The NLR-Annotator Tool Enables Annotation of the Intracellular Immune Receptor Repertoire.
- Steuernagel B John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
- Witek K Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
- Krattinger SG Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland.
- Ramirez-Gonzalez RH John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
- Schoonbeek HJ John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
- Yu G John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
- Baggs E Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom.
- Witek AI Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
- Yadav I School of Agricultural Biotechnology, Dr. G.S. Khush Laboratories, Punjab Agricultural University, Ludhiana-141 004, Punjab, India.
- Krasileva KV Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
- Jones JDG Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
- Uauy C John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
- Keller B Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland.
- Ridout CJ John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
- Wulff BBH John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom brande.wulff@jic.ac.uk.
- 2020-03-19
Published in:
- Plant physiology. - 2020
English
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 intrafamily sequence homology hinder 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 up-regulation 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.
- Language
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- English
- Open access status
- bronze
- Identifiers
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- DOI 10.1104/pp.19.01273
- PMID 32184345
- Persistent URL
- https://sonar.ch/global/documents/244896
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