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Croll, Daniel
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Croll, Daniel
Affiliation principale
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Professeur ordinaire
Email
daniel.croll@unine.ch
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Voici les éléments 1 - 10 sur 43
- PublicationRestriction temporaireThe complex genetic landscape of fungicide resistance evolution in "Zymoseptoria tritici"La résistance aux fongicides chez les agents pathogènes des cultures représente un défi important pour l'agriculture durable et la sécurité alimentaire mondiale. La pression de sélection des fongicides a été sélectionnée pour les populations fongiques résistantes menaçant l'efficacité à long terme des fongicides et nécessitant une compréhension plus approfondie des mécanismes génétiques sous-jacents à la résistance. Les mutations du site cible, telles que celles de Cyp51, sont bien établies comme principaux facteurs de résistance, et les méthodes traditionnelles de génétique directe basées sur des criblages de mutagenèse de souches de référence ont aidé à prédire la mutation de résistance. Néanmoins, les enquêtes sur le terrain ont systématiquement révélé des mécanismes alternatifs. Une limitation majeure de la recherche sur la résistance est que la variabilité naturelle au sein des populations d'agents pathogènes donne lieu à des mécanismes de résistance complexes qui ne peuvent pas toujours être reproduits in vitro. Ces mécanismes impliquent souvent des adaptations polygéniques, des variations structurelles ou des changements d'expression génétique, qui sont difficiles à capturer dans des environnements de laboratoire contrôlés mais sont essentiels pour comprendre l'évolution de la résistance dans le monde réel. Les genome wide association studies (GWAS) offrent une alternative puissante aux criblages de mutagenèse en exploitant la variabilité naturelle au sein des populations d'agents pathogènes à grande échelle. En analysant diverses souches fongiques exposées à des applications de fongicides, GWAS peut identifier les mécanismes de résistance façonnés par les pressions de sélection du monde réel, offrant une compréhension plus complète de l'évolution de la résistance aux fongicides. À cette fin, nous avons constitué un panel génomique européen de Zymoseptoria tritici, le principal pathogène du blé, couvrant 1394 souches collectées sur 15 ans dans 27 pays d'Europe, un continent où les fongicides sont utilisés depuis longtemps et de manière diversifiée. Nous nous concentrons sur la principale classe de fongicides utilisée en agriculture en Europe, les demethylation inhibitors (DMI). En intégrant deux approches de phénotypage, trois méthodes de génotypage et six DMI largement utilisés sur le terrain au cours des 20 dernières années, notre analyse GWAS a révélé 21 220 variantes génétiques et 158 gènes candidats associés à la résistance aux DMI, offrant une vue complète de l'architecture génétique sous-jacente à l'évolution de la résistance. Nos résultats ont révélé une diversification importante dans la séquence codante de Cyp51, avec des modèles géographiques distincts émergeant au fil du temps. Nous avons ensuite établi un atlas de résistance aux fongicides, révélant la base génétique de la résistance à plus de 40 fongicides. Dans ce chapitre, nous avons développé un pipeline simplifié capable d'identifier les déterminants génétiques de la résistance en deux semaines. En exploitant une approche de génotypage sans référence, CNV, TE, SNP, Indels et sans référence, nous avons identifié 2 280 gènes candidats liés à la résistance aux fongicides, soit une multiplication par dix du paysage de résistance précédemment connu. Nos efforts de cartographie ont été validés par des expériences fonctionnelles, confirmant le rôle de SdhC1, Mfs1 et β-tubulin dans la médiation de la résistance. Ces résultats soulignent la puissance de cette approche pour capturer la variabilité naturelle et révéler les réponses adaptatives à la sélection des fongicides dans les populations fongiques. L'atlas de résistance aux fongicides qui en résulte offre une perspective sans précédent à l'échelle du continent sur l'évolution de la résistance, offrant un outil essentiel pour une application de fongicides guidée avec précision et une gestion durable de la résistance. Enfin, dans cette étude, nous avons exploré la dynamique évolutive de la résistance aux fongicides en Europe. Grâce à l'analyse de la fréquence des allèles sur huit sites européens et deux périodes de temps, nous avons découvert des preuves claires d'une évolution convergente, où la résistance est apparue indépendamment dans plusieurs populations. Alors que la résistance au DMI présentait les changements adaptatifs les plus forts, la résistance à l'inhibiteur de la succinate déshydrogénase (SDHI) est restée globalement faible. Malgré l'augmentation rapide de la résistance aux fongicides depuis le début des années 2010, seule une petite fraction du génome était soumise à une sélection positive, soulignant les contraintes et la prévisibilité de l'évolution de la résistance sous une pression fongicide soutenue. En intégrant les perspectives génomiques, phénotypiques et évolutives, cette thèse établit un cadre complet pour comprendre la résistance aux fongicides dans des conditions naturelles. Les résultats fournissent des informations essentielles sur les mécanismes moléculaires et évolutifs à l'origine de la résistance et soulignent l'importance de la variabilité naturelle dans la formation de la résistance au-delà des criblages de mutagenèse. Le développement d'un atlas de résistance aux fongicides permet des mesures de contrôle plus ciblées et informe la conception de stratégies antifongiques de nouvelle génération pour atténuer la propagation de la résistance. Fungicide resistance in crop pathogens presents a significant challenge to sustainable agriculture and global food security. Fungicide application has selected for resistant fungal populations threatening the long-term efficacy of fungicides and requiring a deeper understanding of the genetic mechanisms underlying resistance. Target-site mutations, such as those in Cyp51, are well established as primary drivers of resistance, and traditional forward genetics methods based on mutagenesis screens of reference strains have helped predict resistance mutation. Nevertheless, field surveys have consistently revealed alternative mechanisms. A major limitation in resistance research is that natural variability within pathogen populations gives rise to complex resistance mechanisms that cannot always be replicated in vitro. These mechanisms often involve polygenic adaptations, structural variations, or gene expression changes, which are difficult to capture in controlled laboratory settings but are critical for understanding real-world resistance evolution. Genome-wide association studies (GWAS) provide a powerful alternative to mutagenesis screens by leveraging natural variability within large-scale pathogen populations. By analyzing diverse fungal strains exposed to fungicide applications, GWAS can identify resistance mechanisms shaped by real-world selection pressures offering a more comprehensive understanding of fungicide resistance evolution. For this purpose, we assembled a European genome panel of Zymoseptoria tritici, the major wheat pathogen, spanning 1,394 strains collected over 15 years from 27 countries in Europe, a continent with a long and diverse application of fungicides. We focus on the main fungicide class applied in agriculture in Europe, the demethylation inhibitors (DMI). By integrating two phenotyping approaches, three genotyping methods, and six DMIs widely used in the field over the past 20 years, our GWAS analysis uncovered 21,220 genetic variants and 158 candidate genes associated with DMI resistance, providing a comprehensive view of the genetic architecture underlying resistance evolution. Our findings revealed extensive diversification in the Cyp51 coding sequence, with distinct geographic patterns emerging over time. We then established a fungicide resistance atlas, uncovering the genetic basis of resistance across more than 40 fungicides. In this thesis, we developed a streamlined pipeline capable of identifying genetic determinants of resistance within two weeks. By leveraging on a CNV, TE, SNPs, Indels and reference free genotyping approach, we identified 2,280 candidate genes linked to fungicide resistance—a tenfold expansion of the previously known resistance landscape. Our mapping efforts were further validated through functional experiments, confirming the role of SdhC1, Mfs1, and β-tubulin in mediating resistance. These findings highlight the power of this approach in capturing natural variability and revealing adaptive responses to fungicide selection in fungal populations. The resulting fungicide resistance atlas provides an unprecedented, continent-wide perspective on resistance evolution, offering a vital tool for precision-guided fungicide application and sustainable resistance management. Finally, in this study we explored the evolutionary dynamics of fungicide resistance in Europe. Through allele frequency analysis across eight European sites and two timeframes, we uncovered clear evidence of convergent evolution, where resistance emerged independently in multiple populations. While DMI resistance exhibited the strongest adaptive shifts, succinate dehydrogenase inhibitor (SDHI) resistance remained weak overall. Despite the rapid rise of fungicide resistance since the early 2010s, only a small fraction of the genome was under positive selection, highlighting the constraints and predictability of resistance evolution under sustained fungicide pressure. By integrating genomic, phenotypic, and evolutionary perspectives, this thesis establishes a comprehensive framework for understanding fungicide resistance in natural conditions. The findings provide essential insights into the molecular and evolutionary mechanisms driving resistance and emphasize the importance of natural variability in shaping resistance beyond mutagenesis screens. The development of a fungicide resistance atlas enables more targeted control measures and informs the design of next-generation antifungal strategies to mitigate resistance spread.
- PublicationAccès libreGiant transposons promote strain heterogeneity in a major fungal pathogen(2024-10-08T00:00:00Z)
; - PublicationAccès libreGenomic Signatures of Domestication in a Fungus Obligately Farmed by Leafcutter Ants(2024-10-04T00:00:00Z)
; Shik, Jonathan ZThe naturally selected fungal crop (Leucoagaricus gongylophorus) farmed by leafcutter ants shows striking parallels with artificially selected plant crops domesticated by humans (e.g. polyploidy, engorged nutritional rewards, and dependence on cultivation). To date, poorly resolved L. gongylophorus genome assemblies based on short-read sequencing have constrained hypotheses about how millions of years under cultivation by ants shaped the fungal crop genome and potentially drove domestication. We use PacBio HiFi sequencing of L. gongylophorus from the leafcutter ant Atta colombica to identify 18 putatively novel biosynthetic gene clusters that likely cemented life as a cultivar (e.g. plant fragment degradation, ant-farmer communication, and antimicrobial defense). Comparative analyses with cultivated and free-living fungi showed genomic signatures of stepwise domestication transitions: (i) free-living to ant-cultivated: loss of genes conferring stress response and detoxification; (ii) hyphal food to engorged nutritional rewards: expansions of genes governing cellular homeostasis, carbohydrate metabolism, and siderophore biosynthesis; and (iii) detrital provisioning to freshly cut plant fragments: gene expansions promoting cell wall biosynthesis, fatty acid metabolism, and DNA repair. Comparisons across L. gongylophorus fungi farmed by 3 leafcutter ant species highlight genomic signatures of exclusively vertical clonal propagation and widespread transposable element activity. These results show how natural selection can shape domesticated cultivar genomes toward long-term ecological resilience of farming systems that have thrived across millennia. - PublicationAccès libreCopy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen(2024-07-08T00:00:00Z)
- PublicationAccès librePopulation-level transposable element expression dynamics influence trait evolution in a fungal crop pathogen(2024-03-13T00:00:00Z)
; ; The rapid adaptive evolution of microbes is driven by strong selection pressure acting on genetic variation. How adaptive genetic variation is generated within species and how such variation influences phenotypic trait expression is often not well understood though. We focused on the recent activity of transposable elements (TEs) using deep population genomics and transcriptomics analyses of a fungal plant pathogen with a highly active content of TEs in the genome. causes one of the most damaging diseases on wheat, with recent adaptation to the host and environment being facilitated by TE-associated mutations. We obtained genomic and RNA-sequencing data from 146 isolates collected from a single wheat field. We established a genome-wide map of TE insertion polymorphisms in the population by analyzing recent TE insertions among individuals. We quantified the locus-specific transcription of individual TE copies and found considerable population variation at individual TE loci in the population. About 20% of all TE copies show transcription in the genome suggesting that genomic defenses such as repressive epigenetic marks and repeat-induced polymorphisms are at least partially ineffective at preventing the proliferation of TEs in the genome. A quarter of recent TE insertions are associated with expression variation of neighboring genes providing broad potential to influence trait expression. We indeed found that TE insertions are likely responsible for variation in virulence on the host and potentially diverse components of secondary metabolite production. Our large-scale transcriptomics study emphasizes how TE-derived polymorphisms segregate even in individual microbial populations and can broadly underpin trait variation in pathogens.IMPORTANCEPathogens can rapidly adapt to new hosts, antimicrobials, or changes in the environment. Adaptation arises often from mutations in the genome; however, how such variation is generated remains poorly understood. We investigated the most dynamic regions of the genome of a major fungal pathogen of wheat. We focused on the transcription of transposable elements. A large proportion of the transposable elements not only show signatures of potential activity but are also variable within a single population of the pathogen. We find that this variation in activity is likely influencing many important traits of the pathogen. Hence, our work provides insights into how a microbial species can adapt over the shortest time periods based on the activity of transposable elements. - PublicationAccès libreQuantitative pathogenicity and host adaptation in a fungal plant pathogen revealed by whole-genome sequencing(2024-03-02T00:00:00Z)
; - PublicationAccès libreRecent reactivation of a pathogenicity-associated transposable element is associated with major chromosomal rearrangements in a fungal wheat pathogen(2024-02-09T00:00:00Z)
- PublicationAccès libreTwo-speed genomes of Epichloe fungal pathogens show contrasting signatures of selection between species and across populations(2024-02-01T00:00:00Z)
; Leuchtmann, AdrianAntagonistic selection between pathogens and their hosts can drive rapid evolutionary change and leave distinct molecular footprints of past and ongoing selection in the genomes of the interacting species. Despite an increasing availability of tools able to identify signatures of selection, the genetic mechanisms underlying coevolutionary interactions and the specific genes involved are still poorly understood, especially in heterogeneous natural environments. We searched the genomes of two species of Epichloe plant pathogen for evidence of recent selection. The Epichloe genus includes highly host-specific species that can sterilize their grass hosts. We performed selection scans using genome-wide SNP data from seven natural populations of two co-occurring Epichloe sibling species specialized on different hosts. We found evidence of recent (and ongoing) selective sweeps across the genome in both species. However, selective sweeps were more abundant in the species with a larger effective population size. Sweep regions often overlapped with highly polymorphic AT-rich regions supporting the role of these genome compartments in adaptive evolution. Although most loci under selection were specific to individual populations, we could also identify several candidate genes targeted by selection in sweep regions shared among populations. The genes encoded small secreted proteins typical of fungal effectors and cell wall-degrading enzymes. By investigating the genomic signatures of selection across multiple populations and species, this study contributes to our understanding of complex adaptive processes in natural plant pathogen systems. - PublicationAccès libre
- PublicationAccès libreA systematic screen for co-option of transposable elements across the fungal kingdom(2024-01-20T00:00:00Z)
; ; How novel protein functions are acquired is a central question in molecular biology. Key paths to novelty include gene duplications, recombination or horizontal acquisition. Transposable elements (TEs) are increasingly recognized as a major source of novel domain-encoding sequences. However, the impact of TE coding sequences on the evolution of the proteome remains understudied. Here, we analyzed 1237 genomes spanning the phylogenetic breadth of the fungal kingdom. We scanned proteomes for evidence of co-occurrence of TE-derived domains along with other conventional protein functional domains. We detected more than 13,000 predicted proteins containing potentially TE-derived domain, of which 825 were identified in more than five genomes, indicating that many host-TE fusions may have persisted over long evolutionary time scales. We used the phylogenetic context to identify the origin and retention of individual TE-derived domains. The most common TE-derived domains are helicases derived from Academ, Kolobok or Helitron. We found putative TE co-options at a higher rate in genomes of the Saccharomycotina, providing an unexpected source of protein novelty in these generally TE depleted genomes. We investigated in detail a candidate host-TE fusion with a heterochromatic transcriptional silencing function that may play a role in TE and gene regulation in ascomycetes. The affected gene underwent multiple full or partial losses within the phylum. Overall, our work establishes a kingdom-wide view of putative host-TE fusions and facilitates systematic investigations of candidate fusion proteins.