BUSCADOR RECOLECTA

Differentially expressed genes were selected with DESeq2 (p-adj > 0.01, log2 FC ± 1.5)., Peer reviewed

Native pH and location (also illustrated in a map) is indicated for each water., Peer reviewed

Peer reviewed

Peer reviewed

Percentage of DEGs in each of the manually curated functional categories and the hypergeometric enrichment text are shown for the environmental soil and water conditions for the up- (_UP) and downregulated (_DOWN) genes. Hypergeometric statistical analysis was conducted in R package stats., Peer reviewed

Output tables of the KEGG and GO enrichment analysis conducted on general and exclusive up- and downregulated DEGs from water and soil conditions., Peer reviewed

Peer reviewed

A) RNA sampling conditions from environmental (soil and mineral water) and previously obtained samples (rich B medium reference and three in planta conditions). B) Transcriptomic data analysis pipeline. First, raw RNA-seq data quality was evaluated with FastQC (v.0.11.5), trimmed with trimGalore (v.0.6.1) and potential rRNA contaminants were filtered out with the SortMeRNA software (v.4.2.0). Reads were mapped with Bowtie2 (v. 2.4.4) and alignments quantified with FADU v. 1.8. The R. solanacearum UY031 genome GCF_001299555.1_ASM129955v1 was used. DEG analyses were performed with Deseq2 (v. 1.34.0). Genes with |log2(fold-change)|>1.5 and adjusted p-value <0.01 were considered as differentially expressed (DEG) when compared to the reference medium. The UpsetR package (v. 1.4.0) (90) was used to detect unique DEG and intersections among the in the different conditions. Deseq2 transformed counts normalized for sample size were used for principal component analysis. C) DEGs in the different conditions. Bars show the total number of up- (yellow) and downregulated (blue) genes for each condition compared to the reference Rich B medium. The line graph and the right Y axis indicate the percentage of DEGs. Drawings created with BioRender., Peer reviewed

Dot plots of the KEGG (left) and GO (right) enrichment analyses of differentially expressed genes (DEGs) from soil (brown) and water (blue) conditions. Dot sizes represent the number of genes associated with each term and dot colour indicates the p. adjusted value. The gene ratio represented in the X axis is the proportion of associated genes to a term from the total gene set. The DEGs were extracted with DEseq2 using the thresholds: p-adj.value > 0.01 and log 2 FC ± 1.5 and ClusterProfiler was used to calculate the enrichment., Peer reviewed

R. solanacearum cultures grown overnight in rich B medium were washed and diluted to OD600 = 0.1 in water and luminescence and OD600 values were measured over a 24h period. Relative luminescence units (RLU) were normalised by bacterial concentration measured as OD600. RLU values were divided by 1000 to facilitate visualisation., Peer reviewed