Intraspecies diversity reveals a subset of highly variable plant immune receptors and predicts their binding sites

Abstract

Evolution of recognition specificities by the immune system depends on the generation of receptor diversity, and connecting binding of new antigens with initiation of downstream signalling. In plant immunity, these functions are enabled by the family of innate Nucleotide-Binding Leucine Rich Repeat (NLR) receptors. In this paper we surveyed the NLR complements of 62 ecotypes of Arabidopsis thaliana and 54 lines of Brachypodium distachyon and identified a limited number of NLR subfamilies responsible for generation of new receptor specificities. We show that the predicted specificity-determining residues cluster on the surfaces of Leucine Rich Repeat domains, but the location of the clusters varies between NLR subfamilies. By comparing NLR phylogeny, allelic diversity, and known functions of the Arabidopsis NLRs, we formulate a hypothesis for emergence of direct and indirect pathogen sensing receptors, and of the autoimmune NLRs. These findings reveal the recurring patterns of evolution of innate immunity and inform NLR engineering efforts.