*3.5. Functional Enrichment Analysis of DEGs*

To explore the biological functions of DEGs in the four groups, GO enrichment analysis was performed. In total, 5133 of 11,633 DEGs in the four comparisons were annotated with GO terms and assigned to three categories: molecular function (MF), biological process (BP), and cellular component (CC) (Figure 4; Table S3). Under HS, the GO terms "photosynthesis, light harvesting" (GO:0009765), "DNA conformation change" (GO:0071103), "nucleosome assembly" (GO:0006334), "DNA packaging" (GO:0006323), "chromatin assembly" (GO:0031497), "nucleosome organization" (GO:0034728), and "chromatin assembly or disassembly" (GO:0006333) were the most commonly enriched components in the BP category in 17-03 and H1023 (Figure 4; Table S4). The most commonly enriched components were "cell wall" (GO:0005618) and "external encapsulating structure" (GO:0030312) in the CC category and "nucleosome binding" (GO:0031491) in the MF category in 17-03 and H1023 (Figure 4; Table S4). However, "DNA replication" (GO:0006260), "DNA replication initiation" (GO:0006270), "protein folding" (GO:0006457), and "protein-DNA complex assembly" (GO:0065004) in the BP category, "protein-DNA complex" (GO:0032993) in the CC category, and "nucleosomal DNA binding" (GO:0031492) in the MF category were only enriched in 17-03 (Table S4). For the recovery stage after HS, the most significantly enriched GO terms differed between 17-03 and H1023. In 17-03, DEGs were most enriched in "translation" (GO:0006412), "peptide biosynthetic process" (GO:0043043), "peptide metabolic process" (GO:0006518), "amide biosynthetic process" (GO:0043604), "cellular amide metabolic process" (GO:0043603), and "organonitrogen compound biosynthetic process" (GO:1901566) in the BP category (Table S4). "Ribosome" (GO:0005840), "nonmembrane-bounded organelle" (GO:0043228), and "intracellular non-membrane-bounded organelle" (GO:0043232) were the top three CC categories (Table S4). The terms of the MF category were "structural constituent of ribosome" (GO:0003735) and "structural molecule activity" (GO:0005198) (Table S4).

**Figure 4.** Gene ontology (GO) classifications of differentially expressed genes (DEGs) in the comparison groups CK1\_vs\_T1 (**a**), CK2\_vs\_T2 (**b**), CK1\_vs\_M1 (**c**), and CK2\_vs\_M2 (**d**). The DEGs were assigned to three categories: biological process (BP), cellular component (CC), and molecular function (MF). The *X*-axis indicates the top ten most significantly enriched BP, CC, and MF categories. The *Y*-axis indicates -log10 (*p*-value).

We performed KEGG pathway analysis to examine the pathways in which DEGs were involved. The significantly enriched pathways involved in HS and recovery responses are shown in Figure 5 and Table S5. The common significantly enriched pathways under HS were identified, such as "photosynthesis–antenna proteins" (cann00196), "ribosome biogenesis in eukaryotes" (cann03008), "fatty acid elongation" (cann03008), "anthocyanin biosynthesis" (cann00942), and "glycine, serine and threonine metabolism" (cann00260) (Figure 5 and Table S5). However, the significantly enriched KEGG pathways during recovery were different. The term "ribosome" (cann03010) was the most significantly enriched in 17-03, whereas "photosynthesis–antenna proteins" (cann00196), "carbon fixation in photosynthetic organisms" (cann00710), "porphyrin and chlorophyll metabolism" (cann00860), and "carotenoid biosynthesis" (cann00906) were the most significantly enriched in H1023 (Figure 5 and Table S5).

**Figure 5.** The significantly enriched pathways in comparison groups CK1\_vs\_T1, CK2\_vs\_T2, CK1\_vs\_M1, and CK2\_vs\_M2. The *X*-axis indicates the significantly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and the *Y*-axis indicates the percentage of a specific category of genes in the main category.
