The NLR-Annotator tool enables annotation of the intracellular immune receptor repertoire

Burkhard Steuernagel, Kamil Witek, Simon G. Krattinger, Ricardo H. Ramirez-Gonzalez, Henk-jan Schoonbeek, Guotai Yu, Erin Baggs, Agnieszka Witek, Inderjit Yadav, Ksenia V Krasileva, Jonathan D Jones, Cristobal Uauy, Beat Keller, Christopher James Ridout, Brande B Wulff

Research output: Contribution to journalArticlepeer-review

94 Scopus citations


Disease resistance genes encoding nucleotide-binding and leucine-rich repeat (NLR) intracellular immune receptor proteins detect pathogens by the presence of pathogen effectors. Plant genomes typically contain hundreds of NLR-encoding genes. The availability of the hexaploid wheat (Triticum aestivum) cultivar Chinese Spring reference genome allows a detailed study of its NLR complement. However, low NLR expression and high intra-family sequence homology hinders their accurate annotation. Here we developed NLR-Annotator, a software tool for in silico NLR identification independent of transcript support. Although developed for wheat, we demonstrate the universal applicability of NLR-Annotator across diverse plant taxa. We applied our tool to wheat and combined it with a transcript-validated subset of genes from the reference gene annotation to characterize the structure, phylogeny and expression profile of the NLR gene family. We detected 3,400 full-length NLR loci of which 1,560 were confirmed as expressed genes with intact open reading frames. NLRs with integrated domains mostly group in specific subclades. Members of another subclade predominantly locate in close physical proximity to NLRs carrying integrated domains, suggesting a paired helper-function. Most NLRs (88%) display low basal expression (in the lower 10 percentile of transcripts). In young leaves subjected to biotic stress we found upregulation of 266 of the NLRs. To illustrate the utility of our tool for the positional cloning of resistance genes, we estimated the number of NLR genes within the intervals of mapped rust resistance genes. Our study will support the identification of functional resistance genes in wheat to accelerate the breeding and engineering of disease-resistant varieties.
Original languageEnglish (US)
Pages (from-to)pp.01273.2019
JournalPlant Physiology
Issue number2
StatePublished - Mar 17 2020

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: We thank the IWGSC for early access to the RefSeq v1.0 of Chinese Spring, our colleagues Yajuan Yue and JIC Horticultural Services for plant husbandry, and the NBI Computing Infrastructure for Science (CiS) group for HPC maintenance. We thank David Swarbreck and Gemy Kaithakottil for technical support with Web Apollo. We thank Tobin Florio ( for the artwork in Figure 1.


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