Fig. 2: In planta transcriptome analysis of cotton-V. dahliae interactions.

a Correlation analysis of the FPKM for differentially expressed genes (DEGs) in the V991 transcriptome between different time points from 3-21 days post infection (dpi). Pearson correlation of the FPKM was used to define the similarity of gene expression patterns among different time points. Values and colors indicated Pearson’s correlation coefficient. b Correlation analysis of the FPKM for DEGs in the cotton (V991) transcriptome between different time points from 3-21 dpi. c GO enrichment analysis of the stage-specific response to DEGs in the V991 transcriptome. DEGs that are upregulated at Stage I are named Type 1; DEGs that are upregulated at Stage II are named Type 2. The gene ratio is the number of DEGs divided by the total number of genes associated with a specific pathway. The color key corresponds to p_value for the enrichment score. p_value was determined by Fisher’s exact test. d GO enrichment analysis of stage-specific responses to DEGs in the cotton(V991) transcriptome. The color key corresponds to p_value for the enrichment score. p_value was determined by Fisher’s exact test. e Cluster heatmap of reported virulence-related genes in the V991 and 1cd3-2 transcriptomes. f Expression profiling of DEGs between two stages in cotton (V991) and cotton (1cd3-2) transcriptomes. CK indicates cotton seedlings without inoculation with V991 or 1cd3-2. Source data are provided as a Source Data file.