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This study used a comprehensive multi-omics framework integrating 7-year gap temporal RNA-Seq, PoolSeq Whole Genome, and functional analyses, to uncover resistance escalation mechanisms in Anopheles funestus Africa-wide. Spatiotemporal analyses (2014\u20132021) reveal massive overexpression of novel genes (V-ATPase, tubulin alpha-1, transposase), alongside canonical resistance genes (P450s, cuticular proteins, chemosensory). Epigenetic regulators (histone H3\/4, glycine N-methyltransferase) were greatly overexpressed in highly resistant mosquitoes, suggesting resistance modulation. P450-based signatures of selective sweep were detected with a drastic change in the rp1 and the P450 CYP9K1 in Central Africa. Noticeably, genomic variations at the cytochrome P450 reductase (CPR) gene were selected including a N70I mutation in Malawi [0% (2009)\u201380% (2021)] and a 5.9\u2005kb promoter duplication in Ghana. Transgenic expression in Drosophila confirmed CPR-70I enhances pyrethroid resistance when co-expressed with P450-CYP6P9a, uncovering a novel CPR-mediated mechanism in intensely resistant mosquitoes. This study highlights novel candidate genes for marker development to track the spread of intensely resistant mosquitoes across Africa.<\/jats:p>","DOI":"10.1093\/molbev\/msaf251","type":"journal-article","created":{"date-parts":[[2025,10,2]],"date-time":"2025-10-02T11:58:59Z","timestamp":1759406339000},"source":"Crossref","is-referenced-by-count":5,"title":["Genomic Drivers of Pyrethroid Resistance Escalation in the Malaria Vector\n                    <i>Anopheles funestus<\/i>\n                    Across Africa"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5671-2299","authenticated-orcid":false,"given":"Mahamat","family":"Gadji","sequence":"first","affiliation":[{"name":"Department of Vector Genomics, Centre for Research in Infectious Diseases (CRID) , P.O. BOX 13591, Yaound\u00e9 ,","place":["Cameroon"]},{"name":"Department of Microbiology, University of Yaound\u00e9 1 , P.O. 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