Supplemental Online Files for the manuscript entitled “Salicylic acid perturbs sRNA-gibberellin regulatory network in immune response of potato to Potato virus Y infection” submitted to Frontiers in Plant Science:

• Supplemental Online File 1. sRNA regulatory network connecting endogenous miRNAs, phasiRNAs and their targets. For each predicted interaction, miRNA/phasiRNA identifiers, the target transcript identifiers, short gene name, full descriptions and MapMan ontology annotations (GoMapMan; (Ramšak et al., 2014) are shown. Additionally, PHAS loci and their producing phasiRNAs are also included. 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, interaction properties were also included (see Dataset S6 and S7). Additionally, for each sRNA the log₂FC and p-values among different comparisons are given and the log₂FC ratios of target transcripts between PVY^NTN and mock inoculated Désirée or NahG-Désirée plants (from the study of Stare et al. 2015). – statistically not significant (FDR p > 0.05); NA – not analyzed or not available; NR – not relevant.  D – Désirée; NahG – NahG-Désirée; M – mock; P – PVY^NTN.

 

• Supplemental Online File 2. sRNA regulatory network connecting miRNAs, phasiRNAs, PVY-derived siRNAs (vsiRNAs) and their targets. For each predicted interaction, miRNA/phasiRNA identifiers, the target transcript identifiers, short gene name, full descriptions and MapMan ontology annotations (GoMapMan; Ramšak et al., 2014) are shown. Additionally, PHAS loci and their producing phasiRNAs are also included. 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, interaction properties were also included (see Dataset S6, S7 and S9). Additionally, for each sRNA the log₂FC and p-values among different comparisons are given and the log₂FC ratios of target transcripts between PVY^NTN and mock inoculated Désirée or NahG-Désirée plants (from the study of Stare et al. 2015). – statistically not significant (FDR p > 0.05); NA – not analyzed or not available; NR – not relevant.  D – Désirée; NahG – NahG-Désirée; M – mock; P – PVY^NTN.

 

Links to public database entries associated with the project:

• microarray gene expression dataset of cv. Désirée response to PVY (GEO:GSE58593)
• smallRNA-Seq and degradome-Seq dataset of cv. Désirée response to PVY (GEO: GSE84967)
• smallRNA-Seq of potatoes infected with various viruses (SRA: SRP083247)