R Gene Genealogy Recovers Expected Patterns
The maximum likelihood genealogy constructed from the NBARC domains of the R genes of the draft genomic assembly recovers the deep evolutionary divergence between CNL-type and TNL-type R genes that has been reported in many other studies (Meyers et al., 2003; Mun et al., 2017; Neupane et al., 2018). The instances of individual R genes nesting incongruently within the wrong clade may be attributable to N-domain switching via recombination, which, to the best of our reckoning, has yet to be observed. More likely, it may be due to misidentification of upstream nucleotide sequence as incidentally translating to peptide sequence that meets the identity threshold for one of the diagnostic motifs that places those R genes in the wrong categorization.
PERFORMANCE OF RENSEQ FOR R GENE ENRICHMENT