Transcriptome analysis of the response of domesticated emmer wheat (Triticum turgidum subsp. dicoccum) to single vs. mixed infections with Zymosptoria tritici and Puccinia graminis

Domesticated emmer wheat transcriptomes under single vs mixed infections with Zymoseptoria tritici and Puccinia graminis This dataset contains RNA-seq data and transcript-level quantifications supporting the study of domesticated emmer wheat (Triticum turgidum subsp. dicoccum, accession MG5323) responding to single and mixed infections by Zymoseptoria tritici and Puccinia graminis f. sp. tritici (stem rust). Leaves were sampled under four treatments: Mock (M), Z. tritici (Z), P. graminis (P), and mixed Z+P (ZP), with three biological replicates per treatment (12 libraries total). Contents: Raw reads (FASTQ, paired-end): one R1 and one R2 file per library for re-alignment or alternative quantification pipelines. Transcript quantifications (quant.sf, Salmon): one file per library, generated against the Svevo (durum) reference transcriptome. Standard Salmon columns include Name (TRITD transcript ID), Length, EffectiveLength, TPM, NumReads. Differential expression summary: ztsr_svevo_de_summary.xlsx. One consolidated table that merges the contrast-specific DE results into a single sheet. Added columns: contrast and direction. Typical columns retained from edgeR outputs include gene_id, logFC, logCPM, LR, PValue, FDR. DE summary README: ztsr_svevo_de_summary_README.md. Explains how the DE files were merged and documents the columns present. Enrichment results: ztsr_svevo_gesa_results.xlsx. g:Profiler functional enrichment outputs for gene sets derived from the differential expression contrasts. Columns typically include source (namespace, e.g., GO:BP, GO:MF, GO:CC), term_name, term_id, adjusted_p_value, negative_log10_of_adjusted_p_value, term_size, query_size, intersection_size, effective_domain_size, and intersections (comma-separated TRITD gene IDs). Enrichment README: ztsr_svevo_gesa_results_README.md. Sheet-by-sheet and column-level guidance for interpreting ztsr_svevo_gesa_results.xlsx. Annotated analysis script: ztsr_svevo_r_scripts_annotated.txt. The original R workflow with clarified comments describing each step without adding new information beyond the manuscript. Script README: ztsr_svevo_r_scripts_README.md. Brief guide to inputs, outputs, and package requirements of the R workflow. Salmon quant results README: ztsr_svevo_salmon_quant_results_README.md. Generic description of Salmon quant.sf files (format, columns, typical use) applicable to all libraries here. Table 1 - Quant files only (columns 1 to 4) Host Treatment_1 Treatment_2 Salmon quantification T. turgidum ssp. dicoccum Mock Mock mmc_ztsr_svevo_501_quant.sf T. turgidum ssp. dicoccum Mock Mock mmc_ztsr_svevo_502_quant.sf T. turgidum ssp. dicoccum Mock Mock mmc_ztsr_svevo_503_quant.sf T. turgidum ssp. dicoccum Z. tritici Mock mzc_ztsr_svevo_504_quant.sf T. turgidum ssp. dicoccum Z. tritici Mock mzc_ztsr_svevo_505_quant.sf T. turgidum ssp. dicoccum Z. tritici Mock mzc_ztsr_svevo_506_quant.sf T. turgidum ssp. dicoccum Mock P. graminis mmsr_ztsr_svevo_507_quant.sf T. turgidum ssp. dicoccum Mock P. graminis mmsr_ztsr_svevo_508_quant.sf T. turgidum ssp. dicoccum Mock P. graminis mmsr_ztsr_svevo_509_quant.sf T. turgidum ssp. dicoccum Z. tritici P. graminis mzsr_ztsr_svevo_510_quant.sf T. turgidum ssp. dicoccum Z. tritici P. graminis mzsr_ztsr_svevo_511_quant.sf T. turgidum ssp. dicoccum Z. tritici P. graminis mzsr_ztsr_svevo_512_quant.sf Table 2 - Read files only (columns 4 to 6) Salmon quantification FASTQ: R1 FASTQ: R2 mmc_ztsr_svevo_501_quant.sf P29206_501_S1_L003_R1_001.fastq.gz P29206_501_S1_L003_R2_001.fastq.gz mmc_ztsr_svevo_502_quant.sf P29206_502_S2_L003_R1_001.fastq.gz P29206_502_S2_L003_R2_001.fastq.gz mmc_ztsr_svevo_503_quant.sf P29206_503_S3_L003_R1_001.fastq.gz P29206_503_S3_L003_R2_001.fastq.gz mzc_ztsr_svevo_504_quant.sf P29206_504_S4_L003_R1_001.fastq.gz P29206_504_S4_L003_R2_001.fastq.gz mzc_ztsr_svevo_505_quant.sf P29206_505_S5_L003_R1_001.fastq.gz P29206_505_S5_L003_R2_001.fastq.gz mzc_ztsr_svevo_506_quant.sf P29206_506_S6_L003_R1_001.fastq.gz P29206_506_S6_L003_R2_001.fastq.gz mmsr_ztsr_svevo_507_quant.sf P29206_507_S7_L003_R1_001.fastq.gz P29206_507_S7_L003_R2_001.fastq.gz mmsr_ztsr_svevo_508_quant.sf P29206_508_S8_L003_R1_001.fastq.gz P29206_508_S8_L003_R2_001.fastq.gz mmsr_ztsr_svevo_509_quant.sf P29206_509_S9_L003_R1_001.fastq.gz P29206_509_S9_L003_R2_001.fastq.gz mzsr_ztsr_svevo_510_quant.sf P29206_510_S10_L003_R1_001.fastq.gz P29206_510_S10_L003_R2_001.fastq.gz mzsr_ztsr_svevo_511_quant.sf P29206_511_S11_L003_R1_001.fastq.gz P29206_511_S11_L003_R2_001.fastq.gz mzsr_ztsr_svevo_512_quant.sf P29206_512_S12_L003_R1_001.fastq.gz P29206_512_S12_L003_R2_001.fastq.gz Notes on format and use: quant.sf tables were used to build transcript and gene matrices and to run differential expression across M, Z, P, and ZP (3 replicates each). FASTQ files provide the raw reads for independent re-processing. ztsr_svevo_de_summary.xlsx aggregates the per-contrast DE results and keeps edgeR statistics as columns where present. ztsr_svevo_gesa_results.xlsx lists functional terms significantly associated with DE gene sets and the overlapping TRITD genes driving each term. ztsr_svevo_r_scripts_annotated.txt and its README describe the analysis steps used to generate the results from the Salmon outputs. DOI: 10.5281/zenodo.17337983