Fig. 3: Transcriptional responses triggered by lignin-related aromatic compounds.

Venn diagrams comparing the distribution of unique and shared upregulated genes in conditions containing (a) 4-hydroxybenzaldehyde (4HBZ), benzaldehyde (BZD), or 4-hydroxybenzoate (4HBA) (b) 4HBZ, vanillin (VAN), or syringaldehyde (SYALD) and (c) Lignin-derived compounds - LDC-I and LDC-II conditions. d Gene ontology (GO) enrichment analysis of up regulated genes based on one-side Fisher’s exact test as implemented in the clusterProfiler R package⁷⁷. Circles’ size and color represent the counts and adjusted p-values, respectively. Gene ratio corresponds to the number of DEGs related to a GO term divided by the total number of genes associated with that GO term in the X. citri 306 genome. The differential expression in each condition was compared to XVM2m(G) following the criteria log₂ Fold Change ≥1 and p-adjusted ≤ 0.05. The analysis of other conditions is in Supplementary Fig. 4. e Gene set enrichment analysis based on weighted Kolmogorov–Smirnov statistic and Over Representation Analysis (ORA) to define modules function as implemented in the CEMiTool package³¹. The size and intensity of the circles correspond to the normalized enrichment score (NES) for the module in each condition, indicating biological functions enriched in each module. Positive NES reflects transcriptional activity above the median, whereas negative NES corresponds to transcriptional activity below the median in each condition. COALC coniferyl alcohol, MIX aldehyde mixture. Source data are provided as a source data file.