Additional file 1 of RNA silencing is a key regulatory mechanism in the biocontrol fungus Clonostachys rosea-wheat interactions

Additional file 1: Table S1: Sample-by-sample mRNA and sRNA mapping results on wheat and C. rosea. Table S2: Wheat and C. rosea transcripts differentially expressed during interactions in this study. Analysis carried out through DESeq2 v. 1.28.1 with default parameters. The adjusted p-value threshold was fixed at 0.05, and minimum log2(FC) was set at 1.5. Table S3: Gene ontology terms (GOs) enriched in wheat and C. rosea genes upregulated or downregulated during Cr-Wr. The analysis was done with BLAST2GO, using a Fisher test corrected with the FDR method. The adjusted p-value threshold was set at 0.05. Table S4: Wheat genes of interest upregulated or downregulated during the interaction with C. rosea WT. Table S5: The top 20 highly upregulated or downregulated wheat genes during C. rosea-wheat interactions compared to the wheat control. Table S6: Differentially expressed wheat genes with a role in cell wall synthesis or modification, resistance, or induction of defense reactions, as well as C. rosea CAZymes or effectors. All the genes were upregulated or downregulated in Cr-Wr but not in Δdcl1-Wr and Δdcl2-Wr. Log2Fc values are in bold when significant (adjusted p-value < 0.05). Table S7: The top 20 highly upregulated wheat genes or downregulated C. rosea genes during the interactions with wheat roots. Table S8: Sequence, length, and expression level of detected expressed milRNAs. Note that in this analysis, the conditions “Δdcl1-Wr” and “Δdcl2-Wr” were compared with “Cr-Wr” and not to the control in the differential expression analysis. This way, the conditions involving mutants (Δdcl1-Wr and Δdcl2-Wr) were compared directly with the same condition with the WT (Cr-Wr) rather than with C. rosea in vitro or non-inoculated wheat. Table S9: Transcripts predicted to be targeted by putative milRNAs. At least two target prediction tools have predicted all putative targets, and they show opposite expressions to the targeting milRNAs (a target needs to be upregulated when the targeting milRNA is downregulated). Note that in this analysis, the conditions “Δdcl1-Wr” and “Δdcl2-Wr” were compared with “Cr-Wr” and not to the control in the differential expression analysis. This way, the conditions involving mutants (Δdcl1-Wr and Δdcl2-Wr) were compared directly with the same condition with the WT (Cr-Wr) rather than with C. rosea in vitro or non-inoculated wheat. Table S10: List of primers used in this study.