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.