A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana

Anna Lena Van de Weyer, Freddy Monteiro, Oliver J. Furzer, Marc T. Nishimura, Volkan Cevik, K. Witek, Jonathan D.G. Jones, Jeffery L. Dangl, Detlef Weigel, F. Bemm

Research output: Contribution to journalArticlepeer-review

188 Citations (SciVal)


Infectious disease is both a major force of selection in nature and a prime cause of yield loss in agriculture. In plants, disease resistance is often conferred by nucleotide-binding leucine-rich repeat (NLR) proteins, intracellular immune receptors that recognize pathogen proteins and their effects on the host. Consistent with extensive balancing and positive selection, NLRs are encoded by one of the most variable gene families in plants, but the true extent of intraspecific NLR diversity has been unclear. Here, we define a nearly complete species-wide pan-NLRome in Arabidopsis thaliana based on sequence enrichment and long-read sequencing. The pan-NLRome largely saturates with approximately 40 well-chosen wild strains, with half of the pan-NLRome being present in most accessions. We chart NLR architectural diversity, identify new architectures, and quantify selective forces that act on specific NLRs and NLR domains. Our study provides a blueprint for defining pan-NLRomes. In plants, NLR proteins are important intracellular receptors with roles in innate immunity and disease resistance. This work provides a panoramic view of this diverse and complicated gene family in the model species A. thaliana and provides a foundation for the identification and functional study of disease-resistance genes in agronomically important species with complex genomes.

Original languageEnglish
Pages (from-to)1260-1272.e14
Number of pages13
Issue number5
Early online date22 Aug 2019
Publication statusPublished - 22 Aug 2019


  • disease resistance genes
  • genomics
  • innate immunity
  • integrated domains
  • NLR
  • plant immunity
  • RenSeq
  • sequence capture
  • SMRT sequencing
  • targeted enrichment

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)


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