Manipulation of Vacuole-Mediated Redox Homeostasis by Cyst Nematode Effectors Promotes Feeding Site Formation and Parasitism

The mapped reads of each sample were assembled using StringTie (v2.2.3) (Pertea et al., 2015) in a reference-based approach. Read counts mapped to each gene were quantified using FeatureCounts (v2.0.6). Differential gene expression analysis was performed with the DESeq2 R package (1.42.0), applying the following significance thresholds: padj = 0.05 and |log2(fold change) | = 1. Raw read counts were normalized to transcripts per kilobase million (TPM) for gene expression quantification. For downstream analyses, read counts were averaged across three biological replicates. The resulting clusters were visualized with the RSEM software. Gene Ontology (GO) enrichment analysis was conducted using the clusterProfiler R package (v4.8.1). Additionally, clusterProfiler was employed to test the statistical enrichment of differentially expressed genes in KEGG pathways.