*3.3. Identification of Differentially Expressed Genes (DEGs)*

Based on the RNA-seq experiment, 24,448 expressed genes were identified in the pepper leaves (Table S2). Among these expressed genes, 11,633 DEGs were identified in 17-03 and H1023 among the four groups (Figure 2a; Table S3). Of the 11,633 DEGs, 7327 (3435 upregulated and 3892 downregulated) and 7778 (4025 upregulated and 3753 downregulated) DEGs were identified in groups CK1\_vs\_T1 and CK2\_vs\_T2, respectively (Figure 2a,b); 5185 DEGs were common between the two groups (Figure 2a); however, 2142 and 2593 DEGs were specially differentially expressed in CK1\_vs\_T1 and CK2\_vs\_T2, respectively (Figure 2a). Approximately, 3338 (2021 upregulated and 1317 downregulated) and 4822 (2256 upregulated and 2566 downregulated) DEGs were identified in groups CK1\_vs\_M1 and CK2\_vs\_M2, respectively (Figure 2b); there were 1934 common DEGs and 1404 and 2888 DEGs specially differentially expressed DEGs in CK1\_vs\_M1 and CK2\_vs\_M2, respectively (Figure 2a). Interestingly, 1229 common DEGs were identified among all four groups (Figure 2a).

**Figure 2.** Expression analysis of differentially expressed genes (DEGs) in 17-03 and H1023 leaves after 3 d heat treatment at 42 ◦C and 1 d recovery at 25 ◦C. Numbers of DEGs in 17-03 and H1023 at different times (**a**). Numbers of up- and down regulated DEGs in 17-03 and H1023 at different times (**b**).
