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Characterizing the genetic diversity of\n                      <jats:italic>Ae. aegypti<\/jats:italic>\n                      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\u2019 large genome size. Reduced-representation approaches offer a cost-effective alternative, yet a standardized genome-wide marker set for population genetic studies of\n                      <jats:italic>Ae. aegypti<\/jats:italic>\n                      is lacking.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      We developed a targeted amplicon sequencing panel for cost-effective, high-throughput genotyping across 291 loci distributed throughout the\n                      <jats:italic>Ae. aegypti<\/jats:italic>\n                      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.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      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\n                      <jats:italic>Ae. aegypti<\/jats:italic>\n                      and yields individual genetic admixture estimates consistent with WGS results.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      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\n                      <jats:italic>Ae. aegypti<\/jats:italic>\n                      , particularly in resource-limited settings.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s13071-026-07370-9","type":"journal-article","created":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T17:04:50Z","timestamp":1776272690000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A targeted amplicon sequencing panel for cost-effective high-throughput genotyping of Aedes aegypti"],"prefix":"10.1186","volume":"19","author":[{"given":"Josquin","family":"Daron","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alicia","family":"Lecuyer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laurence","family":"Ma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pegah","family":"Marzooghi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mallery I.","family":"Breban","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Kyrylos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"I\u2019ah","family":"Donovan-Banfield","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Seth N.","family":"Redmond","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Louis","family":"Lambrechts","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2026,4,15]]},"reference":[{"key":"7370_CR1","doi-asserted-by":"publisher","first-page":"854","DOI":"10.1093\/biosci\/biy119","volume":"68","author":"JR Powell","year":"2018","unstructured":"Powell JR, Gloria-Soria A, Kotsakiozi P. 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