add identification of r-gene clusters assay and protocol

assays/IdentificationOfClustersOfR-genes/protocols/IdentificationOfPhysicalClustersOfR-genes.md

+## Identification of physical clusters of *R*-genes
+
+*R*-genes were classified as belonging to a cluster when more than on *R*-gene was located in a region of 200 kilobases (kb) on a chromosome (Van de Weyer et al., 2019). Since Jupe et al. (2013) performed their analysis on an earlier release of the tomato genome assembly (ITAG2.4 release, Tomato Genome Consortium, 2012), the positions of all tomato *R*-genes had to be re-defined (Table S1). Positions of *RDCs* were verified using Blastn v2.6.0 (Altschul et al., 1990; Camacho et al., 2009) against the tomato (ITAG4.0; Hosmani et al., 2019) and potato genomes (PGSC_DM_v4.03; Potato Genome Sequencing Consortium, 2011; Table S1). All *R*-genes without defined chromosomal positions (39 genes in tomato) were classified as *R*-genes with unknown clustering.
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