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Cell. 2019 Aug 22;178(5):1260-1272.e14. doi: 10.1016/j.cell.2019.07.038.

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

Author information

1
Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
2
Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain.
3
Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK.
4
Department of Biology, Colorado State University, Fort Collins, CO 80523, USA.
5
The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK; Milner Centre for Evolution & Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK.
6
The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK.
7
The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK. Electronic address: jonathan.jones@tsl.ac.uk.
8
Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Electronic address: dangl@email.unc.edu.
9
Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany. Electronic address: weigel@weigelworld.org.

Abstract

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.

KEYWORDS:

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

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