# Comparative Transcriptomics for Pepper (_Capsicum annuum_ L.) under Cold Stress and after Rewarming
## 3 Results
### Response of Key Unigenes to Photosynthesis, Plant Hormone Signal Transduction, and DDR Processes  
To further understand the response of photosynthesis, plant hormone signal transduction, and DDR processes to cold and recovery processes, DEGs related to seven pathways (including carbon fixation in photosynthetic organisms, photosynthesis, photosynthesis-antenna proteins, plant hormone signal transduction, DNA replication, HR, and MMR) were annotated. Under cold-rewarm treatments, 52, 21, and 6 DEGs were classified into photosynthesis, photosynthesis-antenna proteins, and carbon fixation in photosynthetic organisms pathways, respectively (Figure 4). In CT and CS, the changes in the regulation of DEGs related to photosynthetic electron transport, photosynthesis-antenna proteins, and carbon fixation in photosynthetic organisms were basically consistent, in which light-harvesting complex II chlorophyll a/b binding protein (LHC) (_Capana10g000141_ and  
Figure 3: GO terms and pathways were significantly enriched in pepper under cold–rewarm treatments. (**a**) Significant enrichment of GO terms in the cold treatment groups. Deep red represents the higher number of DEGs, Deep blue represents the lower number of DEGs. (**b**) Significant enrichment of KEGG pathways in the cold treatment groups. Deep red color represents the higher numbers of DEGs; deep green color represents the lower numbers of DEGs. Capana09g001520), plastocyanin (_petE_) (_Capana04g000129_), ferredoxin (_petF_) (_Capana08g001896_ and _Capana10g001106_), and ribulose bisphosphate carboxylase (Rubisco) (_Capana02g002781_ and _Capana02g002784_) were firstly upregulated in T1 group; then subsequently downregulated; and finally, significantly decreased in T4 group (Figure 4a,b). Attractively, compared with CS, DEGs involved in photosystem I, photosystem II, Cytochrome b6/f complex, and F-type ATPase were significantly upregulated in T1 and T2 groups of CT (Figure 4a). These DEGs mainly included encoding photosystem I P700 apoprotein (_psaA_) (_Capana00g002019_ and _Capana07g00048_), photosystem II P680 reaction center D2/D1 protein (_psbA/psbD_) (_Capana11g002217_/Capana03g001477), photosystem II CP43 chlorophyll apoprotein (_psbC_) (Capana03g001476 and _Capana00g001698_), photosystem II CP47 chlorophyll apoprotein (_psbB_) (Capana00g001154), cytochrome b6 (_petB_) (Capana01g003214), ATP synthase cf1 (CF1) (_Capana00g000237_ and _Capana03g003995), and ATP synthase cf0 (CF0) (_Capana04g000951_). Plant hormone signal transduction plays an important role in plant response to cold stress. The DEGs were mainly enriched in auxin, abscisic acid (ABA), and jasmonic acid (JA) pathways (Figure 5). These might be important hormones related to pepper resistance to cold stress and rewarding recovery. In the two pepper cultivars, most of the genes such as the auxin transporter-like protein (_AUXI_), transport inhibitor response 1 (_TIR1_), and auxin-responsive protein IAA (_IAA_), Auxin response factor (_ARF_), Gretchen Hagen3 (_GH3_), and small auxin up RNA (_SAUR_) had little changes in T2 and T3 group, but their expression levels decreased significantly in T4 group. However, the expression levels of _IAA8_ (Capana00g000845) and _SAUR_ (Capana03g001923) were significantly increased in T4 group. The expression levels of abscisic acid signal transduction related genes did not change significantly under T2 and T3 group, but the expression levels of most genes includ  
Figure 4: DEGs involved in photosynthesis, photosynthesis\(-\)antenna proteins, and carbon fixation in photosynthetic organisms pathways. (**a**) DEGs shared in photosynthesis and comparison of their expression patterns in CT and CS. (**b**) Comparison of DEGs expression patterns in photosynthesis\(-\)antenna proteins. (**c**) Comparison of DEGs expression patterns in carbon fixation in photosynthetic organisms. The log2 FC values were used for mapping. Red color represents high gene expressions; green color represents low gene expressions.