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Abstract Genomic clusters of immune genes, including those encoding nucleotide-binding leucine-rich repeat (NLR) proteins, are a model for exploring the dynamics of genomic regions in flux. Rapid sequence evolution of immune genes, including NLRs, and variation in their gene content, may enable long-lived plants, which lack adaptive immune systems, to keep pace with the fast evolution of pathogens. To explore the patterns and processes shaping the evolution of NLR gene content in a genus of long-lived tree species, we unified the annotation of NLR genes across 11 accessions (or 15 haplotypes) from the genusCitrusand its relatives, including three new diploid genome assemblies. A majority of NLRs were arranged in genomic clusters composed of paralogous genes, typically from a single gene family. Even larger clusters, with 10 or more NLRs, were limited to genes derived from one or few gene families. These patterns suggested that genomic clustering of NLRs arose through local expansion of phylogenetically related NLRs, but the mechanistic processes driving these patterns are not clear. Local gene duplication can be mediated by multiple processes, including transposon-mediated gene capture and subsequent proliferation, and non-allelic repair of double stranded breaks, including unequal recombination. Examples of retrotransposon-mediated duplication of NLRs were identified, but these were not sufficient to explain massive regional expansions. Signatures of unequal recombination are challenging to identify. Focusing on recent lineage-specific sequence duplications, at least one case of unequal recombination was identified, supporting a role for unequal recombination in shaping genomic variation in these regions. 

Plants and animals detect biomolecules termed microbe-associated molecular patterns (MAMPs) and induce immunity. Agricultural production is severely impacted by pathogens which can be controlled by transferring immune receptors. However, most studies use a single MAMP epitope and the impact of diverse multicopy MAMPs on immune induction is unknown. Here, we characterized the epitope landscape from five proteinaceous MAMPs across 4,228 plant-associated bacterial genomes. Despite the diversity sampled, natural variation was constrained and experimentally testable. Immune perception in bothArabidopsisand tomato depended on both epitope sequence and copy number variation. For example, Elongation Factor Tu is predominantly single copy, and 92% of its epitopes are immunogenic. Conversely, 99.9% of bacterial genomes contain multiple cold shock proteins, and 46% carry a nonimmunogenic form. We uncovered a mechanism for immune evasion, intrabacterial antagonism, where a nonimmunogenic cold shock protein blocks perception of immunogenic forms encoded in the same genome. These data will lay the foundation for immune receptor deployment and engineering based on natural variation. 

Plant–pathogen interactions result in disease development in a susceptible host. Plants actively resist pathogens via a complex immune system comprising both surface-localized receptors that sense the extracellular space as well as intracellular receptors recognizing pathogen effectors. To date, the majority of cloned resistance genes encode intracellular nucleotide-binding leucine-rich repeat receptor proteins. Recent discoveries have revealed tandem kinase proteins (TKPs) as another important family of intracellular proteins involved in plant immune responses. Five TKP genes—barley Rpg1 and wheat WTK1 (Yr15), WTK2 (Sr60), WTK3 (Pm24), and WTK4—protect against devastating fungal diseases. Moreover, a large diversity and numerous putative TKPs exist across the plant kingdom. This review explores our current knowledge of TKPs and serves as a basis for future studies that aim to develop and exploit a deeper understanding of innate plant immunity receptor proteins. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license . 

Michelmore, R.W., Coaker, G. et 38 al. (2017). Foundational and translational research opportunities to improve plant health. Molec. Plant-Microbe Interact. 30:515-516. Full article on line: https://doi.org/10.1094/MPMI-01-17-0010-CR.