# Comparative Transcriptomics for Pepper (_Capsicum annuum_ L.) under Cold Stress and after Rewarming
## 3 Results
### Functional Annotation of DEGs under Cold-Rewarming Treatments  
The DEGs were significantly (Wallenius test, Q-value \(\leq\) 0.001) enriched to 51 GO terms in comparisons between one or more groups (Supplementary Table S3), which were classified into the \"biological process\", \"cellular component\", and \"molecular function\" categories. The top 10 GO terms in each category, ranked by the number of DEGs, varied with treatment stages, suggesting that the functional responses were different at each stage. Amongst the biological process, the most represented terms including \"protein phosphorylation\" (GO:0006468) and \"regulation of transcription, DNA-templated\" (GO:0006355) followed by \"transcription, DNA-templated\" (GO:0006351) and \"defense response\" (GO:0006952) were reprogrammed in both CT and CS (Figure 3a). Concerning the cellular component, the major GO terms related to cell part and organelle were enriched upon cold treatment (Figure 3a). For molecular function, the terms with more DEGs were \"DNA binding\" (GO:0003677), \"protein serine/threonine kinase activity\" (GO:0004674), and \"transcription factor activity\" (GO:0003700), showing the importance of these terms in the progress of cold stress response (Figure 3a).  
According to Q-value, it was found that the differences in GO terms were significantly enriched between different groups. Compared with CS, the GO terms--such as \"regulation of transcription, DNA-templated\" (GO:0006355), \"photosystem II\" (GO:0009523), \"transcription factor activity\" (GO:0003700)--showed significant enrichment in the early cold treatment of CT. In addition, the GO terms that only enriched significantly in CT included \"transcription, DNA-templated\" (GO:0006351), \"cell redox homeostasis\" (GO:0045454), \"chloroplast thylakoid membrane\" (GO:0009535), etc. The above GO terms may be responsible for the difference in cold tolerance between CT and CS. In the rewarming treatment, it was found that \"flavonoid biosynthetic process\" (GO:0009813) and \"translation\" (GO:0006412) showed significant enrichment simultaneously in CT and CS.  
According to the results of KEGG annotation and enrichment analysis (Supplementary Table S4), the significantly DEGs from both the CT and CS under cold-rewarm treatments were classified into 16 KEGG pathways (\(p\)-value \(\leq\) 0.005) (Figure 3b). The pathways with the higher number of candidate genes included \"metabolic pathways (sly01100)\", \"plant hormone signal transduction (sly04075)\", and \"phenylpropanol biosynthesis (sly00940)\". Compared with CS, these pathways, including \"photosynthesis-antenna proteins (sly00196)\", \"oxidative phosphorylation (sly00190)\", \"homologous recombination (HR) (sly03440)\", \"DNA replication (sly03030)\", and \"mismatch repair (MMR) (sly03430)\" appeared earlier in CT during cold stress (Figure 3b). In the rewarming stage, there were common pathways in CT and CS, such as \"photosynthesis-antenna proteins (sly00196)\", \"plant hormone signal transduction (sly04075)\", \"phenylpropanol biosynthesis (sly00940)\", \"glutathione metabolism (sly00480)\", etc., while \"DNA replication (sly03030)\" only occurred in CT.