Table 1.
Deltamethrin resistance levels.
Table 2.
Sequencing and mapping statistics.
Fig 1.
Gene families affected by DE genes in resistant populations.
Genes showing a fold change ≥ 3 in either directions, and q-value ≤ 0.001 in any resistant population as compared to all susceptible strains were considered differentially expressed. Biological categories mostly affected were identified by comparing their proportion between all genes detected by RNA-seq and those being differentially expressed using a one-sided Fisher’s exact test (*** p ≤ 0.001).
Fig 2.
Transcription profiles of detoxification enzymes associated with deltamethrin resistance.
Color scale shows the mean Log2 Fold Change between resistant populations and all susceptible strains. Stars indicate a fold change q value ≤ 0.001. Black ‘+’ marks indicate a significant positively correlation between Log2 transcription ratios and Log2 CNVs (Pearson’s r ≥ 0.7 and p ≤ 0.05). Grey ‘+’ marks indicate genes belonging to genomic clusters displaying CNV associated with deltamethrin resistance as reported in [28].
Fig 3.
Promoter elements potentially associated with the up regulation of detoxification genes in resistant populations.
Only variations correlated with transcription level and favouring the binding of potential enhancer elements are shown. Potential initiation sites (Inr) and TATA boxes are indicated. For each gene, variations detected in the upstream region are shown as empty and filled dots depending on the significance of the correlation between their allele frequency and gene transcription level.
Fig 4.
Gene families affected by polymorphism variations in resistant populations.
The frequency of each gene family was compared between all detected polymorphic SNPs (top) and both differential SNPs (Diff SNPs) and non-synonymous differential SNPs (NS Diff SNPs) using a one-sided Fisher’s exact test (*p ≤ 0.05,*** p ≤ 0.001).
Table 3.
Overview of SNP analysis.
Fig 5.
Non-synonymous differential SNPs affecting detoxification genes.
Color scale shows the mean allele frequency variation between each resistant strain and all susceptible strains. Yellow/blue colors indicate an increase/decrease frequency of the variant allele in the resistant population respectively. Chromosome, supercontig, base position, nucleotide variation (ref>var), strand, position in cDNA, position in protein, amino-acid change (ref>var), gene accession and gene name are indicated. Stars indicate genes previously affected by NS Diff SNPs as reported in [28]. Boxed amino acid changes indicate variations likely affecting substrate binding site.