# Effects of Temperature on Growth and Isoprene Metabolism Pathway in _Eucomnia ulmoides_ [PERSON]
## 3 Results
### Transcriptome Data Analyses  
#### 3.4.1 Transcriptome Data Quality  
Leaves of the plants treated at 25 \({}^{\circ}\)C (control) and 35 \({}^{\circ}\)C (HT) for 40 days were collected. A total of six samples were subjected to RNA-Seq, yielding raw reads of 40, 885, 940-43, 679, 536 (Table 2). Clean reads were in the range of 40, 082, 724-43, 233, 386 after the removal of low-quality bases (accession number: PRJNA1030736). The Q20 probability of the samples, indicating a base quality of >20, ranged from 96.46% to 97.59%, and the Q30 probability, indicating a base quality of >30, ranged from 90.87% to 93.19%. The comparison reference rate to the reference genome exceeded 95.28%, indicating the high sequencing quality of the _E. ulmoides_ leaf samples and their suitability for further bioinformatics analysis.  
The analysis revealed 2309 DEGs after HT treatment compared with the control. Of these, 1608 genes were upregulated and 701 genes were downregulated (Figure 4). This suggests that DEGs were primarily enriched in the upregulated expression pathway after HT treatment.  
\begin{table}
\begin{tabular}{c c c c c c c} \hline
**Sample Name** & **Raw Reads** & **Clean Reads** & **Q20 (\%)** & **Q30 (\%)** & **Mapped Read (\%)** & **GC Content (\%)** \\ \hline control-1 & 40,885,940 & 40,082,724 & 96.46 & 90.87 & 95.28 & 47.16 \\ control-2 & 41,794,830 & 41,135,962 & 96.80 & 91.52 & 95.55 & 46.97 \\ control-3 & 41,940,464 & 41,265,186 & 97.34 & 92.71 & 95.93 & 47.23 \\ HT-1 & 43,679,536 & 43,233,386 & 97.38 & 92.70 & 95.65 & 47.12 \\ HT-2 & 42,241,678 & 43,233,386 & 97.46 & 92.89 & 95.75 & 47.05 \\ HT-3 & 43,511,804 & 43,079,342 & 97.59 & 93.19 & 95.81 & 47.10 \\ \hline \end{tabular}
\end{table}
Table 2: Data quality assessment statistics sheet.  
Figure 3: Impact of temperature on rubber and total triterpene contents in _E. ulmoides_ seedling leaves: (**A**) change in rubber content; (**B**) change in total triterpene content. Note: “NS” and different letters above the bar represent insignificant and significant differences, respectively, between the control and treatment (_p_ < 0.05).  
3.4.2. GO and KEGG Enrichment Analysis of DEGs  
The annotation of DEGs in _E. ulmoides_ using the GO database revealed enrichment in three functional categories: molecular function, cellular components, and biological processes. In the biological process category, there was a notable focus on nitrogen compound metabolism (325), macromolecule metabolism (303), regulation of primary metabolism (165), and protein ubiquitination (23). In the molecular function category, emphasis was on catalytic activity (112), binding function (356), kinase activity (61), and protein ubiquitination transfer (23). In terms of cellular components, the major concentrations were in the cytoplasm (531) and plastids (142) (Figure 5A).  
Figure 4: The number of differentially expressed genes in HT-vs-control groups.  
Figure 5: _Cont_.  
The annotation of DEGs into metabolic pathways and KEGG enrichment analysis revealed significant results. The DEGs were mainly enriched in five major categories of processes when comparing HT treatment with the control. These categories included cellular processes, environmental information processing, genetic information processing, metabolism, and organic systems. In terms of metabolic processes, the main enrichments were observed in carbohydrate metabolism (104), biosynthesis of secondary metabolites (87), and metabolism of terpenoids and ketones (31). Environmental information processing was enriched in signal transduction (127), and membrane transport (3). These findings suggest that HT treatment might have accelerated carbohydrate metabolism as well as terpene production and efflux (Figure 5B).