Library Enrichment Calculations
The fasta files containing the annotated R genes for each Illumina library were concatenated into a fasta containing every observed R gene from the Illumina dataset (hence, a “Pan-NLRome”). Reads from each Illumina RenSeq library, as well as eleven 1X-depth WGS libraries from seven S. integrifolium , two S. perfoliatum , one S. laciniatum and one S. terebinthinaceum , were mapped to the Pan-NLRome using bwa mem (Li 2013). The fraction out of the total reads in the library that mapped to the Pan-NLRome with a SAM CIGAR mapping score of between 148M-151M was calculated, representing reads that mapped to an R gene in the Pan-NLRome with between 98.01%-100% identity.