Genomic Profiling of Insecticide Resistance in Malaria Vectors: Insights into Molecular Mechanisms.

Abstract

Malaria control faces challenges from widespread insecticide resistance in major Anopheles species. This study, employing a cross-species approach, integrates RNA-Sequencing, whole-genome sequencing, and microarray data to elucidate drivers of insecticide resistance in Anopheles gambiae complex and An. funestus. Findings show an inverse relationship between genetic diversity and gene expression, with highly expressed genes experiencing stronger purifying selection. These genes cluster physically in the genome, revealing potential coordinated regulation. We identified known and novel candidate insecticide resistance genes, enriched in metabolic, cuticular, and behavioural functions. We also present AnoExpress, a Python package, and an online interface for user-friendly exploration of resistance candidate expression. Despite millions of years of speciation, convergent gene expression responses to insecticidal selection pressures are observed across Anopheles species, providing crucial insights for malaria vector control. This study culminates in a rich dataset that allows us to understand molecular mechanisms, better enabling us to combat insecticide resistance effectively.

Copy number variants underlie the major selective sweeps in insecticide resistance genes inAnopheles arabiensisfrom Tanzania

“…As with Cyp4h17, Gstd3 was also highlighted as consistently differentially expressed in resistant field populations compared to laboratory colonies in a transcriptomic meta-analysis (Ingham and Nagi, 2024), and we further showed equivocal evidence of an association of copy number of this gene with resistance to deltamethrin in our data. Further evidence is needed to determine the importance of this gene in resistance, and the insecticides to which resistance is most strongly conferred.…”

“…We ran simulations assuming that presence / absence of the CNV provided a similar effect size of resistance as was previously found in An. gambiae from Ghana (Nagi et al, 2024) and found that we had 88% power to detect the effect in our data.…”

“…Our agnostic genome-wide scans also revealed an association with deltamethrin resistance around three other detoxification loci: two cytochrome P450 clusters ( Cyp4h16-Cyp4h18 and Cyp12f1 - Cyp12f4 ) and a glutathione-S-transferase cluster ( Gstd ). Cyp4h17 , a member of the first P450 cluster, was highlighted as one of the most strongly upregulated genes in a genome-wide meta-analysis of resistant Anopheles expression data (Ingham and Nagi, 2024), suggesting at a role in resistance, which our data indicate could be against deltamethrin. In the Cyp12f cluster, Cyp12f2 and Cyp12f3 showed allelic imbalance in gene expression in F1 crosses between resistant and susceptible colonies of An.…”

“…1b). The first was centred on the carboxylesterases Coeae1f (AGAP006227) and Coeae2f (AGAP006228), which have been implicated in resistance to PM in West Africa (Nagi et al, 2024). The second peak was centred on another carboxylesterase cluster, Coeae2g (AGAP006723) - Coeae6g (AGAP006727), which has not previously been associated with resistance.…”

“…from Ghana, and have been found in An. arabiensis from Tanzania (Nagi et al, 2024). In our samples, we found the previously identified Coeaexf _Dup2 CNV allele in 74% of samples from Moshi, and 1% of samples from Muleba (Fig.…”