*2.5. Functional Enrichment Analysis of Differentially Expressed Genes*

Genes with an absolute value of |log2fold change| > 1 and a false discovery rate (FDR) < 0.05 were identified as representing significantly differentially expressed genes (DEGs), using DESeq2 in the four comparisons of CK1\_vs\_T1, CK1\_vs\_M1, CK2\_vs\_T2, and CK2\_vs\_M2 [41]. To study the putative functions and pathways of the DEGs in the above four comparisons, gene ontology (GO) functional enrichment analysis was conducted using Blast2GO (version 3.0; https://www.blast2go.com/) (accessed on 10 March 2021) [42]. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation of DEGs was performed using Cytoscape software (version 3.2.0) (https://cytoscape.org/) (accessed on 10 March 2021) with the ClueGO plugin using a hypergeometric test and Benjamini-Hochberg FDR correction (FDR ≤ 0.05) [43]. Transcription factors were predicted using PlantTFDB [44].
