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

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    Type
    Article
    Authors
    Steuernagel, Burkhard
    Witek, Kamil
    Krattinger, Simon G. cc
    Ramirez-Gonzalez, Ricardo H.
    Schoonbeek, Henk-jan
    Yu, Guotai
    Baggs, Erin
    Witek, Agnieszka
    Yadav, Inderjit
    Krasileva, Ksenia V
    Jones, Jonathan D
    Uauy, Cristobal
    Keller, Beat
    Ridout, Christopher James
    Wulff, Brande B
    Date
    2020-03-17
    Online Publication Date
    2020-03-17
    Print Publication Date
    2020-06
    Submitted Date
    2019-10-17
    Permanent link to this record
    http://hdl.handle.net/10754/662267
    
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    Abstract
    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.
    Citation
    Steuernagel, B., Witek, K., Krattinger, S. G., Ramirez-Gonzalez, R. H., Schoonbeek, H., Yu, G., … Wulff, B. B. (2020). The NLR-Annotator tool enables annotation of the intracellular immune receptor repertoire. Plant Physiology, pp.01273.2019. doi:10.1104/pp.19.01273
    Sponsors
    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 (www.flozbox.com/Science.illustrated) for the artwork in Figure 1.
    Publisher
    American Society of Plant Biologists (ASPB)
    Journal
    Plant Physiology
    DOI
    10.1104/pp.19.01273
    Additional Links
    http://www.plantphysiol.org/lookup/doi/10.1104/pp.19.01273
    ae974a485f413a2113503eed53cd6c53
    10.1104/pp.19.01273
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