# Comparative Transcriptomics for Pepper (_Capsicum annuum_ L.) under Cold Stress and after Rewarming
## 4 Discussion
### Response of Photosynthesis and Related Processes to Cold and Rewarming Conditions  
In addition to changes in chlorophyll content, transcriptome data showed that the DEGs related to photosynthesis were significantly enriched in pepper during cold stress and recovery stage. Photosynthesis is one of the most temperature-sensitive processes in plants. Plants could adjust their photosynthetic characteristics to adapt to cold [42]. Previous studies have shown that the reduction of photosynthesis is parallel to a strong decline of PSII photochemistry in various plant species exposed to cold, and suggested PSII as one of the primary targets of cold stress [43; 44]. Arabidopsis were exposed to a relatively moderate cold of 12 \({}^{\circ}\)C, which caused the reduction of PSII reaction center polypeptide _psbA_[45]. In this study, genes in the PSII system including _psbA_ (Capana11g002217), _psbB_ (Capana00g001154), _psbC_ (Capana03g001476 and Capana00g001698), and _psbD_ (Capana03g001477) were down-regulated as cold stress treatment continued, which could affect the photochemical reaction of PSII. In addition to PSII, exposure of various plant species to cold stress can also cause photoinhibition damage in the PSI reaction center [43; 46]. The lower amount of _psaB_ might be also due to downregulation of the genes and/or degradation of PSI to response to the cold stress [47]. Besides, psaA is a core protein and crucial for the functional assembly of PSI [48]. Except for its significant increase in the T1 group, the downregulation of _psaA_ (_Capana00g002019_ and Capana07g00048) under cold stress were also found in this study. However, it seems to be more meaningful to maintain the stability of PSI reaction center complex rather than PSII, which has a much faster repair cycle, as PSI may be the limiting factor for the recovery of photosynthesis in rewarming stage [45]. In T4 group, the above genes were all downregulated. These results indicate that the gene expression of PSI and PSII is difficult to return to normal level after suffered cold stress.  
Furthermore, as an electron transfer enzyme, the Cytochrome b6/f complex can be involved in electron transport to create proton gradient, which drives ATP synthesis in chloroplasts [49; 50]; _petA_, _petB_, and _petD_ are the major chloroplast pet genes that encode the cytochrome b6/f complex [51]. In this study, significant changes of _petB_ (Capana01g003214) occurred only in CT cultivars. Previous studies have shown various LHC compounds involved in several chloroplast functions, including photosynthetic pigment metabolism and photosynthetic electron transport chain, to adapt cold stress [52]. The increase of LHC is beneficial to adjust the organization of photosystem II and photoprotection. In this study, the expression levels of _LHCB4_ (_Capana09g001520) and _LHCA3_ (_Capana10g000141_) in CT were higher than those in CS under T1 and T2 groups, and the _LHCB1_ (Capana08g000679) was only expressed in CT cultivar. The specific expression of these genes under low temperature stress may be an important cause of different cold tolerance. Rubisco also continued to increase after short-term cold stimulus (T1 group); cold increases the affinity of Rubisco for CO\({}_{2}\) relative to O\({}_{2}\) and the solubility of CO\({}_{2}\), which is crucial for C3 photosynthesis plants [53].