High intraspecies allelic diversity in Arabidopsis NLR immune receptors is associated with higher transcription, gene body hypomethylation, and proximity to transposable elements.

Plants rely on Nucleotide-binding, Leucine-rich repeat Receptors (NLRs) for pathogen recognition. Highly variable NLRs (hvNLRs) show remarkable intra-species diversity, while their low variability paralogs (non-hvNLRs) are conserved between ecotypes. At a population level, hvNLRs provide new pathogen recognition specificities, but the association between allelic diversity and genomic and epigenomic features has not been established. Our investigation of NLRs in Arabidopsis Col-0 has revealed that hvNLRs show higher expression, less gene body cytosine methylation, and closer proximity to transposable elements than non-hvNLRs. How these features are established, maintained, and potentially driving the difference in the observed diversity of hv and non-hvNLRs is key to understanding the evolution of plant innate immune receptors.