Rpp8 three-copy paralog intergenic gene conversion polymorphism

Here we examined the population genetics of the three-copy R-gene family of Rpp8. Across Rpp8, nucleotide diversity ranged from double to 27x the genomic background rate and amino acid substitutions were 5 to 16x higher due to intergenic gene conversion (IGC) between the 3 paralogs.  Simulation models suggest IGC coupled with balancing selection to maintain copy number polymorphism drives the high level of diversity we observe in Rpp8.  If we consider paralogs undergoing IGC as analogous to a single gene, then IGC between paralogs could effectively create a heterozygous locus in a predominantly homozygous individual thus establishing reservoirs of variation for the generation of new R-gene recognition specificities via some sort of recombination event.

Bootstrap consensus trees for the maximum parsimony phylogenies of the leucine-rich repeat region (LRR) and non-LRR regions of all three Rpp8 paralogs. Clades comprised of alleles from one paralog are boxed. Green, blue, and orange boxes represent P1, P2, and P3, respectively.

a) Phylogeny of non-LRR region (239 parsimony-informative sites out of 1701 sites).
b) Phylogeny of the framed LRR region for the same accessions as in (a). There were 236 parsimony-informative sites out of 1019 in this phylogeny