Fig. 2

Metatranscriptomics reveals distinct gene expression profiles between symptomatic and non-symptomatic samples. a Bacterial virulence-associated genes significantly upregulated in symptomatic samples compared to non-symptomatic samples. Genes were determined to be significantly different in expression by using the limma package in R (statistical cutoff at FDR < 0.05, and log₂ cutoff at < − 2 and > 2). Genes were separated into different colour-coded categories. b Oak tree defence-associated genes, based on the Swissprot database, upregulated in symptomatic samples compared to non-symptomatic samples. Genes were identified the same way as in a and separated into different categories as colour coded in the figure. Circles in light grey outgoing from the centre indicate the different log₂ fold changes, with respective numbers (5, 8, 11 in a and 5, 7, 9 in b) indicated to the side of the plots. c Geneset Enrichment Analysis highlights the global impact on genesets of infected oak tree cells. Genes with closest homology to Arabidopsis, determined to be statistically significantly altered in expression in symptomatic samples compared to non-symptomatic samples, were used in a geneset enrichment analysis (GSEA). Depicted in the figure are genesets found in the GO and KEGG databases. The figure was made using the GSEA results in the Enrichment Map plugin (Bader Lab) for the Cytoscape software (version 3.2). Red circles signify upregulated genesets, and blue circles signify downregulated genesets