#Immune repertoire notation software#

The warm, wet climates in the wheat belts of India and China, which supply ∼30% of the world’s wheat ( FAOSTAT, 2014), favor the further proliferation of this devastating disease.

In that context, wheat blast, a relatively new disease of wheat, which had until recently been confined to Brazil and other countries in South America, appeared in 2016 in Bangladesh, possibly as a result of importing contaminated grain ( Islam et al., 2016 Abu Sadat and Choi, 2017). The spread of disease into new regions can be attributed to the very success of wheat as a globally traded commodity. For example, wheat stem rust, long considered a vanquished foe of the past, has in the last 20 years caused devastating epidemics in Africa ( Pretorius et al., 2000 Olivera et al., 2015) and eastern Russia ( Shamanin et al., 2016), while in 20, large outbreaks occurred for the first time in more than 50 years in western Europe ( Bhattacharya, 2017 Firpo et al., 2017). The status of wheat ( Triticum spp.) as the world’s most widely grown and important food crop ( FAOSTAT, 2014) is threatened by the emergence and spread of new and old diseases. Our study will support the identification of functional resistance genes in wheat to accelerate the breeding and engineering of disease-resistant varieties. 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. In young leaves subjected to biotic stress, we found up-regulation of 266 of the NLRs. Most NLRs (88%) display low basal expression (in the lower 10 percentile of transcripts). Members of another subclade predominantly locate in close physical proximity to NLRs carrying integrated domains, suggesting a paired helper function. NLRs with integrated domains mostly group in specific subclades. We detected 3,400 full-length NLR loci, of which 1,560 were confirmed as expressed genes with intact open reading frames. 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. Although developed for wheat, we demonstrate the universal applicability of NLR-Annotator across diverse plant taxa.

#Immune repertoire notation software#

Here, we developed NLR-Annotator, a software tool for in silico NLR identification independent of transcript support. However, low NLR expression and high intrafamily sequence homology hinder their accurate annotation. The availability of the hexaploid wheat ( Triticum aestivum) cultivar Chinese Spring reference genome allows a detailed study of its NLR complement. Plant genomes typically contain hundreds of NLR-encoding genes. Disease resistance genes encoding nucleotide-binding and leucine-rich repeat (NLR) intracellular immune receptor proteins detect pathogens by the presence of pathogen effectors.