applications. It should facilitate large-scale genetic studies of Ae. aegypti, particularly in resource-limited settings.