MpPR-1 expression data

MpPR-1 expression data in RPKM (Reads Per Kilobase per Million mapped reads) values from the C-biotype of M. perniciosa in seven biological conditions (dikaryotic mycelium 14 days, basidiomata, germinating spores, green broom, initial necrosis, advanced necrosis, dry broom) were downloaded from the Witches’ Broom Disease Transcriptome Atlas (v. 1.1) (http://bioinfo08.ibi.unicamp.br/atlas/).

MpPR-1 expression data of M. perniciosa treated with plant antifungal compounds were obtained from RNA-seq data (unpublished). The C-BA1a isolate’s necrotrophic mycelia was initially inoculated in 100 mL of liquid MYEA media and cultivated for 5 days under agitation of 150 rpm at 30 °C, then 5 mL of this initial cultivation were transferred to 50 mL of fresh MYEA liquid media containing eugenol (500 µM), α-tomatin (80 µM) or DMSO (250 µL, solvent control) and cultivated again under agitation of 150 rpm at 30 °C for 7 days. The total RNA was extracted using the Rneasy^® Plant Mini Kit (Quiagen, USA) and quantified on a fluorimeter (Qubit, Invitrogen). cDNA libraries were prepared in five biological replicates for each treatment, plus biological control. The cDNA libraries were built from 1000 ng of total RNA using Illumina’s TruSeq RNA Sample Prep kit, as recommended by the manufacturer. The libraries were prepared according to Illumina’s standard procedure and sequenced on Illumina’s HiSeq 2500 sequencer. The quality of raw sequences was assessed with FastQC (v.0.11.7) [66]. Read quantification was performed by mapping the generated reads against 16,084 gene models of the C-BA1a genome using Salmon (v.0.14.1) in mapping-based mode [67]. Read counts were normalized to Transcripts Per Million (TPM) values for plotting. Differential expression analysis was performed with the DESeq2 (v.1.22.2) package using Wald test and Log fold change shrinkage by the apeglm method (IfcThreshold = 0.1, s-value < 0.005) [68]. TPM values and DESeq2 results for MpPR-1 genes in these experimental conditions are available at Additional file 2.

MpPR-1 expression data in TPM for the S-biotype was obtained from RNA-seq libraries of infected MicroTom tomato plants in seven different time points after inoculation (12 h, 24 h, 48 h, 5 days, 10 days, 20 days, 30 days) (unpublished). The quality of raw sequences was assessed with FastQC (v. 0.11.7) [66]. Next, Trimmomatic (v.0.36) [69] was used to remove adaptor-containing and low-quality sequences. Quality-filtered reads were then aligned against the S-MG1 or S-MG2 reference genome using HISAT2 (v.2.1.0) with default parameters [70]. Reads that mapped to coding sequences were counted with featureCounts (v.1.6.3) [71]. TPM values for MpPR-1 genes in these experimental conditions are available at Additional file 3.

MrPR-1 expression data in TPM was obtained from RNA-Seq reads of M. roreri in the biotrophic (30 days after infection) and necrotrophic (60 days after infection) stages of frosty pod rot from [27]. Reads were mapped and quantified with Salmon (v.0.14.1) [67] using 17,910 gene models of M. roreri MCA 2997 (GCA_000488995) available at Ensembl Fungi.