ArticleBMC biology2023
Combined pangenomics and transcriptomics reveals core and redundant virulence processes in a rapidly evolving fungal plant pathogen.
Article in BMC biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 40 citations in OpenAlex.
- TheJournal of fungi (Basel, Switzerland) · 2026Article
- Development of a bioassay-guided genome mining approach for antifungal natural product discovery from pseudomonads.Scientific reports · 2026Article
- EffectorFisher: association of disease phenotype with pangenomic protein-isoform profiles for improved prediction of fungal pathogenicity effectors.Scientific reports · 2026Article
- Phylogenomics of Plasmopara halstedii Reveals Genomic Regions Associated With the Breakdown of Sunflower Downy Mildew Resistance Genes.Molecular ecology · 2026Article
- The poplar pathogenMicrobial genomics · 2026Article
- A Core Effector MoPce1 Is Required for the Pathogenicity of Magnaporthe oryzae by Modulating Catalase-Mediated HMolecular plant pathology · 2026Article
- Isolation and Characterization of Extracellular Vesicles From Ascochyta rabiei, a Necrotrophic Fungal Chickpea Pathogen.Proteomics · 2025Article
- Plant-pathogen interactions: making the case for multi-omics analysis of complex pathosystems.Stress biology · 2025Review
- How genomics can help unravel the evolution of endophytic fungi.World journal of microbiology & biotechnology · 2025Review
- Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen.BMC biology · 2025Article
- A conserved fungal Knr4/Smi1 protein is crucial for maintaining cell wall stress tolerance and host plant pathogenesis.PLoS pathogens · 2025Article
- Unforeseen current and future benefits of uncommon yeast: the Metschnikowia genus.Applied microbiology and biotechnology · 2024Review
- An array of Zymoseptoria tritici effectors suppress plant immune responses.Molecular plant pathology · 2024Article
- Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers?Journal of experimental botany · 2024Article
- Article
- The expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogenMicrobial genomics · 2023Article
- Combined pangenomics and transcriptomics reveals core and redundant virulence processes in a rapidly evolving fungal plant pathogen.BMC biology · 2023Article
- Fungal plant pathogen "mutagenomics" reveals tagged and untagged mutations inFrontiers in plant science · 2023Article
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Authors and funding
10 authors at 4 institutions in 3 countries.
Funding
Abstract
backgroundStudying genomic variation in rapidly evolving pathogens potentially enables identification of genes supporting their "core biology", being present, functional and expressed by all strains or "flexible biology", varying between strains. Genes supporting flexible biology may be considered to be "accessory", whilst the "core" gene set is likely to be important for common features of a pathogen species biology, including virulence on all host genotypes. The wheat-pathogenic fungus Zymoseptoria tritici represents one of the most rapidly evolving threats to global food security and was the focus of this study.
resultsWe constructed a pangenome of 18 European field isolates, with 12 also subjected to RNAseq transcription profiling during infection. Combining this data, we predicted a "core" gene set comprising 9807 sequences which were (1) present in all isolates, (2) lacking inactivating polymorphisms and (3) expressed by all isolates. A large accessory genome, consisting of 45% of the total genes, was also defined. We classified genetic and genomic polymorphism at both chromosomal and individual gene scales. Proteins required for essential functions including virulence had lower-than average sequence variability amongst core genes. Both core and accessory genomes encoded many small, secreted candidate effector proteins that likely interact with plant immunity. Viral vector-mediated transient in planta overexpression of 88 candidates failed to identify any which induced leaf necrosis characteristic of disease. However, functional complementation of a non-pathogenic deletion mutant lacking five core genes demonstrated that full virulence was restored by re-introduction of the single gene exhibiting least sequence polymorphism and highest expression.
conclusionsThese data support the combined use of pangenomics and transcriptomics for defining genes which represent core, and potentially exploitable, weaknesses in rapidly evolving pathogens.
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