SUPPORTING INFORMATION Figure S1. Cotton whitefly infestation within a sealed chamber.

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SUPPORTING INFORMATION Figure S1. Cotton whitefly infestation within a sealed chamber.

Figure S2. Comprehensive evaluation of the RNA-Seq data. (a, b)Analysis of all samples was performed based on FPKM data using PCA. (c) All samples were clustered using the pvclust package. PC3 (6.4%) principal component

HR0-12HR0-24 ZS0-12ZS0-24ZS0-48 Figure S3. Test for differential expression in cotton before and after whitefly infestation. Scatter plot indicates the log2 fold change versus mean. Red indicates DEGs detected with a P-value < 0.01 and a multiple testing adjustment.

HR0-12HR0-24 ZS0-12 ZS0-24ZS0-48 Figure S4. Ven diagram showing the overlap of DEGs detected using different analysis methods.

Figure S5. Pie charts represent GO terms (biological_process level 2) in the various treatment groups. The percentage present DEGs counts.

(a)(c) (d)(c) Figure S6. Network construction of related results. (a) Analysis of network topology through different soft-thresholding limits. (b) Ten modules DEGs were showed by a hierarchical clustering dendrogram. (c) Clustering of the modules. (d) The heatmap shows the eigengene adjacency.

Figure S7. Correlation between qRT-PCR and RNA-Seq results.