*3.5. Sweet Potato Tuberous Roots Transcriptome Analysis at Different Storage Temperatures* 3.5.1. Data Quality Evaluation and Analysis

To gain a better understanding of the physiological changes of sweet potato tuberous roots under different storage temperatures, RNA samples were collected on days 0 (control, C0) and 14 (control and CS group, C14, and CS14). A total of 6.44 Gb to 9.51 Gb clean reads were obtained, and more than 94.0% of the reads had a Q30 quality score (Table S2). The sequencing data were therefore deemed adequate for correlation analysis. Hisat2 was used to align the clean reads with the sweet potato reference genome (https://ipomoea-genome. org/ (accessed on 15 October 2020)), achieving a 77.64–82.57% alignment efficiency. The alignment results are shown in Table S3.

Pearson correlation analysis was performed to validate the gene expression profiles based on the transcripts from nine different samples (Figure 5A). As expected, the results indicated that biological replicates from the same treatment group were highly correlated. Particularly, C0 and C14 were highly correlated, whereas CS14 and C0 were less correlated. The principal component analysis (PCA) (Figure 5B) results coincided with the correlation analysis findings. These findings indicated that the gene expression profile of the CS14 and C0 groups exhibited the most significant differences.

**Figure 5.** Global transcriptomic changes at the control and CS groups after 14 d of storage (C14 and CS14). (**A**) 2D hierarchical clustering, blue indicates a high correlation, purple represents low correlation. (**B**) Principal component analysis (PCA) of the RNA sequencing data of sweet potato tuberous roots samples.
