ArticleBMC biology2018
Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome.
Article in BMC biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
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91 citing papers in PubMed, 221 citations in OpenAlex.
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- Polymorphism and evolutionary origins of accessory chromosomes in the basidiomycete Tremella fuciformis.Nature communications · 2026Article
- Pangenome analysis of nine soybean cyst nematode genomes reveals hidden variation contributing to diversity and adaptation.BMC genomics · 2026Article
- Dynamics of genome evolution in the era of pangenome analysis.Cell genomics · 2026Review
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- The poplar pathogenMicrobial genomics · 2026Article
- Legume Pangenome Construction Using an Iterative Mapping and Assembly Approach.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Zymoseptoria tritici stealth infection is facilitated by stage-specific downregulation of a β-glucanase.The New phytologist · 2025Article
- Comprehensive Annotation of Olfactory and Gustatory Receptor Genes and Transposable Elements Revealed Their Evolutionary Dynamics in Aphids.Molecular biology and evolution · 2025Article
- Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen.Nature communications · 2025Article
- A genomic perspective on fungal diversity and evolution.Nature reviews. Microbiology · 2025Review
- High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons.Microbiome · 2025Article
- Pan-genome analysis reveals genomic variations during enoki mushroom domestication, with emphasis on genetic signatures of cap color and stipe length.Journal of advanced research · 2025Article
- Evolution of antifungal resistance in the environment.Nature microbiology · 2025Review
- Mapping genomic regions associated with temperature stress in the wheat pathogen Zymoseptoria tritici.G3 (Bethesda, Md.) · 2025Article
- Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen.BMC biology · 2025Article
31 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 3 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundStructural variation contributes substantially to polymorphism within species. Chromosomal rearrangements that impact genes can lead to functional variation among individuals and influence the expression of phenotypic traits. Genomes of fungal pathogens show substantial chromosomal polymorphism that can drive virulence evolution on host plants. Assessing the adaptive significance of structural variation is challenging, because most studies rely on inferences based on a single reference genome sequence.
resultsWe constructed and analyzed the pangenome of Zymoseptoria tritici, a major pathogen of wheat that evolved host specialization by chromosomal rearrangements and gene deletions. We used single-molecule real-time sequencing and high-density genetic maps to assemble multiple genomes. We annotated the gene space based on transcriptomics data that covered the infection life cycle of each strain. Based on a total of five telomere-to-telomere genomes, we constructed a pangenome for the species and identified a core set of 9149 genes. However, an additional 6600 genes were exclusive to a subset of the isolates. The substantial accessory genome encoded on average fewer expressed genes but a larger fraction of the candidate effector genes that may interact with the host during infection. We expanded our analyses of the pangenome to a worldwide collection of 123 isolates of the same species. We confirmed that accessory genes were indeed more likely to show deletion polymorphisms and loss-of-function mutations compared to core genes.
conclusionsThe pangenome construction of a highly polymorphic eukaryotic pathogen showed that a single reference genome significantly underestimates the gene space of a species. The substantial accessory genome provides a cradle for adaptive evolution.
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