Abstract
SummaryInfectious 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.
Highlights
Plant immunity relies critically on a repertoire of immunity receptors whose diversity has been shaped by eons of plant-microbe coevolution
A large portion of the latter class comprises nucleotide-binding leucine-rich repeat receptors (NLRs)
Most plant NLRs contain a central nucleotide-binding domain shared by Apaf-1, resistance proteins, and CED4 (NB-ARC, hereafter NB for simplicity), and either a Toll/interleukin-1 receptor (TIR) or coiled-coil (CC) domain at the N terminus (Jones et al, 2016; Monteiro and Nishimura, 2018)
Summary
Plant immunity relies critically on a repertoire of immunity receptors whose diversity has been shaped by eons of plant-microbe coevolution. A large portion of the latter class comprises nucleotide-binding leucine-rich repeat receptors (NLRs). These are encoded by highly polymorphic genes that represent the majority of genetically defined disease-resistance loci (Jones et al, 2016; Kourelis and van der Hoorn, 2018; Monteiro and Nishimura, 2018), with hundreds of NLR genes being found in the typical flowering plant genome (Shao et al, 2016). Most plant NLRs contain a central nucleotide-binding domain shared by Apaf-1, resistance proteins, and CED4 (NB-ARC, hereafter NB for simplicity), and either a Toll/interleukin-1 receptor (TIR) or coiled-coil (CC) domain at the N terminus (Jones et al, 2016; Monteiro and Nishimura, 2018). Similar to animal NLRs, plant NLRs appear to form inflammasome-like structures, or resistosomes, that control cell death following pathogen recognition (Wang et al, 2019a, 2019b)
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