Deltamethrin Selection Drives Transcriptomic Changes in Detoxification, Immune, and Cuticle Genes in Aedes aegypti

Abstract

The rapid global expansion of Aedes aegypti-borne diseases such as dengue, chikungunya, and Zika has positioned this mosquito as a key target for vector control programs. These programs rely heavily on insecticide use, leading to the widespread emergence of insecticide resistance. Understanding the molecular basis of resistance is essential for developing effective management strategies. In this study, we employed a whole-transcriptome (RNA-seq) approach to analyze gene expression in three Ae. aegypti populations from Mexico that underwent four generations of laboratory selection with deltamethrin. Several cytochrome P450 genes (CYP6AG4, CYP6M5, CYP307A1) and a chitin-binding peritrophin-like gene (Ae-Aper50) were significantly overexpressed following selection, supporting roles for both detoxification and midgut protection. We also observed a consistent downregulation of cuticular protein genes in deltamethrin-selected groups relative to the baseline populations, suggesting their involvement in baseline tolerance rather than induced resistance. Additionally, the overexpression of immune- and stress-related genes, including the RNA helicase MOV-10, indicates that insecticide selection may trigger broader physiological responses. These findings highlight complex, multi-pathway transcriptomic changes associated with resistance development in Ae. aegypti.

Keywords: Aedes aegypti; RNA-seq; cuticular proteins; cytochrome P450; deltamethrin selection; immune-related genes; peritrophic matrix.

Figure 1

Clustering of the normalized RNA-seq data: (A) Hierarchical clustering heatmap of the sample-to-sample Pearson’s correlation of the normalized gene expression data assigned to each biological replicate; (B) principal component analysis (PCA) of multiple RNA-seq datasets.

Figure 2

Volcano plots for gene expression for the HUN population experiment. (A) HUNF_S0 vs. NOr, (B) HUNF_S4 vs. HUNF_S0, and (C) HUNF_S4 vs. NOr. The X-axis shows log₂ fold change (FC), where negative and positive values indicate down- and upregulation, respectively. The Y-axis shows −log₁₀ of the adjusted p-value. Detoxification gene families are color-coded as follows: red for carboxylesterases (COEs), blue for cytochrome P450s (CYPs), and black for glutathione S-transferases (GSTs). Cuticular proteins (CPs) are shown in green, salivary gland proteins (SGs) are shown in pink, and genes with unknown functions are shown in gray. In each plot, genes overexpressed in the F_S4 group appear on the right side (>0 on the x-axis). The vertical dotted lines indicate a log₂FC threshold of ±1, and the horizontal dotted line represents the significance cutoff (FDR ≤ 0.01). (D) Venn diagram showing differentially expressed (DGE) genes shared among the comparisons F_S0 vs. NOr, F_S4 vs. F_S0, and F_S4 vs. NOr.

Figure 3

Volcano plots of gene expression in the JC population experiment. (A) JCF_S0 vs. NOr, (B) JCF_S4 vs. JCF_S0, and (C) JCF_S4 vs. NOr. The X-axis shows log₂ fold change (FC), where negative and positive values indicate down- and upregulation, respectively. The Y-axis shows −log₁₀ of the adjusted p-value. Detoxification gene families are color-coded as follows: red for carboxylesterases (COEs), blue for cytochrome P450s (CYPs), and black for glutathione S-transferases (GSTs). Cuticular proteins (CPs) are shown in green, salivary gland proteins (SGs) are shown in pink, and genes with unknown functions are shown in gray. In each plot, genes overexpressed in the F_S4 group appear on the right side (>0 on the X-axis). The vertical dotted lines indicate a log₂FC threshold of ±1, and the horizontal dotted line represents the significance cutoff (FDR ≤ 0.01). (D) Venn diagram showing differentially expressed (DGE) genes shared among the comparisons F_S0 vs. NOr, F_S4 vs. F_S0, and F_S4 vs. NOr.

Figure 4

Volcano plots of gene expression in the MER population experiment. (A) MERF_S0 vs. NOr, (B) MERF_S4 vs. MERF_S0, and (C) MERF_S4 vs. NOr. The X-axis shows log₂ fold change (FC), where negative and positive values indicate down- and upregulation, respectively. The Y-axis shows −log₁₀ of the adjusted p-value. Detoxification gene families are color-coded as follows: red for carboxylesterases (COEs), blue for cytochrome P450s (CYPs), and black for glutathione S-transferases (GSTs). Cuticular proteins (CPs) are shown in green, salivary gland proteins (SGs) are shown in pink, and genes with unknown functions are shown in gray. In each plot, genes overexpressed in F_S4 appear on the right side (>0 on the X-axis). The vertical dotted lines indicate a log₂FC threshold of ±1, and the horizontal dotted line represents the significance cutoff (FDR ≤ 0.01). (D) Venn diagram showing differentially expressed (DGE) genes shared among the comparisons F_S0 vs. NOr, F_S4 vs. F_S0, and F_S4 vs. NOr.

Figure 5

Shared differentially expressed genes (DGEs) in F_S4 vs. F_S0 comparisons across populations. (A) Venn diagram showing overlapping DEGs among F_S4 vs. F_S0 comparisons in HUN, JC, and MER populations. (B) Log₂ fold change expression and functional annotation of the top 10 commonly upregulated and top 10 commonly downregulated DGEs shared across all F_S4 groups. These shared genes represent a consistent transcriptomic response to deltamethrin selection when compared to their respective F_S0 counterparts.