Membrane trafficking in resistance gene-mediated defense against the barley powdery mildew fungus

[1]  Takaki Maekawa,et al.  Evolution and Conservation of Plant NLR Functions , 2013, Front. Immunol..

[2]  J. G. Moseman Isogenic Barley Lines for Reaction to Erysiphe graminis F. Sp. Hordei 1 , 1972 .

[3]  P. Spanu The genomics of obligate (and nonobligate) biotrophs. , 2012, Annual review of phytopathology.

[4]  E. Schleiff,et al.  The Complexity of Vesicle Transport Factors in Plants Examined by Orthology Search , 2014, PloS one.

[5]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[6]  I. Mills,et al.  COP and clathrin-coated vesicle budding: different pathways, common approaches. , 2004, Current opinion in cell biology.

[7]  H. Yoshioka,et al.  Loss of AtPDR8, a plasma membrane ABC transporter of Arabidopsis thaliana, causes hypersensitive cell death upon pathogen infection. , 2006, Plant & cell physiology.

[8]  Marius A. Micluţa,et al.  Coiled-coil domain-dependent homodimerization of intracellular barley immune receptors defines a minimal functional module for triggering cell death. , 2011, Cell host & microbe.

[9]  P. Dodds,et al.  Showdown at the RXLR motif: Serious differences of opinion in how effector proteins from filamentous eukaryotic pathogens enter plant cells , 2011, Proceedings of the National Academy of Sciences.

[10]  Anésia A. Santos,et al.  Immune Receptors and Co-receptors in Antiviral Innate Immunity in Plants , 2017, Front. Microbiol..

[11]  K. Mayer,et al.  Time‐course expression QTL‐atlas of the global transcriptional response of wheat to Fusarium graminearum , 2017, Plant biotechnology journal.

[12]  G. Jürgens,et al.  SNARE complexes of different composition jointly mediate membrane fusion in Arabidopsis cytokinesis , 2013, Molecular biology of the cell.

[13]  P. Schulze-Lefert Knocking on the heaven's wall: pathogenesis of and resistance to biotrophic fungi at the cell wall. , 2004, Current opinion in plant biology.

[14]  P. Schulze-Lefert,et al.  Cell-Autonomous Expression of Barley Mla1 Confers Race-Specific Resistance to the Powdery Mildew Fungus via a Rar1-Independent Signaling Pathway , 2001, Plant Cell.

[15]  Trevor Lithgow,et al.  A Complete Set of SNAREs in Yeast , 2004, Traffic.

[16]  Jonathan D. G. Jones,et al.  Plant pathogens and integrated defence responses to infection , 2001, Nature.

[17]  K. Shirasu The HSP90-SGT1 chaperone complex for NLR immune sensors. , 2009, Annual review of plant biology.

[18]  A. Nakano,et al.  Emp47p and its close homolog Emp46p have a tyrosine-containing endoplasmic reticulum exit signal and function in glycoprotein secretion in Saccharomyces cerevisiae. , 2002, Molecular biology of the cell.

[19]  F. Wieland,et al.  Novel isotypic gamma/zeta subunits reveal three coatomer complexes in mammals. , 2004, Molecular and cellular biology.

[20]  Harald Stenmark,et al.  The Rab GTPase family , 2001, Genome Biology.

[21]  K. Ohnishi,et al.  Molecular chaperons and co-chaperons, Hsp90, RAR1, and SGT1 negatively regulate bacterial wilt disease caused by Ralstonia solanacearum in Nicotiana benthamiana , 2015, Plant signaling & behavior.

[22]  Pari Skamnioti,et al.  Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism , 2010, Science.

[23]  C. Pedersen,et al.  The Barley Powdery Mildew Effector Candidates CSEP0081 and CSEP0254 Promote Fungal Infection Success , 2016, PloS one.

[24]  G. Jürgens,et al.  Co-option of a default secretory pathway for plant immune responses , 2008, Nature.

[25]  D. Kliebenstein Quantification of variation in expression networks. , 2009, Methods in molecular biology.

[26]  Xiaojun Ding,et al.  Receptor-like cytoplasmic kinases integrate signaling from multiple plant immune receptors and are targeted by a Pseudomonas syringae effector. , 2010, Cell host & microbe.

[27]  P. Spanu,et al.  In Planta Proteomics and Proteogenomics of the Biotrophic Barley Fungal Pathogen Blumeria graminis f. sp. hordei* , 2009, Molecular & Cellular Proteomics.

[28]  C. Pedersen,et al.  The Barley Powdery Mildew Candidate Secreted Effector Protein CSEP0105 Inhibits the Chaperone Activity of a Small Heat Shock Protein1[OPEN] , 2015, Plant Physiology.

[29]  P. Trost,et al.  Nuclear Accumulation of Cytosolic Glyceraldehyde-3-Phosphate Dehydrogenase in Cadmium-Stressed Arabidopsis Roots1[C][W] , 2013, Plant Physiology.

[30]  P. Wittkopp,et al.  Genomic sources of regulatory variation in cis and in trans , 2005, Cellular and Molecular Life Sciences CMLS.

[31]  P. Schulze-Lefert,et al.  Barley MLA Immune Receptors Directly Interfere with Antagonistically Acting Transcription Factors to Initiate Disease Resistance Signaling[C][W] , 2013, Plant Cell.

[32]  E. Lagudah,et al.  Cytosolic activation of cell death and stem rust resistance by cereal MLA-family CC–NLR proteins , 2016, Proceedings of the National Academy of Sciences.

[33]  R. Innes,et al.  Recent Advances in Plant NLR Structure, Function, Localization, and Signaling , 2013, Front. Immunol..

[34]  C. Zipfel,et al.  Plant PRRs and the activation of innate immune signaling. , 2014, Molecular cell.

[35]  B. Keller,et al.  Allelic Series of Four Powdery Mildew Resistance Genes at the Pm3 Locus in Hexaploid Bread Wheat1 , 2005, Plant Physiology.

[36]  C. Haley,et al.  Genetical genomics in humans and model organisms. , 2005, Trends in genetics : TIG.

[37]  James K. M. Brown,et al.  Evolution of the EKA family of powdery mildew avirulence-effector genes from the ORF 1 of a LINE retrotransposon , 2015, BMC Genomics.

[38]  P. Schulze-Lefert,et al.  Conservation of NLR-triggered immunity across plant lineages , 2012, Proceedings of the National Academy of Sciences.

[39]  F. Wieland,et al.  COPI-mediated Transport , 2006, The Journal of Membrane Biology.

[40]  Benjamin M. Bolstad,et al.  affy - analysis of Affymetrix GeneChip data at the probe level , 2004, Bioinform..

[41]  J. Parker,et al.  Effector-triggered immunity: from pathogen perception to robust defense. , 2015, Annual review of plant biology.

[42]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[43]  C. Zipfel,et al.  Plants and animals: a different taste for microbes? , 2005, Current opinion in plant biology.

[44]  B. Kobe,et al.  Direct protein interaction underlies gene-for-gene specificity and coevolution of the flax resistance genes and flax rust avirulence genes. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[45]  D. Kliebenstein Quantitative genomics: analyzing intraspecific variation using global gene expression polymorphisms or eQTLs. , 2009, Annual review of plant biology.

[46]  P. Schulze-Lefert,et al.  Diversity at the Mla powdery mildew resistance locus from cultivated barley reveals sites of positive selection. , 2010, Molecular plant-microbe interactions : MPMI.

[47]  F. Govers,et al.  Phytophthora infestans RXLR Effector AVR1 Interacts with Exocyst Component Sec5 to Manipulate Plant Immunity1[OPEN] , 2015, Plant Physiology.

[48]  B. Meyers,et al.  Small RNAs Add Zing to the Zig-Zag-Zig Model of Plant Defenses. , 2016, Molecular plant-microbe interactions : MPMI.

[49]  M. Rossi,et al.  Multiple Roles of ADP-Ribosylation Factor 1 in Plant Cells Include Spatially Regulated Recruitment of Coatomer and Elements of the Golgi Matrix1[W][OA] , 2007, Plant Physiology.

[50]  Lauren S. Ryder,et al.  Effector-Mediated Suppression of Chitin-Triggered Immunity by Magnaporthe oryzae Is Necessary for Rice Blast Disease[C][W] , 2012, Plant Cell.

[51]  Roger P Wise,et al.  A single-amino acid substitution in the sixth leucine-rich repeat of barley MLA6 and MLA13 alleviates dependence on RAR1 for disease resistance signaling. , 2004, The Plant journal : for cell and molecular biology.

[52]  A. Fuglsang,et al.  Interaction of barley powdery mildew effector candidate CSEP0055 with the defence protein PR17c. , 2012, Molecular plant pathology.

[53]  N. Takahashi,et al.  Proteomic snapshot analyses of preribosomal ribonucleoprotein complexes formed at various stages of ribosome biogenesis in yeast and mammalian cells. , 2003, Mass spectrometry reviews.

[54]  R. Terauchi,et al.  Arms race co-evolution of Magnaporthe oryzae AVR-Pik and rice Pik genes driven by their physical interactions. , 2012, The Plant journal : for cell and molecular biology.

[55]  S. Munro,et al.  A genome‐wide RNA interference screen identifies two novel components of the metazoan secretory pathway , 2010, The EMBO journal.

[56]  M. Moscou,et al.  Blufensin1 Negatively Impacts Basal Defense in Response to Barley Powdery Mildew1[W][OA] , 2008, Plant Physiology.

[57]  D. Glawe,et al.  The powdery mildews: a review of the world's most familiar (yet poorly known) plant pathogens. , 2008, Annual review of phytopathology.

[58]  Liam J McGuffin,et al.  Proteogenomics and in silico structural and functional annotation of the barley powdery mildew Blumeria graminis f. sp. hordei. , 2011, Methods.

[59]  D. Kudrna,et al.  Barley putative hypersensitive induced reaction genes: genetic mapping, sequence analyses and differential expression in disease lesion mimic mutants , 2003, Theoretical and Applied Genetics.

[60]  Jörg Durner,et al.  Conserved requirement for a plant host cell protein in powdery mildew pathogenesis , 2006, Nature Genetics.

[61]  Gábor Csárdi,et al.  The igraph software package for complex network research , 2006 .

[62]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[63]  Liam J McGuffin,et al.  Structure and evolution of barley powdery mildew effector candidates , 2012, BMC Genomics.

[64]  A. Bogdanove,et al.  Host-induced gene silencing in barley powdery mildew reveals a class of ribonuclease-like effectors. , 2013, Molecular plant-microbe interactions : MPMI.

[65]  P. Spanu Cereal immunity against powdery mildews targets RNase-Like Proteins associated with Haustoria (RALPH) effectors evolved from a common ancestral gene. , 2017, The New phytologist.

[66]  Antonio Di Pietro,et al.  The Top 10 fungal pathogens in molecular plant pathology. , 2012, Molecular plant pathology.

[67]  I. Somssich,et al.  Nuclear Activity of MLA Immune Receptors Links Isolate-Specific and Basal Disease-Resistance Responses , 2007, Science.

[68]  R. Doerge,et al.  Empirical threshold values for quantitative trait mapping. , 1994, Genetics.

[69]  T. Kuno,et al.  Deletion mutants of AP‐1 adaptin subunits display distinct phenotypes in fission yeast , 2009, Genes to cells : devoted to molecular & cellular mechanisms.

[70]  D. Kliebenstein,et al.  Identifying the molecular basis of QTLs: eQTLs add a new dimension. , 2008, Trends in plant science.

[71]  T. Wicker,et al.  articleWheat gene bank accessions as a source of new alleles of the powdery mildew resistance gene Pm 3 : a large scale allele mining project , 2010 .

[72]  M. Bayer,et al.  An eQTL Analysis of Partial Resistance to Puccinia hordei in Barley , 2010, PloS one.

[73]  G. Palmer Endosomal and AP-3-Dependent Vacuolar Trafficking Routes Make Additive Contributions to Candida albicans Hyphal Growth and Pathogenesis , 2010, Eukaryotic Cell.

[74]  Seonghee Lee,et al.  Host versus nonhost resistance: distinct wars with similar arsenals. , 2015, Phytopathology.

[75]  Z. Fu,et al.  Go in for the kill: How plants deploy effector- triggered immunity to combat pathogens , 2014 .

[76]  P. D. Wit,et al.  How plants recognize pathogens and defend themselves , 2007, Cellular and Molecular Life Sciences.

[77]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[78]  W. Terzaghi,et al.  Characterization of Arabidopsis and Rice DWD Proteins and Their Roles as Substrate Receptors for CUL4-RING E3 Ubiquitin Ligases[W] , 2008, The Plant Cell Online.

[79]  M. Luo,et al.  The wheat Sr50 gene reveals rich diversity at a cereal disease resistance locus , 2015, Nature Plants.

[80]  P. D. de Wit,et al.  Fungal effector proteins. , 2009, Annual review of phytopathology.

[81]  Xin Li,et al.  NLRs in plants. , 2015, Current opinion in immunology.

[82]  In silico analysis of the core signaling proteome from the barley powdery mildew pathogen (Blumeria graminis f.sp. hordei) , 2014, BMC Genomics.

[83]  R. Doerge,et al.  Global eQTL Mapping Reveals the Complex Genetic Architecture of Transcript-Level Variation in Arabidopsis , 2007, Genetics.

[84]  Takaki Maekawa,et al.  Allelic barley MLA immune receptors recognize sequence-unrelated avirulence effectors of the powdery mildew pathogen , 2016, Proceedings of the National Academy of Sciences.

[85]  S. Dinesh-Kumar,et al.  Chloroplastic Protein NRIP1 Mediates Innate Immune Receptor Recognition of a Viral Effector , 2008, Cell.

[86]  Martin Wolfe,et al.  Genetics of Powdery Mildew Resistance in Barley , 1994 .

[87]  Jonathan D. G. Jones,et al.  Nuclear Accumulation of the Arabidopsis Immune Receptor RPS4 Is Necessary for Triggering EDS1-Dependent Defense , 2007, Current Biology.

[88]  Weihui Xu,et al.  Mla- and Rom1-mediated control of microRNA398 and chloroplast copper/zinc superoxide dismutase regulates cell death in response to the barley powdery mildew fungus. , 2014, The New phytologist.

[89]  F. Takken,et al.  A nuclear localization for Avr2 from Fusarium oxysporum is required to activate the tomato resistance protein I-2 , 2013, Front. Plant Sci..

[90]  John K. McCooke,et al.  A chromosome conformation capture ordered sequence of the barley genome , 2017, Nature.

[91]  B. Thomma,et al.  Understanding plant immunity as a surveillance system to detect invasion. , 2015, Annual review of phytopathology.

[92]  T. Kroj,et al.  A novel conserved mechanism for plant NLR protein pairs: the “integrated decoy” hypothesis , 2014, Front. Plant Sci..

[93]  T. Wicker,et al.  Avirulence Genes in Cereal Powdery Mildews: The Gene-for-Gene Hypothesis 2.0 , 2016, Front. Plant Sci..

[94]  S. Dinesh-Kumar,et al.  Novel Positive Regulatory Role for the SPL6 Transcription Factor in the N TIR-NB-LRR Receptor-Mediated Plant Innate Immunity , 2013, PLoS pathogens.

[95]  Yiqun Bao,et al.  Regulation of cytokinesis by exocyst subunit SEC6 and KEULE in Arabidopsis thaliana. , 2013, Molecular plant.

[96]  A. Ellingboe,et al.  Infection kinetics of Erysiphe graminis f. sp. hordei on barley with different alleles at the Ml-a locus , 1983 .

[97]  Mike Tyers,et al.  BioGRID: a general repository for interaction datasets , 2005, Nucleic Acids Res..

[98]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[99]  P. Cosson,et al.  Delta‐ and zeta‐COP, two coatomer subunits homologous to clathrin‐associated proteins, are involved in ER retrieval. , 1996, The EMBO journal.

[100]  Erich Kombrink,et al.  SNARE-protein-mediated disease resistance at the plant cell wall , 2003, Nature.

[101]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[102]  Quanxi Sun,et al.  The HSP90-RAR1-SGT1 based protein interactome in barley and stripe rust , 2015 .

[103]  Jeff H. Chang,et al.  Effector-triggered immunity blocks pathogen degradation of an immunity-associated vesicle traffic regulator in Arabidopsis , 2011, Proceedings of the National Academy of Sciences.

[104]  N. Paris,et al.  Arabidopsis mu A-adaptin interacts with the tyrosine motif of the vacuolar sorting receptor VSR-PS1. , 2004, The Plant journal : for cell and molecular biology.

[105]  S. Elledge,et al.  SGT1 encodes an essential component of the yeast kinetochore assembly pathway and a novel subunit of the SCF ubiquitin ligase complex. , 1999, Molecular cell.

[106]  N. Hayashi,et al.  Blast resistance of CC-NB-LRR protein Pb1 is mediated by WRKY45 through protein–protein interaction , 2013, Proceedings of the National Academy of Sciences.

[107]  Jun Liu,et al.  Quantitative Proteomics Reveals Dynamic Changes in the Plasma Membrane During Arabidopsis Immune Signaling* , 2012, Molecular & Cellular Proteomics.

[108]  David R. Kelley,et al.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.

[109]  Patrick Schweizer,et al.  HIGS: Host-Induced Gene Silencing in the Obligate Biotrophic Fungal Pathogen Blumeria graminis[W][OA] , 2010, Plant Cell.

[110]  J. Bonifacino,et al.  Adaptins: the final recount. , 2001, Molecular biology of the cell.

[111]  A. Nakano,et al.  Reconstitution of Coat Protein Complex II (COPII) Vesicle Formation from Cargo-reconstituted Proteoliposomes Reveals the Potential Role of GTP Hydrolysis by Sar1p in Protein Sorting* , 2004, Journal of Biological Chemistry.

[112]  A. Bogdanove,et al.  Broadly Conserved Fungal Effector BEC1019 Suppresses Host Cell Death and Enhances Pathogen Virulence in Powdery Mildew of Barley (Hordeum vulgare L.). , 2015, Molecular plant-microbe interactions : MPMI.

[113]  Xinnian Dong,et al.  A highway for war and peace: the secretory pathway in plant-microbe interactions. , 2011, Molecular plant.

[114]  P. Cortesi,et al.  Identification and structure of the mating-type locus and development of PCR-based markers for mating type in powdery mildew fungi. , 2011, Fungal genetics and biology : FG & B.

[115]  Seon-In Yeom,et al.  Plant NB-LRR proteins: tightly regulated sensors in a complex manner. , 2015, Briefings in functional genomics.

[116]  J. Luck,et al.  Identification of Regions in Alleles of the Flax Rust Resistance Gene L That Determine Differences in Gene-for-Gene Specificity , 1999, Plant Cell.

[117]  L. Mao,et al.  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. , 1999, Genetics.

[118]  Blake C Meyers,et al.  Evolving disease resistance genes. , 2005, Current opinion in plant biology.

[119]  P. Schweizer,et al.  Large-scale data integration reveals colocalization of gene functional groups with meta-QTL for multiple disease resistance in barley. , 2011, Molecular plant-microbe interactions : MPMI.

[120]  J. Dvorak,et al.  The Gene Sr33, an Ortholog of Barley Mla Genes, Encodes Resistance to Wheat Stem Rust Race Ug99 , 2013, Science.

[121]  H. Koga,et al.  HvCEBiP, a gene homologous to rice chitin receptor CEBiP, contributes to basal resistance of barley to Magnaporthe oryzae , 2010, BMC Plant Biology.

[122]  Fumiaki Katagiri,et al.  The μ Subunit of Arabidopsis Adaptor Protein-2 Is Involved in Effector-Triggered Immunity Mediated by Membrane-Localized Resistance Proteins. , 2016, Molecular plant-microbe interactions : MPMI.

[123]  Akihiko Nakano,et al.  Oligomerization of a cargo receptor directs protein sorting into COPII-coated transport vesicles. , 2003, Molecular biology of the cell.

[124]  L. Stuart,et al.  Effector-triggered versus pattern-triggered immunity: how animals sense pathogens , 2013, Nature Reviews Immunology.

[125]  John P. Rathjen,et al.  Plant immunity: towards an integrated view of plant–pathogen interactions , 2010, Nature Reviews Genetics.

[126]  M. Farrall Quantitative genetic variation: a post-modern view. , 2004, Human molecular genetics.

[127]  Joh. Dros The creation and maintenance of two spring barley varieties , 1957, Euphytica.

[128]  L. Kruglyak,et al.  Gene–Environment Interaction in Yeast Gene Expression , 2008, PLoS biology.

[129]  Andrew R. Russell,et al.  Pseudomonas syringae Effector AvrPphB Suppresses AvrB-Induced Activation of RPM1 but Not AvrRpm1-Induced Activation. , 2015, Molecular plant-microbe interactions : MPMI.

[130]  D. Nettleton,et al.  The knottin-like Blufensin family regulates genes involved in nuclear import and the secretory pathway in barley-powdery mildew interactions , 2015, Front. Plant Sci..

[131]  P. Schulze-Lefert,et al.  NLR functions in plant and animal immune systems: so far and yet so close , 2011, Nature Immunology.

[132]  G. Payne,et al.  The Saccharomyces cerevisiae APS1 gene encodes a homolog of the small subunit of the mammalian clathrin AP‐1 complex: evidence for functional interaction with clathrin at the Golgi complex. , 1994, The EMBO journal.

[133]  J. Beynon,et al.  Host-Parasite Coevolutionary Conflict Between Arabidopsis and Downy Mildew , 2004, Science.

[134]  T. Ueda,et al.  Conserved and Plant-Unique Mechanisms Regulating Plant Post-Golgi Traffic , 2012, Front. Plant Sci..

[135]  L. Kruglyak,et al.  Genetic Dissection of Transcriptional Regulation in Budding Yeast , 2002, Science.

[136]  James K. M. Brown,et al.  Genetic and forma specialis diversity in Blumeria graminis of cereals and its implications for host-pathogen co-evolution. , 2003, Molecular plant pathology.

[137]  Mihaela M. Martis,et al.  A physical, genetic and functional sequence assembly of the barley genome. , 2022 .

[138]  Nathan M. Springer,et al.  Mendelian and Non-Mendelian Regulation of Gene Expression in Maize , 2013, PLoS genetics.

[139]  C. Zipfel Plant pattern-recognition receptors. , 2014, Trends in immunology.

[140]  Zhenbiao Yang,et al.  Analysis of the Small GTPase Gene Superfamily of Arabidopsis1 , 2003, Plant Physiology.

[141]  Hsien-Da Huang,et al.  Arabidopsis Argonaute 2 regulates innate immunity via miRNA393(∗)-mediated silencing of a Golgi-localized SNARE gene, MEMB12. , 2011, Molecular cell.

[142]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[143]  D. Nettleton,et al.  Interaction-Dependent Gene Expression in Mla-Specified Response to Barley Powdery Mildeww⃞ , 2004, The Plant Cell Online.

[144]  B. Meyers,et al.  The Diversification of Plant NBS-LRR Defense Genes Directs the Evolution of MicroRNAs That Target Them , 2016, Molecular biology and evolution.

[145]  M. Stephens,et al.  , comparison with gene expression arrays RNA-seq : An assessment of technical reproducibility and data , 2008 .

[146]  M. Moscou,et al.  Quantitative and Qualitative Stem Rust Resistance Factors in Barley Are Associated with Transcriptional Suppression of Defense Regulons , 2011, PLoS genetics.

[147]  Lu Lu,et al.  Dissection of a QTL Hotspot on Mouse Distal Chromosome 1 that Modulates Neurobehavioral Phenotypes and Gene Expression , 2008, PLoS genetics.

[148]  L. Baxter,et al.  Maintenance of genetic variation in plants and pathogens involves complex networks of gene-for-gene interactions. , 2009, Molecular plant pathology.

[149]  B. Dujon,et al.  Genome-wide nuclear morphology screen identifies novel genes involved in nuclear architecture and gene-silencing in Saccharomyces cerevisiae. , 2002, Journal of molecular biology.

[150]  R. Wing,et al.  Genome Dynamics and Evolution of the Mla (Powdery Mildew) Resistance Locus in Barley Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.002238. , 2002, The Plant Cell Online.

[151]  P. Schulze-Lefert,et al.  RAR1 Positively Controls Steady State Levels of Barley MLA Resistance Proteins and Enables Sufficient MLA6 Accumulation for Effective Resistance , 2004, The Plant Cell Online.

[152]  John D. Storey,et al.  Statistical significance for genomewide studies , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[153]  S. Takamatsu,et al.  Multilocus phylogenetic analyses within Blumeria graminis, a powdery mildew fungus of cereals. , 2007, Molecular phylogenetics and evolution.

[154]  Robert W. Williams,et al.  Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function , 2005, Nature Genetics.

[155]  C. Pedersen,et al.  Identification of eight effector candidate genes involved in early aggressiveness of the barley powdery mildew fungus , 2016 .

[156]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[157]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[158]  S. Chisholm,et al.  Host-Microbe Interactions: Shaping the Evolution of the Plant Immune Response , 2022 .

[159]  Y. Jin,et al.  Genetics of multiple disease resistance in a doubled-haploid population of barley , 1995 .

[160]  James K. M. Brown,et al.  Coevolution between a Family of Parasite Virulence Effectors and a Class of LINE-1 Retrotransposons , 2009, PloS one.

[161]  N. Raikhel,et al.  The Specificity of Vesicle Trafficking: Coat Proteins and SNAREs , 1999, Plant Cell.

[162]  P. Schulze-Lefert,et al.  Recognition Specificity and RAR1/SGT1 Dependence in Barley Mla Disease Resistance Genes to the Powdery Mildew Fungus Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.009258. , 2003, The Plant Cell Online.

[163]  David Mackey,et al.  Elicitors, effectors, and R genes: the new paradigm and a lifetime supply of questions. , 2007, Annual review of phytopathology.

[164]  Marek Żurczak,et al.  Nucleocytoplasmic partitioning of tobacco N receptor is modulated by SGT1. , 2013, The New phytologist.

[165]  R. Herrmann,et al.  Molecular Studies of CtpA, the Carboxyl-terminal Processing Protease for the D1 Protein of the Photosystem II Reaction Center in Higher Plants* , 1996, Journal of Biological Chemistry.

[166]  D. Nettleton,et al.  Quantitative and temporal definition of the Mla transcriptional regulon during barley-powdery mildew interactions. , 2011, Molecular plant-microbe interactions : MPMI.

[167]  D. Hofius,et al.  Membrane trafficking and autophagy in pathogen-triggered cell death and immunity. , 2014, Journal of experimental botany.

[168]  R. Wise,et al.  HvWRKY10, HvWRKY19, and HvWRKY28 regulate Mla-triggered immunity and basal defense to barley powdery mildew. , 2012, Molecular plant-microbe interactions : MPMI.

[169]  H. Quesneville,et al.  The wheat powdery mildew genome shows the unique evolution of an obligate biotroph , 2013, Nature Genetics.

[170]  D. Nettleton,et al.  Stage-specific suppression of basal defense discriminates barley plants containing fast- and delayed-acting Mla powdery mildew resistance alleles. , 2006, Molecular plant-microbe interactions : MPMI.

[171]  J. Glazebrook,et al.  Physical Association of Arabidopsis Hypersensitive Induced Reaction Proteins (HIRs) with the Immune Receptor RPS2* , 2011, The Journal of Biological Chemistry.

[172]  Jonathan D. G. Jones,et al.  Multiple Avirulence Paralogues in Cereal Powdery Mildew Fungi May Contribute to Parasite Fitness and Defeat of Plant Resistance , 2006, The Plant Cell Online.

[173]  Jun Liu,et al.  A receptor-like cytoplasmic kinase phosphorylates the host target RIN4, leading to the activation of a plant innate immune receptor. , 2011, Cell host & microbe.

[174]  A. Pareek,et al.  Cyclophilins: Proteins in search of function , 2013, Plant signaling & behavior.

[175]  R. Panstruga,et al.  Terrific Protein Traffic: The Mystery of Effector Protein Delivery by Filamentous Plant Pathogens , 2009, Science.

[176]  T. Ueda,et al.  Membrane trafficking pathways and their roles in plant-microbe interactions. , 2014, Plant & cell physiology.

[177]  Ken Shirasu,et al.  The RAR1 Interactor SGT1, an Essential Component of R Gene-Triggered Disease Resistance , 2002, Science.

[178]  L. Noël,et al.  xopAC-triggered Immunity against Xanthomonas Depends on Arabidopsis Receptor-Like Cytoplasmic Kinase Genes PBL2 and RIPK , 2013, PloS one.

[179]  T. Boller,et al.  Clathrin-dependent endocytosis is required for immunity mediated by pattern recognition receptor kinases , 2016, Proceedings of the National Academy of Sciences.

[180]  B. Thomma,et al.  Fungal effector Ecp6 outcompetes host immune receptor for chitin binding through intrachain LysM dimerization , 2013, eLife.

[181]  A. Nakano,et al.  Activation of the Rab7 GTPase by the MON1-CCZ1 Complex Is Essential for PVC-to-Vacuole Trafficking and Plant Growth in Arabidopsis[C][W] , 2014, Plant Cell.

[182]  R. Panstruga,et al.  Interaction of a Blumeria graminis f. sp. hordei effector candidate with a barley ARF-GAP suggests that host vesicle trafficking is a fungal pathogenicity target. , 2014, Molecular plant pathology.

[183]  Scott A. Rifkin,et al.  Revealing the architecture of gene regulation: the promise of eQTL studies. , 2008, Trends in genetics : TIG.

[184]  Hyeran Kim,et al.  Cell-autonomous defense, re-organization and trafficking of membranes in plant-microbe interactions. , 2014, The New phytologist.

[185]  A. Ellingboe Genetics and Physiology of Primary Infection by Erysiphe graminis , 1972 .

[186]  S. Howell,et al.  Elements proximal to and within the transmembrane domain mediate the organelle-to-organelle movement of bZIP28 under ER stress conditions. , 2012, The Plant journal : for cell and molecular biology.

[187]  T. D. de Kievit,et al.  Elucidating the Role of Effectors in Plant-Fungal Interactions: Progress and Challenges , 2016, Front. Microbiol..

[188]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[189]  Sheng Yang He,et al.  A Bacterial Virulence Protein Suppresses Host Innate Immunity to Cause Plant Disease , 2006, Science.

[190]  K. Shirasu,et al.  Negative Regulation of PAMP-Triggered Immunity by an E3 Ubiquitin Ligase Triplet in Arabidopsis , 2008, Current Biology.

[191]  Qianhua Shen,et al.  The miR9863 Family Regulates Distinct Mla Alleles in Barley to Attenuate NLR Receptor-Triggered Disease Resistance and Cell-Death Signaling , 2014, PLoS genetics.

[192]  Paul Schulze-Lefert,et al.  Arabidopsis PEN3/PDR8, an ATP Binding Cassette Transporter, Contributes to Nonhost Resistance to Inappropriate Pathogens That Enter by Direct Penetration[W][OA] , 2006, The Plant Cell Online.

[193]  M. Munson,et al.  The Secret Life of Tethers: The Role of Tethering Factors in SNARE Complex Regulation , 2016, Front. Cell Dev. Biol..

[194]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[195]  R. Innes,et al.  Extracellular Vesicles Isolated from the Leaf Apoplast Carry Stress-Response Proteins1[OPEN] , 2016, Plant Physiology.

[196]  F. Cvrčková,et al.  Arabidopsis exocyst subunits SEC8 and EXO70A1 and exocyst interactor ROH1 are involved in the localized deposition of seed coat pectin. , 2010, The New phytologist.