Data for: Parasitic success of the pathogenic plant Phelipanche ramosa (L.) Pomel. (Orobanchaceae) differs in some re-infected vs. naive tomato cultivars

The aim of this study was to investigate whether preinfection with broomrape alters host responses upon a second encounter of the parasite. The files in this repository contain read count tables, R-code, and other files for RNA-sequencing data analysis, incl.:
- Pramosa_rsem_matrix.gene.counts.matrix: Read counts from mapping RNASeq data to broomrape reference transcriptome
- Slycopersicum_rsem_matrix.gene.counts.matrix: Read counts from mapping RNASeq data to tomato reference genome
- Pramosa_DEG_annotated.txt: List of annotated differentially expressed genes (DEGs) for P.ramosa
- Slycopersicum_DEG_annotated.txt: List of annotated differentially expressed genes (DEGs) for tomato
- Pramosa_trinotate_annotation_report.txt and Slycopersicum_trinotate_annotation_report.txt: Annotation reports from trinotate annotation runs for parasite and host
- Pramosa_trinotate_report_gene_ontology_with_parents.txt and Slycopersicum_trinotate_report_gene_ontology_with_parents.txt: GO-term annotation reports from trinotate runs for parasite and host transcripts
- PramSlyc_RNAseqAnalysis.R: R code for the analysis of RNAseq data from parasite and host-read mapping
- GO_terms_description.txt: Translation file for gene ontology descriptions
- AT_terms_description.txt: Translation file for gene descriptions for Arabidopsis thaliana genes