Comparing to Reference Genome
The reference genome, which was sequenced at 21.5 X coverage using PacBio long reads, contained a greater number of R genes in total (873; Table S2), of which 281 and 147 where annotated as CNLs and TNLs, respectively. This compares to the 603 candidates found by NLR-Annotator in the closely related sunflower genome (Toda et al., 2020). It contained a comparable percentage of complete R genes relative to its total number of R genes (50.7%) as the enriched PacBio libraries (58.2%, 54.2%, and 57.3% in the West, Central, and East, respectively). 837 R genes in the reference (as well as the 281 and 147 CNLs and TNLs, respectively) exceeded counts from both the lower-coverage, R-gene-enriched PacBio assemblies or the Illumina short-read assemblies, below, suggesting either that the reference had more R genes (which is plausible as it an interspecific F1) than the rest of the samples and/or that some genes were missed in the enrichment process.