{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T00:57:46Z","timestamp":1792717066784,"version":"4.5.0"},"posted":{"date-parts":[[2025,1,16]]},"group-title":"Genomics","reference-count":138,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,1,16]],"date-time":"2025-01-16T00:00:00Z","timestamp":1736985600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,1,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  The yellow fever mosquito (\n                  <jats:italic>Aedes aegypti<\/jats:italic>\n                  ) is an organism of high medical importance because it is the primary vector for diseases such as yellow fever, Zika, dengue, and chikungunya. Its medical importance has made it a subject of numerous efforts to understand their biology. One such effort, was the development of a high-quality reference genome (AaegL5). However, this reference genome was sourced from a highly inbred laboratory strain with unknown geographic origin. Thus, the reference is not representative of a wild mosquito, let alone one from its native range in sub-Saharan Africa. To better understand the genetic architecture of\n                  <jats:italic>Ae. aegypti<\/jats:italic>\n                  and their sister species, we developed two\n                  <jats:italic>de novo<\/jats:italic>\n                  chromosome-scale genomes with sequences sourced from single individuals: one of\n                  <jats:italic>Ae. aegypti formosus<\/jats:italic>\n                  (Aaf) from Burkina Faso and one of\n                  <jats:italic>Ae. mascarensis<\/jats:italic>\n                  (Am) from Mauritius. Both genomes exhibit high contiguity and gene completeness, comparable to AaegL5. While Aaf exhibits high degree of synteny to AaegL5, it also exhibits several large inversions. We further conducted comparative genomic analyses using our genomes and other publicly available culicid reference genomes to find extensive chromosomal rearrangements between major lineages. Overrepresentation analysis of expanded genes in Aaf, AaegL5, and Am revealed that while the overarching category of genes that have expanded are similar, the specific genes that have expanded differ. Our findings elucidate novel insights into chromosome evolution at both microevolutionary and macroevolutionary scales. The genomic resources we present are additions to the arsenal of biologists in understanding mosquito biology and genome evolution.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>Significance<\/jats:title>\n                  <jats:p>\n                    <jats:italic>Aedes aegypti<\/jats:italic>\n                    is a major arboviral disease vector found throughout the tropics and sub-tropics. Its subspecies differ ecologically, as native sub-Saharan African form feeds on mammals generally and inhabit both sylvatic and domestic areas and the global invasive form preferentially feeds on humans and lives primarily domestic areas. Their medical importance has prompted the development of a high-quality reference genome, but it was sourced from an inbred laboratory strain of unknown origin. Here, we leveraged PacBio HiFi sequencing and HiC sequencing to develop the first de novo genome of\n                    <jats:italic>Ae. aegypti<\/jats:italic>\n                    sampled its native range in Burkina Faso. We also present a de novo genome of\n                    <jats:italic>Ae. mascarensis<\/jats:italic>\n                    , its sister species. Our genomes are comparably contiguous and complete to the reference genome. Comparative genomic analysis using our genomes and other culicid reference genomes reveal extensive chromosomal rearrangements.\n                  <\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2025.01.13.632753","type":"posted-content","created":{"date-parts":[[2025,1,16]],"date-time":"2025-01-16T04:40:18Z","timestamp":1737002418000},"source":"Crossref","is-referenced-by-count":3,"title":["From macro to micro: De novo genomes of Aedes mosquitoes enable comparative genomics among close and distant relatives"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6325-5268","authenticated-orcid":false,"given":"Gen","family":"Morinaga","sequence":"first","affiliation":[{"name":"Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dar\u00edo","family":"Balcazar","sequence":"additional","affiliation":[{"name":"Department of Ecology & Evolution, Yale University, New Haven, CT, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Athanase","family":"Badolo","sequence":"additional","affiliation":[{"name":"Laboratoire d\u2019Entomologie Fondamentale et Appliqu\u00e9e, Universit\u00e9 Joseph Ki-Zerbo, Ouagadougou, Burkina Faso"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diana","family":"Iyaloo","sequence":"additional","affiliation":[{"name":"Vector Biology & Control Division, Ministry of Health & Quality of Life, Curepipe, Mauritius"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luciano","family":"Tantely","sequence":"additional","affiliation":[{"name":"Medical Entomology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Theo","family":"Mouillaud","sequence":"additional","affiliation":[{"name":"L\u2019Institut de recherche pour le d\u00e9veloppment, UMR MIVEGEC, Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Sharakhova","sequence":"additional","affiliation":[{"name":"Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9511-5139","authenticated-orcid":false,"given":"Scott M.","family":"Geib","sequence":"additional","affiliation":[{"name":"USDA-ARS Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, HI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christophe","family":"Paupy","sequence":"additional","affiliation":[{"name":"L\u2019Institut de recherche pour le d\u00e9veloppment, UMR MIVEGEC, Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diego","family":"Ayala","sequence":"additional","affiliation":[{"name":"Medical Entomology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar"},{"name":"L\u2019Institut de recherche pour le d\u00e9veloppment, UMR MIVEGEC, Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffrey R.","family":"Powell","sequence":"additional","affiliation":[{"name":"Department of Ecology & Evolution, Yale University, New Haven, CT, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Gloria-Soria","sequence":"additional","affiliation":[{"name":"Department of Ecology & Evolution, Yale University, New Haven, CT, USA"},{"name":"The Connecticut Agricultural Experiment Station, New Haven, CT, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Soghigian","sequence":"additional","affiliation":[{"name":"Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026041021414272000_2025.01.13.632753v2.1","doi-asserted-by":"publisher","DOI":"10.1093\/aesa\/saab025"},{"key":"2026041021414272000_2025.01.13.632753v2.2","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-022-04590-5"},{"key":"2026041021414272000_2025.01.13.632753v2.3","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-017-3579-8"},{"key":"2026041021414272000_2025.01.13.632753v2.4","doi-asserted-by":"publisher","DOI":"10.1126\/science.1191864"},{"key":"2026041021414272000_2025.01.13.632753v2.5","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-018-4663-4"},{"key":"2026041021414272000_2025.01.13.632753v2.6","doi-asserted-by":"crossref","unstructured":"Ayala D , Ullastres A , Gonz\u00e1lez J. 2014. 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