Figure 3
Spinosad-resistant lines exhibit increased expression of genes associated with either penetration resistance or metabolic resistance. (a) Volcano plot of genes displaying fold change gene expression differences between the resistant C3 line vs 2 susceptible lines (C2 and C5). Genes upregulated in the resistant populations (green) are to the right of the dotted line while genes downregulated in the resistant populations (pink) lie to the left of the dotted line. Genes that exhibit no significant difference in gene expression between the two populations are in grey. Highly significant differences are located higher up on the y-axis where padj is the Benjamin-Hochberg adjusted p-value. Labeled points signify genes that satisfy at least one of the following criteria: (1) have the largest fold change difference between the two groups, (2) have the lowest padj, and (3) are genes known to be involved in insecticide resistance. Labels contain the D. suzukii gene symbol (LOC#########) and the corresponding D. melanogaster gene symbol. Genes known to be involved in conferring resistance are labeled in black while genes labeled in grey are not known to be directly involved in conferring resistance. (b) Volcano plot of genes displaying fold change gene expression differences between the resistant C4 line vs 2 susceptible lines (C2 and C5). The black box denotes the region zoomed-in in the insert. (c) Relative expression (FPKM) of metabolic and cuticular genes (twdl: tweedle; cpr: cuticular protein) in the susceptible (C2 and C5: black) and resistant (C3: maroon; C4: blue) groups extracted from the RNA sequencing data. Each point denotes a biological replicate (n = 3 replicates of 8–10 females per line). Asterisks denote significant p-values as determined by 2-way ANOVA: **p < 0.01, ***p < 0.001, and ****p < 0.0001. (d, e) Top 5 most significant enrichment pathways within the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) Biological Processes (bio proc) categories for genes up- or down-regulated in lines (d) C3 and (e) C4. The x-axis is Fold Enrichment, which is defined as the percentage of differentially expressed genes that belong to each pathway. Point size represents the number of genes (nGenes) within the category while color denotes the false discovery rate (FDR) correction of enrichment p-values.
