difflines20 Teasdale et al 2025 phase 2 long read genomes

Nucleotide-binding leucine-rich repeat (NLR) proteins are a major component of the plant immune system, exhibiting extraordinary sequence, structural, and regulatory variability. Several processes that generate this diversity have been identified, but the evolution of this complex system can only be truly understood if one takes into account the interaction between the different mechanisms and how each relates to the genomic context. Here, we integrate genome-specific full-length transcript, homology and transposable element information to exhaustively annotate 3,789 intact and pseudogenised NLRs in the genomes of 17 diverse accessions of Arabidopsis thaliana. We leveraged graph-based methods to define 121 pangenomic NLR neighbourhoods, which vary greatly in size, gene content, and structural complexity. A key finding is that NLRs exhibit diversity across many complementary axes, and we show that multiple metrics are required to capture the full extent of NLR variation. Our results advance the hypothesis that diversity in how diversity is generated is likely fundamental to the maintenance of a functionally “adaptive” immune system in plant populations, and highlights the need for future mechanistic studies to consider multiple axes of immune diversity.