Plant disease resistance can be seen as a process of dual nature: both qualitative and quantitative. The nature non-self molecules perceived by plants has led to the depiction plant immunity two-layer defence system. first layer is mediated cell surface intracellular pattern recognition receptors (PRRs) which perceive conserved microbial elicitors, termed pathogen-associated molecular patterns (PAMPs). perception these elicitors initiates cascades signalling transcription events, known...

Abstract Background The gene content of a species largely governs its ecological interactions and adaptive potential. A is therefore defined by both core genes shared between all individuals accessory segregating presence-absence variation. There growing evidence that eukaryotes, similar to bacteria, show intra-specific variability in content. However, it remains unknown how functionally relevant such pangenome structure for eukaryotes what mechanisms underlie the emergence highly...

Transposable elements (TEs) are drivers of genome evolution and affect the expression landscape host genome. Stress is a major factor inducing TE activity; however, regulatory mechanisms underlying de-repression poorly understood. Plant pathogens excellent models to dissect impact stress on TEs. The process plant infection induces for pathogen, virulence factors (i.e., effectors) located in TE-rich regions become expressed. To dynamics contributions virulence, we analyzed four strains wheat...

Genome evolution is driven by the activity of transposable elements (TEs). The spread TEs can have deleterious effects including destabilization genome integrity and expansions. However, precise triggers expansions remain poorly understood because size typically investigated only among deeply divergent lineages. Here, we use a large population genomics dataset 284 individuals from populations across globe Zymoseptoria tritici, major fungal wheat pathogen. We built robust map genome-wide TE...

Invasive microbial species constitute a major threat to biodiversity, agricultural production and human health. Invasions are often dominated by one or small number of genotypes, yet the underlying factors driving invasions poorly understood. The chestnut blight fungus Cryphonectria parasitica first decimated North American chestnut, more recent outbreak threatens European stands. To unravel invasion southeastern Europe, we sequenced 230 genomes predominantly strains. Genotypes outside zone...

Fungal genome sizes exhibit more than a 100-fold variation, largely driven by the expansion of repetitive sequences such as transposable elements (TEs). Genomic defenses have evolved to counteract TE proliferation through silencing mechanisms operating at epigenetic or transcript level. In fungi, repeat-induced point mutation (RIP) targets TEs recognizing and inducing mutagenesis. However, prevalence RIP across fungal kingdom fidelity canonical C-to-T signatures remain unclear. this study,...

Recombination suppression can evolve in sex or mating-type chromosomes, autosomal supergenes, with different haplotypes being maintained by balancing selection. In the invasive chestnut blight fungus Cryphonectria parasitica, a genomic region was suggested to lack recombination and be partially physically linked (MAT) locus based on segregation analyses. Using hundreds of available C. parasitica genomes generating new high-quality genome assemblies, we show that ca. 1.2 Mb proximal lacks...

Fungicide resistance in crop pathogens poses severe challenges to sustainable agriculture. Demethylation inhibitors (DMIs) are critical for controlling diseases but face rapid gains the field. Even though main molecular basis of is well established, field surveys have repeatedly revealed alternative mechanisms. The European continent particular has seen and heterogeneous azole past decades. Here, we establish a large genome panel dissect genetic architecture emerging major wheat pathogen...

The range of hosts that parasites can infect is a key determinant the emergence and spread disease. Yet, impact host variation on evolution parasite genomes remains unknown. Here, we show codon optimization underlies genome adaptation in broad parasites. We found longer proteins encoded by fungi likely increase natural selection these species. Accordingly, correlates with across fungal kingdom. At species level, biased patterns synonymous substitutions underpin increased generalist but not...

Plant pathogens with a broad host range are able to infect plant lineages that diverged over 100 million years ago. They exert similar and recurring constraints on the evolution of unrelated populations. Plants generally respond quantitative disease resistance (QDR), form immunity relying complex genetic determinants. In most cases, molecular determinants QDR how they evolve is unknown. Here we identify in Arabidopsis thaliana gene mediating against Sclerotinia sclerotiorum, agent white mold...

Abstract Species harbor extensive structural variation underpinning recent adaptive evolution. However, the causality between genomic features and induction of new rearrangements is poorly established. Here, we analyze a global set telomere-to-telomere genome assemblies fungal pathogen wheat to establish nucleotide-level map variation. We show that emergence pesticide resistance has been disproportionally driven by rearrangements. use machine learning train model on events based 30...

Summary Quantitative disease resistance ( QDR ) is a form of plant immunity widespread in nature, and the only one active against broad host range fungal pathogens. The genetic determinants are complex largely unknown, thought to rely partly on genes controlling morphology development. We used genome‐wide association mapping Arabidopsis thaliana identify ARPC 4 as associated with necrotrophic pathogen Sclerotinia sclerotiorum . Mutants impaired showed enhanced susceptibility S. , defects...

A bstract Genome evolution is driven by the activity of transposable elements (TEs). The spread TEs can have deleterious effects including destabilization genome integrity and expansions. However, precise triggers expansions remain poorly understood because size typically investigated only among deeply divergent lineages. Here, we use a large population genomics dataset 284 individuals from populations across globe Zymoseptoria tritici , major fungal wheat pathogen. We built robust map...

Plant pathogens cause substantial crop losses in agriculture production and threaten food security. Plants evolved the ability to recognize virulence factors have repeatedly escaped recognition due rapid evolutionary change at pathogen loci (i.e. effector genes). The presence of transposable elements (TEs) close physical proximity genes can important consequences for gene regulation sequence evolution. Species-wide investigations remain rare hindering our predict evolvability.Here, we...

Abstract Transposable elements (TEs) are key drivers of genomic variation contributing to recent adaptation in most species. Yet, the evolutionary origins and insertion dynamics within species remain poorly understood. We recapitulate spread pathogenicity-associated Styx element across five that last diverged ∼11 000 years ago. show likely originated Zymoseptoria fungal pathogen genus underwent multiple independent reactivation events. Using a global 900-genome panel wheat tritici, we assess...

Fungal plant pathogens produce secreted proteins adapted to function outside fungal cells facilitate colonization of their hosts. In many cases such as for fungi from the Sclerotiniaceae family repertoire and remains elusive. Sclerotiniaceae, whereas Sclerotinia sclerotiorum Botrytis cinerea are cosmopolitan broad host-range pathogens, borealis has a psychrophilic lifestyle with low optimal growth temperature, narrow host range geographic distribution. To spread successfully, S. must...

Abstract Transposable elements (TEs) are drivers of genome evolution and affect the expression landscape host genome. Stress is a major factor inducing TE activity, however regulatory mechanisms underlying de-repression poorly understood. Key unresolved questions whether different types stress differentially induce activity TEs respond differently to same stress. Plant pathogens excellent models dissect impact on TEs, because lifestyle transitions off impose exposure variety conditions. We...

Abstract Invasive microbial species constitute a major threat to biodiversity, agricultural production and human health. Invasions are often dominated by one or small number of genotypes, yet the underlying factors driving invasions poorly understood. The chestnut blight fungus Cryphonectria parasitica first decimated American recent outbreak threatens European trees. To unravel mechanisms underpinning invasion south-eastern Europe, we sequenced 188 genomes predominantly strains. Genotypes...

Summary Transposable elements (TEs) are key drivers of genomic variation contributing to recent adaptation in most species. Yet, the evolutionary origins and insertion dynamics within species remain poorly understood. We recapitulate spread pathogenicity-associated Styx element across five that last diverged ∼11,000 years ago. show likely originated Zymoseptoria fungal pathogen genus underwent multiple independent reactivation events. Using a global 900-genome panel wheat Z. tritici, we...

Abstract Background The gene content of a species largely governs its ecological interactions and adaptive potential. A is therefore defined by both core genes shared between all individuals accessory segregating presence-absence variation. There growing evidence that eukaryotes, similar to bacteria, show intra-specific variability in content. However, it remains unknown how functionally relevant such pangenome structure for eukaryotes what mechanisms underlie the emergence highly...

Abstract Recombination suppression often evolves in sex chromosomes and around mating-type loci. In the invasive chestnut blight fungus Cryphonectria parasitica (Ascomycota), a genomic region was previously suggested to lack recombination be partially linked (MAT) locus based on analysis of few progenies. Using hundreds available C. genomes generating several new high-quality genome assemblies from native introduced range pathogen, we show that ca. 1.2 Mb proximal lacks worldwide....