The Venn diagram (Fig 1) shows no shared DEGs across the three comparison groups (CK1_vs_CP1, CK2_vs_CP2, CK3_vs_CP3). This is biologically implausible; if CP treatment consistently activates the phenylpropanoid pathway across storage times, one would expect at least some overlapping DEGs (e.g., core transcription factors or structural genes).
How do you explain that not a single gene was differentially expressed at all three time points? Could this indicate that your DEG identification thresholds (FDR < 0.05, |log2FC| ≥ 1) are too stringent, or alternatively, does this suggest technical variability between biological replicates that undermines the reliability of the temporal comparison? Please provide the raw read counts for the key candidate genes (OsPAL, OsFLS, etc.) across all time points to verify this surprising result.