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.