Fig. 5: Transcriptional responses to XyGOs in X. citri.
a Volcano plot of RNA-seq data highlighting differentially expressed genes (DEGs; blue circles = downregulated and purple circles = upregulated). In yellow are DEGs acting on processes important for virulence or XyG utilization. Genes were considered differentially expressed according to Wald test implemented in DESeq2. p-values were adjusted for multiple tests using the Benjamini-Hochberg (BH) method implemented in DESeq2. Thresholds: p-adjusted < 0.05 and | log2 Fold Change| > 1. b Transcription levels of XyGUL genes, downstream genes encoding xylose metabolism and MFS transporter in RNA-seq experiments. Data shown as mean ± SE from four biologically independent experiments (n = 4) (open circles). Threshold: BH adjusted p-value < 0.05. c Gene ontology (GO) enrichment analysis of DEGs. Circles size and color represent the counts and BH adjusted p-values, respectively, according to the legend at the left. Gene ratio is the number of DEGs related to a GO term divided by the total number of annotated DEGs. Categories were considered enriched based on hypergeometric test, implemented in the clusterProfiler 3.14.3R/Bioconductor enrich function60. d Clustered heat map of RT-qPCR data of hrp genes color-coded according to the log2 (−1 to +6) of the mean normalized expression relative to the control (numbers inside the boxes). Two-tailed t test: *, p < 0.001; **; p < 0.0001; Xyl = xylose, Glc = glucose and Gal = galactose. See details in Supplementary Fig. 25.
