Identification of Novel Gene Clusters Potentially Associated with Insecticide Resistance in <em>Anopheles gambiae s.l.</em>
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Despite the increasing emergence of resistance, insecticide-based tools remain the main strategies used so far for vector control in Africa. In the absence of more effective alternatives, monitoring and screening for new resistance mechanisms remain the main strategies to ensure the continued deployment of current vector control tools. Here, we used the whole genome sequencing data from the Anopheles gambiae 1000 Genomes Project to investigate potential novel insecticide resistance genes in the Anopheles gambiae complex. We used a broad range of genomic data analysis techniques to identify and examine genetic variation in the potential new resistance genes identified. The results showed elevated Garud H12 values in the genomic regions of the 2L chromosome corresponding to the aldehyde oxidase cluster genes (AGAP006220, AGAP006221, AGAP006224, AGAP006225 and AGAP006226). The findings show a high occurrence of the two most common haplotypes in the populations, suggesting a recent selective sweep in this region driven by positive selection. In addition, single nucleotide polymorphisms (SNPs) have been identified in these genes with frequencies up to 100%, including 569, 691, 1433, 978, and 811 non-synonymous SNPs in AGAP006220, AGAP006221, AGAP006224, AGAP006225, and AGAP006226, respectively. Copy number variation (CNVs) such as deletions and amplifications were also identified in these genes at low frequencies (&lt;12%). The analysis of population structure analysis revealed evidence of adaptive and geographic gene flow between An. gambiae and An. coluzzii, confirming the historical connectivity between both species. These findings showed the potential role of aldehyde oxidase genes in the resistance of An. gambiae s.l. populations to insecticides. This study emphasized the importance of genomic surveillance for identifying new potential genes involved in the adaptation of malaria vectors to ecological changes.