MOA2010-05_3C_sRNAomics_bioinformatics_sRNA-targets-in-silico

Version 1

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 was set (Ramšak et al., 2014). For each sRNA-target interaction, alignment score value (based on the scoring schema: G: U wobble pairings - each 0.5 scores, insertions/ deletions (indels – 2.0) and all other non-canonical Watson-Crick pairings – 1.0.), UPE (unpaired energy required to open secondary structure around sRNAˈs target site on the mRNA), the position (miRNA_start, miRNA_end, target_start, target_end) and the aligned sequence (miRNA_aligned_fragment and target_aligned_fragment) have been obtained. Moreover, the information whether the interaction was also confirmed by degradome-sequencing was added (Y – YES; N – NO). Additionally, for each sRNA the log2FC and p-values among different comparisons are given and the log2FC ratios of target transcripts between PVYNTN and mock inoculated Désirée or NahG-Désirée plants; yellow – upregulated; blue – downregulated; – statistically not significant (FDR p > 0.05). NA – not analyzed or not available. D – Désirée; NahG – NahG-Désirée; M – mock; P – PVYNTN.