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 StNIBv1 gene identifier was set (Ramšak et al., 2014). For each vsiRNA-target interaction, degradome category (Addo-Quaye et al., 2009), its p-value (the chance is the total number of peaks of the given category divided by the effective transcriptome size, where 'n' is the number of transcripts), TStart (one-based start position of the alignment within the transcript, TStop (one-based stop position of the alignment within the transcript), TSLice (one-based position of the alignment opposite position 10 of the query, MFEperfect (Minimum free energy of a perfectly matched site), MFEsite (Minimum free energy of the alignment), MFEratio (MFEsite / MFE_perfect) and number of mismatches are given. Additionally, 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.
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Created: 4th Mar 2019 at 17:20
Last updated: 4th Mar 2019 at 17:32
Last used: 24th Oct 2021 at 17:51