Additional file 2 of Early transcriptional changes of heavy metal resistance and multiple efflux genes in Xanthomonas campestris pv. campestris under copper and heavy metal ion stress

Additional file 2: Supplemental Table 1. Read quality and mapping statictics of Illumina reads from copper stress and control treatments involving Xcc BrA1. Supplemental Table 2. qPCR primers and target genes for validation of Transcriptomic results. Supplemental Table 3. qPCR primer gene targets. Targets were identified in Xcc BrA1 from genomes characterised in Ramnarine, Jayaraman and Ramsubhag (2022). Ramnarine, Stephen D. B., Jr., Jayaraj Jayaraman, and Adesh Ramsubhag. 2022. "Comparative genomics of the black rot pathogen Xanthomonas campestris pv. campestris and non-pathogenic co-inhabitant Xanthomonas melonis from Trinidad reveal unique pathogenicity determinants and secretion system profiles." PeerJ 9 (e12632). Supplemental Table 4. Ct values for qPCR experiments on CuSo4.5H2O exposed cells at 15 (C15), 60 (C60) and 240 (C240) mins. Concentrations are given as 0p - 0ppm/0mM, 200p - 200ppm/0.8mM and 300p - 300ppm/ 1.2mM. Supplemental Table 5. Average log2FC values of gene targets under tolerant and resistant copper stress at 15 min, 1 hr and 4hr exposure time points. Supplemental Table 6. Ct values from qPCR experiments where by cells were exposed to different heavy metal concentrations for 1 hr. Supplemental Table 7. Average Log2FC values for MDR efflux pumps and other targets under heavy metal stress at the 1hr exposure. Supplemental Table 8. Upregulated genes (logFC ≥ 1). Supplemental Table 9. Downregulated genes (logFC ≤ 1). Supplemental Table 10. Low expression genes (logFC < 1 or > -1). Supplemental Table 11. Differentially expressed mobile elements, IS and Tn elements at the initial timepoint sampled. Refer to linked multifasta and annotation files to correlate with GeneID. Supplemental Table 12. KEGG BRITE categories summarizing significantly enriched DEGs (up, downregulated and low expression). Supplemental Table 13. Enriched KEGG Pathways (ShinyGO). Supplemental Table 14. Enriched Biological Processes (BP) GO terms (ShinyGO). Supplemental Table 15. Enriched Molecular Function (MF) GO terms (ShinyGO). Supplemental Table 16. Gene cluster classification, predicted function and probable metal-binding sites.