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Population and Evolutionary Genetics Subfamily-specific functionalization of diversified immune receptors in wild barley

https://doi.org/10.1101/352278
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Advanced backcross QTL analysis in barley (Hordeum vulgare L.)
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Coiled-Coil Domain-Dependent Homodimerization of Intracellular Barley Immune Receptors Defines a Minimal Functional Module for Triggering Cell Death
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RIN4 Interacts with Pseudomonas syringae Type III Effector Molecules and Is Required for RPM1-Mediated Resistance in Arabidopsis
inferredcites →https://doi.org/10.1016/s0092-8674(03)00036-9openalex-snapshot
Initiation of RPS2-Specified Disease Resistance in Arabidopsis Is Coupled to the AvrRpt2-Directed Elimination of RIN4
inferredcites →https://doi.org/10.1038/23260openalex-snapshot
Dynamics of disease resistance polymorphism at the Rpm1 locus of Arabidopsis
inferredcites →https://doi.org/10.1038/msb.2011.75openalex-snapshot
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
inferredcites →https://doi.org/10.1038/nature01588openalex-snapshot
Fitness costs of R-gene-mediated resistance in Arabidopsis thaliana
inferredcites →https://doi.org/10.1038/nature05286openalex-snapshot
The plant immune system
inferredcites →https://doi.org/10.1038/nature13439openalex-snapshot
The long-term maintenance of a resistance polymorphism through diffuse interactions
inferredcites →https://doi.org/10.1038/nature22043openalex-snapshot
A chromosome conformation capture ordered sequence of the barley genome
inferredcites →https://doi.org/10.1038/nbt.1754openalex-snapshot
Integrative genomics viewer
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Full-length transcriptome assembly from RNA-Seq data without a reference genome
inferredcites →https://doi.org/10.1038/ni.2083openalex-snapshot
NLR functions in plant and animal immune systems: so far and yet so close
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nplants.2015.186openalex-snapshot
The wheat Sr50 gene reveals rich diversity at a cereal disease resistance locus
inferredcites →https://doi.org/10.1038/nprot.2013.084openalex-snapshot
De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity
inferredcites →https://doi.org/10.1073/pnas.0602577103openalex-snapshot
Direct protein interaction underlies gene-for-gene specificity and coevolution of the flax resistance genes and flax rust avirulence genes
inferredcites →https://doi.org/10.1073/pnas.1605483113openalex-snapshot
Cytosolic activation of cell death and stem rust resistance by cereal MLA-family CC–NLR proteins
inferredcites →https://doi.org/10.1073/pnas.1612947113openalex-snapshot
Allelic barley MLA immune receptors recognize sequence-unrelated avirulence effectors of the powdery mildew pathogen
inferredcites →https://doi.org/10.1073/pnas.1615933113openalex-snapshot
Structural insights into plant NLR immune receptor function
inferredcites →https://doi.org/10.1073/pnas.1800168115openalex-snapshot
Extant fold-switching proteins are widespread
inferredcites →https://doi.org/10.1074/jbc.m114.616532openalex-snapshot
The N-Terminal Domain of the Tomato Immune Protein Prf Contains Multiple Homotypic and Pto Kinase Interaction Sites
inferredcites →https://doi.org/10.1080/713608055openalex-snapshot
Genetics of Powdery Mildew Resistance in Barley
inferredcites →https://doi.org/10.1093/bioinformatics/btp696openalex-snapshot
pegas: an R package for population genetics with an integrated–modular approach
inferredcites →https://doi.org/10.1093/bioinformatics/bts091openalex-snapshot
Unipro UGENE: a unified bioinformatics toolkit
inferredcites →https://doi.org/10.1093/bioinformatics/btv428openalex-snapshot
dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering
inferredcites →https://doi.org/10.1093/bioinformatics/btw361openalex-snapshot
STRUM: structure-based prediction of protein stability changes upon single-point mutation
inferredcites →https://doi.org/10.1093/genetics/153.4.1929openalex-snapshot
The Mla (Powdery Mildew) Resistance Cluster Is Associated With Three NBS-LRR Gene Families and Suppressed Recombination Within a 240-kb DNA Interval on Chromosome 5S (1HS) of Barley
inferredcites →https://doi.org/10.1093/molbev/msj030openalex-snapshot
Application of Phylogenetic Networks in Evolutionary Studies
inferredcites →https://doi.org/10.1093/molbev/msr121openalex-snapshot
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
inferredcites →https://doi.org/10.1093/molbev/mst030openalex-snapshot
FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection
inferredcites →https://doi.org/10.1093/nar/gkt381openalex-snapshot
Scalable web services for the PSIPRED Protein Analysis Workbench
inferredcites →https://doi.org/10.1093/nar/gkv236openalex-snapshot
IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences: Figure 1.
inferredcites →https://doi.org/10.1094/mpmi-01-14-0009-ropenalex-snapshot
Three-Dimensional Modeling and Diversity Analysis Reveals Distinct AVR Recognition Sites and Evolutionary Pathways in Wild and Domesticated WheatPm3 RGenes
inferredcites →https://doi.org/10.1094/mpmi-23-4-0497openalex-snapshot
Diversity at theMlaPowdery Mildew Resistance Locus from Cultivated Barley Reveals Sites of Positive Selection
inferredcites →https://doi.org/10.1104/pp.105.062406openalex-snapshot
Allelic Series of Four Powdery Mildew Resistance Genes at the Pm3 Locus in Hexaploid Bread Wheat
inferredcites →https://doi.org/10.1104/pp.105.073510openalex-snapshot
Mutations in the NB-ARC Domain of I-2 That Impair ATP Hydrolysis Cause Autoactivation
inferredcites →https://doi.org/10.1105/tpc.002238openalex-snapshot
Genome Dynamics and Evolution of theMla(Powdery Mildew) Resistance Locus in Barley[W]
inferredcites →https://doi.org/10.1105/tpc.009258openalex-snapshot
Recognition Specificity and RAR1/SGT1 Dependence in Barley Mla Disease Resistance Genes to the Powdery Mildew Fungus
inferredcites →https://doi.org/10.1105/tpc.104.023382openalex-snapshot
Interaction-Dependent Gene Expression inMla-Specified Response to Barley Powdery Mildew[W]
inferredcites →https://doi.org/10.1105/tpc.106.042614openalex-snapshot
A Genome-Wide Survey of R Gene Polymorphisms in Arabidopsis
inferredcites →https://doi.org/10.1105/tpc.107.053611openalex-snapshot
Crystal Structures of Flax Rust Avirulence Proteins AvrL567-A and -D Reveal Details of the Structural Basis for Flax Disease Resistance Specificity
inferredcites →https://doi.org/10.1105/tpc.107.056036openalex-snapshot
The Coiled-Coil and Nucleotide Binding Domains of the Potato Rx Disease Resistance Protein Function in Pathogen Recognition and Signaling
inferredcites →https://doi.org/10.1105/tpc.112.107201openalex-snapshot
The Rice Resistance Protein Pair RGA4/RGA5 Recognizes the Magnaporthe oryzae Effectors AVR-Pia and AVR1-CO39 by Direct Binding
inferredcites →https://doi.org/10.1105/tpc.13.2.337openalex-snapshot
Cell-Autonomous Expression of Barley Mla1 Confers Race-Specific Resistance to the Powdery Mildew Fungus via a Rar1-Independent Signaling Pathway
inferredcites →https://doi.org/10.1105/tpc.16.00435openalex-snapshot
Recognition of the Magnaporthe oryzae Effector AVR-Pia by the Decoy Domain of the Rice NLR Immune Receptor RGA5
inferredcites →https://doi.org/10.1105/tpc.17.00180openalex-snapshot
The Intracellular Immune Receptor Sw-5b Confers Broad-Spectrum Resistance to Tospoviruses through Recognition of a Conserved 21-Amino Acid Viral Effector Epitope
inferredcites →https://doi.org/10.1110/ps.4010102openalex-snapshot
Assessment of the ability to model proteins with leucine‐rich repeats in light of the latest structural information
inferredcites →https://doi.org/10.1111/j.1365-313x.2004.02032.xopenalex-snapshot
A single‐amino acid substitution in the sixth leucine‐rich repeat of barley MLA6 and MLA13 alleviates dependence on RAR1 for disease resistance signaling
inferredcites →https://doi.org/10.1111/j.1365-313x.2009.04078.xopenalex-snapshot
Prf immune complexes of tomato are oligomeric and contain multiple Pto‐like kinases that diversify effector recognition
inferredcites →https://doi.org/10.1111/j.1365-313x.2010.04445.xopenalex-snapshot
The wheat Mla homologue TmMla1 exhibits an evolutionarily conserved function against powdery mildew in both wheat and barley
inferredcites →https://doi.org/10.1111/j.1439-0523.1987.tb01181.xopenalex-snapshot
Genetical Studies of Resistance of Powdery Mildew in Barley Lines Derived from Hordeum spontaneum Collected from Israel
inferredcites →https://doi.org/10.1111/nph.14097openalex-snapshot
Molecular genetics and evolution of disease resistance in cereals
inferredcites →https://doi.org/10.1111/nph.14943openalex-snapshot
A dominant‐interfering camta3 mutation compromises primary transcriptional outputs mediated by both cell surface and intracellular immune receptors in Arabidopsis thaliana
inferredcites →https://doi.org/10.1111/nph.15077openalex-snapshot
Targeted resequencing reveals genomic signatures of barley domestication
inferredcites →https://doi.org/10.1126/science.1136372openalex-snapshot
Nuclear Activity of MLA Immune Receptors Links Isolate-Specific and Basal Disease-Resistance Responses
inferredcites →https://doi.org/10.1126/science.1158868openalex-snapshot
Metamorphic Proteins
inferredcites →https://doi.org/10.1126/science.1239028openalex-snapshot
The Gene Sr33, an Ortholog of Barley Mla Genes, Encodes Resistance to Wheat Stem Rust Race Ug99
inferredcites →https://doi.org/10.1126/science.aao4810openalex-snapshot
Loss of AvrSr50 by somatic exchange in stem rust leads to virulence for Sr50 resistance in wheat
inferredcites →https://doi.org/10.1146/annurev.phyto.46.081407.104740openalex-snapshot
The Powdery Mildews: A Review of the World's Most Familiar (Yet Poorly Known) Plant Pathogens
inferredcites →https://doi.org/10.1186/s12864-016-3011-9openalex-snapshot
Genome analysis and avirulence gene cloning using a high-density RADseq linkage map of the flax rust fungus, Melampsora lini
inferredcites →https://doi.org/10.1186/s12915-016-0235-8openalex-snapshot
Integrated decoys and effector traps: how to catch a plant pathogen
inferredcites →https://doi.org/10.1371/journal.pgen.1002764openalex-snapshot
Detecting Individual Sites Subject to Episodic Diversifying Selection
inferredcites →https://doi.org/10.1371/journal.ppat.1000970openalex-snapshot
Balanced Nuclear and Cytoplasmic Activities of EDS1 Are Required for a Complete Plant Innate Immune Response
inferredcites →https://doi.org/10.1371/journal.ppat.1002752openalex-snapshot
Structure-Function Analysis of Barley NLR Immune Receptor MLA10 Reveals Its Cell Compartment Specific Activity in Cell Death and Disease Resistance
inferredcites →https://doi.org/10.1371/journal.ppat.1003123openalex-snapshot
The Tomato Prf Complex Is a Molecular Trap for Bacterial Effectors Based on Pto Transphosphorylation
inferredcites →https://doi.org/10.2210/pdb2ncg/pdbopenalex-snapshot
The CC domain structure from the wheat stem rust resistance protein Sr33 challenges paradigms for dimerization in plant NLR proteins
inferredcites →https://doi.org/10.3389/fimmu.2013.00297openalex-snapshot
Evolution and Conservation of Plant NLR Functions
inferredcites →https://doi.org/10.7554/elife.08709openalex-snapshot
Structural basis of pathogen recognition by an integrated HMA domain in a plant NLR immune receptor
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