add R-gene data set study

studies/R-geneDataSet/protocols/R-geneData.md

+## *R*-gene Data Set
+
+The lists of the *R*-gene repertoires of *S. lycopersicum* and *S. tuberosum* were retrieved from Jupe et al. (2013). *R*-genes were classified as “full-length” NBS-LRRs if they contained both NBS and LRR domains as identified using InterPro (Mitchell et al., 2019). A slightly modified pipeline as described by Jupe et al. (2013) was used to verify their novel *R*-genes (Figure S2). These novel *R*-genes were designated by the authors as *R gene discovery consortium (RDC)* genes. Using AUGUSTUS (version 3.3.1), a gene-prediction tool developed by Stanke et al. (2008), we analyzed these *RDC* genes for coding regions and searched for NBS and LRR domains using InterPro. *RDCs* were classified as true *R*-genes if they possessed a coding region and an NBS-LRR domain. Otherwise they were excluded from further analysis. In cases in which multiple splice variants were identified, the longest splice variant was analyzed. The well-established *R*-genes *Pto* (Martin et al., 1993) and *EDS1* (Hu et al., 2005) from tomato were included in the dataset. In total, the expression patterns of 359 *R*-genes of tomato and 581 *R*-genes of potato were analyzed.
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