{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T18:42:20Z","timestamp":1785436940698,"version":"3.56.0"},"posted":{"date-parts":[[2025,9,30]]},"group-title":"Genomics","reference-count":61,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,9,30]],"date-time":"2025-09-30T00:00:00Z","timestamp":1759190400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"crossref","award":["ANR-10-LABX-62-IBEID"],"award-info":[{"award-number":["ANR-10-LABX-62-IBEID"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"crossref","award":["ANR-20-CE35-0002"],"award-info":[{"award-number":["ANR-20-CE35-0002"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"crossref","award":["ANR-10-INBS-09"],"award-info":[{"award-number":["ANR-10-INBS-09"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"crossref"}]},{"id":[{"id":"https:\/\/ror.org\/022nw7x84","id-type":"ROR","asserted-by":"publisher"}]},{"award":["1S10OD030363-01A1"],"award-info":[{"award-number":["1S10OD030363-01A1"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,9,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  The mosquito\n                  <jats:italic>Aedes aegypti<\/jats:italic>\n                  is the primary vector for several medically significant arboviruses, including dengue, Zika, chikungunya, and yellow fever. Studying the genetic diversity of\n                  <jats:italic>Ae. aegypti<\/jats:italic>\n                  is crucial for understanding its evolutionary history, population dynamics, and the effectiveness of vector control methods. Due to the large genome size of\n                  <jats:italic>Ae. aegypti<\/jats:italic>\n                  , whole-genome sequencing (WGS) is often cost-prohibitive for large-scale studies. Recent advances in reduced-representation methods, aiming to reduce costs by sequencing only a small portion of the genome, provide cost-effective alternatives. However, a standardized set of genome-wide markers specifically designed for population genetic studies of\n                  <jats:italic>Ae. aegypti<\/jats:italic>\n                  remains unavailable. Here, we present a targeted amplicon sequencing panel designed for cost-effective, high-throughput genotyping across 291 loci distributed throughout the\n                  <jats:italic>Ae. aegypti<\/jats:italic>\n                  genome. Our\n                  <jats:italic>in silico<\/jats:italic>\n                  analyses indicate that this amplicon panel effectively replicates population structure analyses typically derived from WGS data. We demonstrate that the amplicon panel accurately discriminates between diverse laboratory colonies of\n                  <jats:italic>Ae. aegypti<\/jats:italic>\n                  and consistently measures individual genetic admixture to a degree comparable with WGS. By enabling high-throughput genotyping at a reduced cost, we anticipate that our targeted amplicon sequencing panel will facilitate large-scale genotyping studies of\n                  <jats:italic>Ae. aegypti<\/jats:italic>\n                  for vector surveillance and population structure analyses, especially in resource-limited settings.\n                <\/jats:p>","DOI":"10.1101\/2025.09.28.679043","type":"posted-content","created":{"date-parts":[[2025,9,30]],"date-time":"2025-09-30T19:45:14Z","timestamp":1759261514000},"source":"Crossref","is-referenced-by-count":0,"title":["A targeted amplicon sequencing panel for cost-effective high-throughput genotyping of\n                  <i>Aedes aegypti<\/i>"],"prefix":"10.64898","author":[{"given":"Josquin","family":"Daron","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alicia","family":"Lecuyer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurence","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pegah","family":"Marzooghi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mallery I.","family":"Breban","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Kyrylos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"I\u2019ah","family":"Donovan-Banfield","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seth N.","family":"Redmond","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5958-2138","authenticated-orcid":false,"given":"Louis","family":"Lambrechts","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2025100309200923000_2025.09.28.679043v1.1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msq148"},{"key":"2025100309200923000_2025.09.28.679043v1.2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.094052.109"},{"key":"2025100309200923000_2025.09.28.679043v1.3","doi-asserted-by":"publisher","DOI":"10.1111\/mec.12276"},{"key":"2025100309200923000_2025.09.28.679043v1.4","doi-asserted-by":"publisher","DOI":"10.1126\/science.abd3663"},{"key":"2025100309200923000_2025.09.28.679043v1.5","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.12737"},{"key":"2025100309200923000_2025.09.28.679043v1.6","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1111\/1755-0998.12682","article-title":"Effective mosquito and arbovirus surveillance using metabarcoding","volume":"18","year":"2018","journal-title":"Mol Ecol Resour"},{"key":"2025100309200923000_2025.09.28.679043v1.7","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2010.2469"},{"key":"2025100309200923000_2025.09.28.679043v1.8","doi-asserted-by":"publisher","DOI":"10.1016\/S2542-5196(24)00276-6"},{"key":"2025100309200923000_2025.09.28.679043v1.9","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.12357"},{"key":"2025100309200923000_2025.09.28.679043v1.10","doi-asserted-by":"crossref","first-page":"13893","DOI":"10.1038\/s41598-022-17822-8","article-title":"High-throughput barcoding method for the genetic surveillance of insecticide resistance and species identification in Anopheles gambiae complex malaria vectors","volume":"12","year":"2022","journal-title":"Sci Rep"},{"key":"2025100309200923000_2025.09.28.679043v1.11","doi-asserted-by":"crossref","unstructured":"Cannon, M.V. , Bogale, H.N. , Bhalerao, D. , Keita, K. , Camara, D. , Barry, Y. , Keita, M. , Coulibaly, D. , Kone, A.K. , Doumbo, O.K. , Thera, M.A. , Plowe, C.V. , Travassos, M.A. , Irish, S.R. , Yeroshefsky, J. , Dorothy, J. , Prendergast, B. , St Laurent, B. , Fritz, M.L. , Serre, D. , 2021. 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