A5010389174- Plant-Microbe Interactions and Immunity
- Plant Pathogenic Bacteria Studies
- Plant Virus Research Studies
- Plant Parasitism and Resistance
- Plant Disease Resistance and Genetics
- Nuclear Structure and Function
- Microbial Natural Products and Biosynthesis
- Plant Pathogens and Fungal Diseases
- RNA Research and Splicing
- Fungal Biology and Applications
- RNA modifications and cancer
- Fungal and yeast genetics research
- Transgenic Plants and Applications
- Wheat and Barley Genetics and Pathology
- Rice Cultivation and Yield Improvement
- Photosynthetic Processes and Mechanisms
- Plant responses to water stress
- Plant nutrient uptake and metabolism
- Genomics and Phylogenetic Studies
- Plant Gene Expression Analysis
- Yeasts and Rust Fungi Studies
- Biochemical and biochemical processes
- Plant Pathogens and Resistance
- Mycorrhizal Fungi and Plant Interactions
- CRISPR and Genetic Engineering
University of California, Berkeley
2018-2024
Joint Genome Institute
2022
Lawrence Berkeley National Laboratory
2022
Innovative Genomics Institute
2020
Effector-triggered immunity (ETI) in plants involves a large family of nucleotide-binding leucine-rich repeat (NLR) immune receptors, including Toll/IL-1 receptor-NLRs (TNLs) and coiled-coil NLRs (CNLs). Although various NLR receptors are known, mechanistic understanding function ETI remains unclear. The TNL Recognition XopQ 1 (Roq1) recognizes the effectors HopQ1 from Xanthomonas Pseudomonas, respectively, which activates resistance to euvesicatoria gardneri an Enhanced Disease...
Significance Susceptibility (S) genes are plant that facilitate pathogen infection. Inactivation of S has been considered a promising strategy to obtain broad-spectrum and durable resistance in crops. We characterized two orthologs the Arabidopsis gene DMR6 tomato: SlDMR6-1 SlDMR6-2 . show SlDMR6-1, but not SlDMR6-2, is associated with immunity. Remarkably, Sldmr6-1 mutants display enhanced bacterial, oomycete, fungal pathogens. This phenotype correlates increased levels defense hormone...
Elucidating the similarity and diversity of pathogen effectors is critical to understand their evolution across fungal phytopathogens. However, rapid divergence that diminishes sequence similarities between putatively homologous has largely concealed roots effector evolution. Here we modelled structures 26,653 secreted proteins from 14 agriculturally important phytopathogens, six non-pathogenic fungi one oomycete with AlphaFold 2. With 18,000 successfully predicted folds, performed...
Summary Nucleotide‐binding and leucine‐rich repeat immune receptors (NLRs) provide resistance against diverse pathogens. To create comparative NLR resources, we conducted gene enrichment sequencing (RenSeq) with single‐molecule real‐time of PacBio for 18 accessions in Solanaceae, including 15 five wild tomato species. We investigated the evolution a class NLRs, CNLs extended N‐terminal sequences previously named Solanaceae Domain. Through genomic analysis, revealed that (exCNLs) anciently...
Summary In response to jasmonates (JAs), the JA receptor Coronatine Insensitive 1 (COI1) recruits JA‐zinc‐finger inflorescence meristem (ZIM)‐domain (JAZ) family repressors for destruction regulate plant growth, development, and defense. As Arabidopsis encodes 13 JAZ repressors, their functional specificity, diversity, redundancy in JA/COI1‐mediated responses remain unclear. We generated a broad range of jaz mutants based on phylogenetic relationship investigate roles responses. The group I...
Structural biology has the potential to illuminate evolution of pathogen effectors and their commonalities that cannot be readily detected at primary sequence level. Recent breakthroughs in protein structure modeling have demonstrated feasibility predict folds without depending on homologous templates. These advances enabled a genome-wide computational structural approach help understand proteins based predicted folds. In this study, we employed prediction methods secretome destructive fungal
Many resistance genes deployed against pathogens in crops are intracellular nucleotide-binding (NB) leucine-rich repeat (LRR) receptors (NLRs). The ability to rationally engineer the specificity of NLRs will be crucial response newly emerging crop diseases. Successful attempts modify NLR recognition have been limited untargeted approaches or depended on previously available structural information knowledge pathogen-effector targets. However, this is not for most NLR-effector pairs. Here, we...
Rice (Oryza sativa) is of paramount importance for global nutrition, supplying at least 20% calories. However, water scarcity and increased drought severity are anticipated to reduce rice yields globally. We explored stomatal developmental genetics as a mechanism improving resilience in while maintaining yield under climate stress. CRISPR/Cas9-mediated knockouts the positive regulator development STOMAGEN its paralog EPIDERMAL PATTERNING FACTOR-LIKE10 (EPFL10) yielded lines with ∼25% 80%...
Fungal pathogens deploy a set of molecules (proteins, specialized metabolites, and sRNAs), so-called effectors, to aid the infection process. In comparison other plant pathogens, smut fungi have small genomes secretomes 20 Mb around 500 proteins, respectively. Previous comparative genomic studies shown that many secreted effector proteins without known domains, i.e., novel, are conserved only in Ustilaginaceae family. By analyzing 11 species within Ustilaginaceae, we identified 53 core...
Abstract Elucidating the evolution of pathogen effector molecules is critical to understand infection mechanisms fungal phytopathogens and ensure crop security. However, rapid diversification that diminishes sequence similarities between homologous effectors has largely concealed roots evolution. We predicted folds 26,653 secreted proteins from 21 species with AlphaFold performed structure-guided comparative analyses on two aspects evolution: uniquely expanded families common present across...
Abstract Sr50, an intracellular nucleotide-binding leucine-rich repeat receptor (NLR), confers resistance of wheat against stem rust caused by the fungal pathogen Puccinia graminis f. sp. tritici . The recognizes effector AvrSr50 through its C-terminal domain, initiating a localized cell death immune response. However, this immunity is compromised mutations in effector, as escape mutant QCMJC , which evades Sr50 detection. In study, we employed iterative computational structural analyses and...
Wildfires drastically impact the soil environment, altering organic matter, forming pyrolyzed compounds, and markedly reducing diversity of microorganisms. Pyrophilous fungi, especially species from orders Pezizales Agaricales, are fire-responsive fungal colonizers post-fire that have historically been found fruiting on burned thus may encode mechanisms processing these compounds in their genomes. fungi diverse. In this work, we explored sequenced six new genomes pyrophilous isolated after...
Bacterial spot, caused by Xanthomonas species, is a devastating disease of tomato (Solanum lycopersicum) and pepper (Capsicum annuum) (Schwartz et al., 2015). The recessively inherited resistance, bacterial spot 5 (bs5), in (hereafter referred to as Cabs5) can confer resistance against different strains (Jones 2002). Cabs5 characterized the absence symptoms, faint chlorosis at site infection, reduced growth. Remarkably, commercial varieties containing bs5 allele show durable effectively...
Abstract Plants possess cytoplasmic immune receptors called nucleotide-binding leucine-rich repeat (NLRs) that recognize the presence of a pathogen through range mechanisms: direct binding effectors or indirect recognition effector actions. The has been shown to be mediated NLR’s (LRR) domain. Accurate prediction amino acids involved in these interactions can greatly enhance understanding and inform efforts engineer new resistance. In this study, we utilized two homologous NLR resistance...
Abstract Tetraploid durum wheat Triticum turgidum subsp. cv ‘Kronos’ has extensive genetic variation resources, including a sequenced and cataloged ethyl methanesulfonate (EMS) mutagenized population. To utilize this allelic diversity, we screened over 2,000 mutant lines identified 30 enhanced disease resistance (EDR) mutants in forward field screen against stripe rust. Sixteen of the EDR have persistent to rust after four years, several showed differential responses other fungal pathogens,...
Abstract Magnaporthe oryzae relies on a diverse collection of secreted effector proteins to reprogram the host metabolic and immune responses for pathogen’s benefit. Characterization effectors is thus critical understanding biology infection mechanisms this phytopathogen. In rapid, divergent evolution, structural information has potential illuminate unknown aspects that sequence analyses alone cannot reveal. It recently become feasible reliably predict protein structures without depending...
Abstract Background Nucleotide-binding and leucine-rich repeat immune receptors (NLRs) are an important component of plant immunity that provides resistance against diverse pathogens. NLRs often exist as large gene families, the members which display multi-domain architectures (MDAs) evolve through various mechanisms duplications selections. Results We conducted enrichment sequencing (RenSeq) with single-molecule real time (SMRT) PacBio for 18 accessions in Solanaceae including 15 wild...
Abstract Solanum habrochaites LA1353 is a self-incompatible, highly heterozygous wild tomato that useful germplasm resource for the study of metabolism, reproduction and disease resistance. We generated draft genome assembly with PacBio HiFi reads annotations, which underscored expansion gene families associated metabolite-production, self-incompatibility, DNA regulation immunity. After manually curating intracellular nucleotide-binding leucine-rich repeat immune receptors (NLRs), we found...
Abstract Zymoseptoria tritici is the most economically significant fungal pathogen of wheat in Europe. However, despite importance this pathogen, molecular interactions between and host during infection are not well understood. Herein, we describe use two libraries cloned Z . effectors that were screened to identify effector candidates with putative pathogen‐associated pattern (PAMP)‐triggered immunity (PTI)‐suppressing activity. The from each library transiently expressed Nicotiana...
Abstract Rice ( Oryza sativa ) is of paramount importance for global nutrition, supplying at least 20% calories. However, water scarcity and increased drought severity are anticipated to reduce rice yields globally. stomatal developmental genetics were explored as a mechanism improve resilience while maintaining yield under climate stress. CRISPR/Cas9-mediated knockouts EPFL10 STOMAGEN yielded lines with c. 80% 25% wild-type density, respectively. epfl10 moderate reductions in densities able...