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. 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 language | English |
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Pages (from-to) | 1260-1272.e14 |
Number of pages | 13 |
Journal | Cell |
Volume | 178 |
Issue number | 5 |
Early online date | 22 Aug 2019 |
DOIs | |
Publication status | Published - 22 Aug 2019 |
Funding
We thank Florian Jupe for sharing methods before publication, Eunyoung Chae for contributing with alleles for bait design, Burkhard Steuernagel for assistance with demultiplexing, and Johannes Hofberger and Eric Schranz for providing sequences for an early version of the bait library. J.L.D. is an Investigator of the Howard Hughes Medical Institute. We would like to thank three anonymous reviewers, whose comments improved the quality and readability of the manuscript. This work was supported by a grant from the Gordon and Betty Moore Foundation to the 2Blades Foundation ( GBMF4725 ) (J.D.G.J., J.L.D., D.W.); by the Gatsby Charitable Foundation (O.J.F., K.W., J.D.G.J.); by BBSRC grants BB/M003809/1 , BB/P021646/1 , and BB/L009293/1 (O.J.F., J.D.G.J.); by NSF grant IOS-1758400 (J.L.D.); the Howard Hughes Medical Institute (J.L.D.); the European Research Council (Advanced Grant IMMUNEMESIS 340602 ); and the Max Planck Society (D.W.). The ORCIDs for authors are as follows: 0000-0002-5180-897X (A.-L.V.d.W.), 0000-0002-9080-6715 (F.M.), 0000-0002-3536-9970 (O.J.F.), 0000-0003-4666-6900 (M.T.N.), 0000-0002-3545-3179 (V.C.), 0000-0003-0659-5562 (K.W.), 0000-0002-4953-261X (J.D.G.J.), 0000-0003-3199-8654 (J.L.D.), 0000-0002-2114-7963 (D.W.), and 0000-0001-6557-4898 (F.B.).
Keywords
- disease resistance genes
- genomics
- innate immunity
- integrated domains
- NLR
- plant immunity
- RenSeq
- sequence capture
- SMRT sequencing
- targeted enrichment
ASJC Scopus subject areas
- General Biochemistry,Genetics and Molecular Biology
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Volkan Cevik
- Department of Life Sciences - Senior Lecturer
- Milner Centre for Evolution
Person: Research & Teaching