*2.6. Di*ff*erential RNA Expression Analysis*

Raw read counts obtained from RNAseq were normalized and assessed for di fferential expression using the Statistical Software "R" version 3.6.0 and the package DESeq2 [28,29]. Log2 fold change threshold of 2 and a 5% false discovery rate (FDR) were used as cut-o ff values for continuing to the annotation step. R scripts are available on Bioconductor (https://bioconductor.org/) from the package developers and were adapted for the data presented in this paper. The same technique was repeated for the discovery of di fferentially expressed small RNA, with target gene identification done using psRNATarget [27]. Gene annotations for *S. tuberosum* and *A. thaliana* were obtained from the Ensembl Plants database (http://plants.ensembl.org). *Arabidopsis* homologs with >50% identity to the original potato gene were input into the online DAVID Bioinformatics Resources version 6.8 (https://david.ncifcrf.gov/) for functional annotation clustering and KEGG pathway mapping analyses.
