Pangenomic context reveals the extent of intraspecific plant NLR evolution

Nucleotide-binding leucine-rich repeat (NLR) proteins are major components of the plant immune system, recognizing pathogen effectors and triggering defense responses. Because of the diversity of pathogen effector repertoires, NLRs have extraordinary sequence, structural, and regulatory variability. Although processes contributing to NLR diversity have been identified, the precise evolution of NLRs in their genomic context and along the multiple axes of diversity has been difficult to trace. We integrate genome-specific full-length transcript, homology, and transposable element information to annotate 3,789 NLRs in 17 diverse Arabidopsis thaliana accessions. We define 121 pangenomic NLR neighborhoods, which vary greatly in size, content, and complexity. NLRs are diverse across many axes, and multiple metrics are required to fully capture NLR variation. Based on these findings, we propose that diversity in diversity generation is fundamental to maintaining a functionally “adaptive” immune system in plants and that mechanistic studies should consider multiple axes of immune system diversity.