3.5.2. Unigene Annotation Statistics

Unigene function annotation was conducted using the COG, GO, KEGG, KOG, Pfam, Swissprot, eggnog, and NR databases (Table S4). A total of 24,045 single genes were annotated in eight databases, of which the NR database had the highest annotation rate, with 31,000 annotations, accounting for 99.52% of the total annotated genes.

3.5.3. DEG Screening and Annotation Analysis Comparison of Two DEG Groups

Degseq was used to identify differentially expressed genes (DEGs) in C0 vs. C14 and C0 vs. CS14. The screening criteria were fold change ≥2 and FDR < 0.01. Compared with the C0, 602 unigenes were upregulated, and 466 were downregulated in C14, whereas more genes were differentially expressed in the CS14 group (4850 upregulated and 5086 downregulated) (Table 1). The two groups of DEGs were annotated using the COG, eggnog, NR, Pfam, Swissprot, GO, and KEGG databases. The number of annotated genes is shown in Table S5, and the annotation ratio of the NR database was the highest (>95%).

**Table 1.** Statistics of the number of deferentially expressed genes.


### GO Database Annotation Analysis

The GO annotation system includes three main branches: cellular component, molecular function, and biological process. The two groups of DEGs were classified into 53 functional subgroups (Figure S1). As indicated in Table S6, in terms of cellular components, the DEGs were mainly associated with seven functional sub-categories: "cell", "membrane", "macroscopic complex", "organelle", "organelle part", "membrane part", and "cell part". Regarding molecular function, DEGs were mainly associated with the two functional subclasses of "catalytic activity" and "binding". For the biological process classification, the DEGs were mainly enriched in pathways associated with "biological process", "cellular process", "single organization process", "response to stimulus", "localization", "biological regulation", and "cellular component organization or biogenesis". Regarding the differences in DEG ratios between the two groups, the "cell", "membrane-enclosed lumen", "macroscopic complex", "organelle", "organelle part", "cell part", "structural molecular activity", "growth and cellular component organization or biogenesis" process ratios exhibited marked differences (e.g., up to 40-fold differences). Moderately low temperatures had an important effect on the aforementioned processes at the transcriptome level in sweet potato tuberous roots stored for 14 d.
