Data files

Novel miRNAs and/or novel MIR loci identified in PVYNTN- and mock-inoculated samples of cv. Désirée and NahG-Désirée potato plants. List of novel/known miRNAs with novel MIR loci. For each miRNA, sequence, length, class (C – conserved or N – novel), miRNA family, the genome locations, strand, the predicted hairpin precursor (pre-miRNA) sequences and the location in genome (MIR loci), their lengths, minimal folding energy index (MFEI; calculated as described by Zhang et al. (2006) as well as gene ...

PHAS loci identified by genome and transcriptome-wide phasing analysis. List of genome locations for the all identified non-coding PHAS loci or transcript identifiers (IDs) for protein-coding PHAS loci together with the lengths of their producing phasiRNAs. For the protein-coding PHAS loci, transcript full description, protein domains (obtained from PFAM database; Finn et al. 2016), MapMan ontology annotation (from GoMapMan;(Ramšak et al. 2014)) and log2 ratio of gene expression between PVYNTN-infected ...

Predicted targets of endogenous small RNAs (sRNAs) by in silico approach. For each predicted interaction, miRNAs/phasiRNA ID, the target transcript identifiers, representative gene identifier, short gene name, full descriptions, MapMan ontology annotations (GoMapMan; (Ramšak et al., 2014)) and predicted target regulation (cleavage or translational repression) are shown. Short names for potato genes were inferred from Arabidopsis thaliana orthologs where applicable, else the StNIB_v1 gene identifier ...

sRNA regulatory network connecting endogenous miRNAs, phasiRNAs and their targets.

sRNA regulatory network connecting miRNAs, phasiRNAs, PVY-derived siRNAs (vsiRNAs) and their targets.

Table connecting MOA degradome pool identifiers to GEO identifiers.

Experimentally validated targets of endogenous sRNAs by Degradome-Seq. For each identified interaction, miRNAs/phasiRNA ID, the target transcript identifiers, representative gene identifier, full descriptions, and MapMan ontology annotations (GoMapMan; (Ramšak et al., 2014)) are shown. Short names for potato genes were inferred from Arabidopsis thaliana orthologs where applicable, else the StNIB_v1 gene identifier was set (Ramšak et al., 2014). For each sRNA-target interaction, degradome category ...

Targets of PVY-derived siRNAs identified by Degradome-Seq. For each predicted interaction, PVYNTN-derived siRNAs (vsiRNAs), the target transcript identifiers, representative gene identifier, full descriptions and MapMan ontology annotations (GoMapMan; (Ramšak et al., 2014)) are shown. Short names for potato genes were inferred from Arabidopsis thaliana orthologs where applicable, else the StNIB_v1 gene identifier was set (Ramšak et al., 2014). For each vsiRNA-target interaction, degradome category ...

List of identified proteins and their counts; using MaxQuant software for selected MOA proteomics pool identifiers.

List of identified peptides using MaxQuant software for selected MOA proteomics pool identifiers.

Differentially expressed proteins between various comparison groups (Sheet: comparisons), with log2-fold changes and Benjamini-Hochberg FDR corrected p-values given for MaxQuant quantified proteins.

List of identified proteins and their counts; using spectral counts (Proteome Discoverer) for selected MOA proteomics pool identifiers.

List of identified peptides using spectral counts (Proteome Discoverer) for selected MOA proteomics pool identifiers.

Differentially expressed proteins between various comparison groups (Sheet: comparisons), with log2-fold changes and Benjamini-Hochberg FDR corrected p-values given for spectral count (Proteome Discoverer) quantified proteins.

Concentrations of seven different plant hormones (ABA, GA3, OPDA, JA, IAA and SA) as determined by gas chromatography coupled with mass spectrometry (GC-MS) for MOA samples.

Significant changes for a set of hormones between treatment-genotype groups as determined by ANOVA followed by LSD post hoc analysis (FDR < 0.05) using the Agricolae R package.

File describing the phenotypic observations taken on potato plants, namely spot necroses, vein necroses, chlorotic spots, yellowing and mechanicam damage.

Measurements of photosynthetic activity, namely net photosynthesis (Pn), stomatal conductance (Cond), actual photochemical efficiency (Fv’/Fm’), potential photochemical activity (Fv/Fm), chlorophyll content (SPAD) and electron transport rate (ETR).

Statistical analysis of measurements of photosynthetic parameters.

qPCR measured values of Potato virus Y (PVY).

Table connecting MOA Investigation sample ID's and GEO sample identifiers.

QC filtered and RSN normalised values for all MOA samples with microarray measurements.

Differential expression of genes between various comparison groups (Sheet: comparisons), with log2-fold changes and Benjamini-Hochberg FDR corrected p-values given.

Validation of microarray results by RT-qPCR. RT-qPCR measurements for eight genes: biologically relevant for photosynthesis chlorophyll a-b binding protein (CAB, CAB_NEW) and RuBisCO activase (RA); for defense response three classes of β-1,3-glucanases (Glu-I, Glu-II, Glu-III) and pathogenesis-related protein1b (PR-1b); and for sugar metabolism granule bound starch synthase I (GBSSI) and cell wall invertase (INV).

RT-qPCR assays for microarray validation described using the MIQE standard.

Table connecting MOA sample identifiers to GEO identifiers related to sRNAomics dataset.

miRNAs and their counts identified in the MOA samples for sRNA-Seq.

miRNAs and their RPM normalised counts identified in the MOA samples for sRNA-Seq.

Differential expression of miRNAs between various comparison groups (Sheet: comparisons), with log2-fold changes and Benjamini-Hochberg FDR corrected p-values given.