R Gene Counts by Geographic Region
The Illumina R gene assemblies ranged from 2.2 Mb to 51 Mb, and averaged
15 Mb in size. We detected an average of 386.3, 410.0, and 414.0 R genes
in plants sourced from the Western, Central, and Eastern prairies,
respectively (left facet of Figure 4A). The plants averaged 47.38
(West), 48.69 (Central), and 45.14 (East) TNL genes, and 166.1 (West),
171.3 (Central), and 175.3 (East) CNL genes (Table S2).
The PacBio R gene assemblies ranged from 4.9 Mb to 13 Mb, but averaged 8
Mb. Within this dataset, we only had three plants per region, so the
inferential power was lower, but our confidence in the contigs assembled
was higher due to longer reads. We found an average of 355.0, 563.3, and
592.7 R genes in the Western, Central, and Eastern prairies,
respectively (right facet of Figure 4A). Within this dataset, we found
an average of 54.00 (West), 81.67 (Central), and 81.33 (East) TNLs, and
121.3 (West), 158.7 (Central) and 159 (East) CNLs (Table S2). As
compared to the Illumina data, PacBio assemblies resulted in more
“complete”, as compared to “partial” genes for both intact and
pseudogenized R genes (Figure 4B), indicating that many of the R genes
predicted as pseudogenes in the Illumina data likely represent complete
genes that are mis-categorized due to assembly limitations.