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 the genetic diversity of Ae. aegypti is essential to understand its evolutionary history and population dynamics and to evaluate vector control strategies. However, whole-genome sequencing (WGS) is often cost-prohibitive at scale due to the species' large genome size. 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 developed a targeted amplicon sequencing panel for cost-effective, high-throughput genotyping across 291 loci distributed throughout the Ae. aegypti genome. We evaluated its performance by comparing patterns of population structure and genetic admixture inferred from the amplicon sequences with those obtained from WGS data. RESULTS: In silico analyses demonstrate that the amplicon panel reliably reproduces population structure patterns typically observed with WGS. It also effectively distinguishes among diverse laboratory colonies of Ae. aegypti and yields individual genetic admixture estimates consistent with WGS results. CONCLUSIONS: This targeted amplicon sequencing panel enables high-throughput genotyping at reduced cost and provides a practical alternative to WGS for population genetic and genomic surveillance studies. It should facilitate large-scale genotyping of Ae. aegypti, particularly in resource-limited settings.