Biology subjects

Stukenbrock, E.

Publications and source records attributed to Stukenbrock, E..

9 recordsLinked to original sources

bioRxiv2026

An effector protein that protects a fungal pathogen from the plant microbiota during host colonisation

Zymoseptoria tritici is the causal agent of Septoria tritici blotch, one of the most economically important wheat diseases worldwide. One of the few cloned wheat resistance genes against Z. tritici, Stb6, recognizes the secreted fungal effector AvrStb6. Although AvrStb6 has been extensively studied as an avirulence determinant, its biological function during host colonization remains unknown. Based on the amphipathic nature of the predicted structure of AvrStb6, we hypothesized the effector to function as a membrane-active antimicrobial protein. However, in vitro growth inhibition assays demonstrated that AvrStb6 does not directly inhibit the growth of wheat-associated bacteria across multiple bacterial genera and experimental conditions. Instead, microbiome analyses of wheat apoplastic fluid revealed shifts in bacterial abundance associated with the presence or absence of AvrStb6 in a susceptible cultivar (without Stb6-induced resistance). This prompted us to further explore other putative microbiome-related functions of AvrStb6. In vitro confrontation assays further showed that deletion of AvrStb6 increased the sensitivity of Z. tritici to antagonistic wheat-associated bacteria, particularly Pseudomonas and Pantoea spp. This phenotype was conserved across independent fungal genetic backgrounds and across virulent and avirulent AvrStb6 variants. Fluorescence-based co-culture assays additionally showed reduced fungal growth and increased bacterial proliferation in the absence of AvrStb6 during interactions with Pseudomonas spp., but not with the control bacterium Escherichia coli. Finally, biochemical assays demonstrated that AvrStb6 associates with the Z. tritici cell wall in vitro, whereas other secreted fungal effectors do not. Collectively, our findings identify a previously uncharacterized role of AvrStb6 in protecting Z. tritici from antagonistic wheat-associated bacteria by associating with the fungal cell wall. More broadly, this work highlights that fungal effectors may contribute to microbial competition and ecological adaptation beyond their established roles in host immune recognition. Author summaryPlant pathogens secrete proteins that help them colonize their hosts. Some of these proteins are recognized by plant immune receptors and trigger disease resistance, but their original biological functions often remain unclear. We investigated the role of AvrStb6, a protein produced by the wheat pathogen that causes Septoria tritici blotch. AvrStb6 is best known because it is recognized by a wheat resistance gene, yet its contribution to fungal growth and survival has remained unknown. We initially tested whether AvrStb6 directly inhibits bacteria that live on wheat leaves, but found no evidence that it acts as an antimicrobial protein. Instead, we discovered that AvrStb6 influences interactions between the pathogen and wheat-associated bacteria. Fungal strains lacking AvrStb6 were more sensitive to several bacterial species that naturally occur in wheat, particularly members of the genera Pseudomonas and Pantoea. We also found that AvrStb6 can associate with the fungal cell wall, suggesting that it helps protect the pathogen during encounters with antagonistic bacteria. Our findings reveal an unexpected role for a fungal effector in microbial competition and show that pathogen proteins traditionally studied in the context of plant immunity can also influence interactions with other microbes. This work highlights the importance of considering the broader microbial community when studying plant-pathogen systems.

pathology↗

bioRxiv2024

Sequencing of historical plastid genomes reveal exceptional genetic diversity in early domesticated rye plants

In medieval central Europe, rye was one of the most important agricultural crops. Its properties of frost resistance, general resilience and resistance to many pathogens made it invaluable for medieval farmers. Rye has a distinct domestication history compared to other cereal crops and was not domesticated directly from its wild ancestors, like barley and wheat. Rye is considered to be a "secondary domesticate", i.e. a crop with domestication traits that initially evolved as an arable weed but eventually was intentionally sown and propagated as a crop. To study the history of rye domestication, genetic sequences of present-day plant populations as well as material from historical samples can provide insights into the temporal and spatial signatures of domestication. In this study we combined archaeobotanical methods and ancient DNA sequencing of well-preserved, historical rye material to study patterns of genetic diversity across four centuries. We first applied archaeobotanical methods to characterize rye material acquired from construction material ranging from the 14th to 18th century from different locations in Germany. Next, we extracted DNA to sequence complete chloroplast genomes of six individual samples. We compared the 115,000 bp chloroplast genomes of historical rye samples to chloroplast genomes of other cereal crops and identified 217 single nucleotide variants exclusive to historical samples. By comparing the aDNA chloroplast samples with modern rye chloroplasts, we show that the genetic variation in ancient rye populations was exceptionally high compared to samples from contemporary rye cultivars. This confirms that late domestication and selective breeding have reduced genetic variation in this important crop species only in the last few centuries. HighlightsO_LIHistorical plant material covering four centuries was obtained from half-timbered houses from five locations in Germany C_LIO_LIIntegrative archaeobotanical analyses and ancient DNA sequencing provided insights into genetic diversity of rye plants from historical farmland fields. C_LIO_LISequence analyses of complete assembled chloroplast genomes reveal expectational diversity in rye populations. C_LIO_LILate domestication of rye preserved genetic diversity over centuries. The more recent intensification of rye breeding has however conferred a considerable loss of genetic diversity in this important crop. C_LI

evolutionary biology↗

bioRxiv2023

Deep population structure linked to host vernalization requirement in the barley net blotch fungal pathogen

Invasive fungal pathogens pose a substantial threat to widely cultivated crop species, owing to their capacity to adapt to new hosts and new environmental conditions. Gaining insights into the demographic history of these pathogens and unraveling the mechanisms driving coevolutionary processes are crucial for the development of durably effective disease management programs. Pyrenophora teres is a significant fungal pathogen of barley, consisting of two lineages, Ptt and Ptm, with global distributions and demographic histories reflecting barley domestication and spread. However, the factors influencing the population structure of P. teres remain poorly understood, despite the varietal and environmental heterogeneity of barley agrosystems. Here, we report on the population genomic structure of P. teres in France and globally. We used genotyping-by-sequencing to show that Ptt and Ptm can coexist in the same area in France, with Ptt predominating. Furthermore, we showed that differences in the vernalization requirement of barley varieties were associated with population differentiation in France and at a global scale, with one population cluster found on spring barley and another population cluster found on winter barley. Our results demonstrate how cultivation conditions, possibly associated with genetic differences between host populations, can be associated with the maintenance of divergent invasive pathogen populations coexisting over large geographic areas. This study not only advances our understanding of the coevolutionary dynamics of the Pt-barley pathosystem but also prompts further research on the relative contributions of adaptation to the host versus adaptation to abiotic conditions in shaping Ptt populations. Impact statementMany invasive fungal pathogens have successfully followed major crop species throughout their intercontinental range, but continue to represent dynamic biotic threats. During their geographic expansion, invasive fungal populations were subjected to heterogeneous environmental conditions, or different populations of hosts, which could result in adaptation processes. Understanding this history of colonization can allow us to better prevent the emergence of infectious diseases of crops, and to better control them. One such fungus, Pyrenophora teres, negatively impacts barley production globally by causing net blotch disease. In this study, we characterized the genetic makeup of P. teres in France and how it compares with what can be sampled in other regions of the world. We found that both the net and spot forms of Pyrenophora teres can be in the same area in France, but the spot form is more common. We also discovered that the net form populations associated with winter and spring barley are different, which was not known until now. This study opens up numerous experimental perspectives aimed at evaluating whether the two populations of net form are adapted to their hosts or to the conditions of cultivation of their hosts, with the goal of implementing measures that force the pathogen to maladaptation. Data summaryGBS data are available under BioProject PRJEB66440. Single nucleotide polymorphism and reference genome assembly are available under doi: https://doi.org/10.5281/zenodo.10021844. Reads used for genome assembly are available under the BioProject PRJEB66476. The authors confirm all supporting data, code, and protocols have been provided within the article or through supplementary data files.

evolutionary biology↗

bioRxiv2023

Segmental Duplications Drive the Evolution of Accessory Regions in a Major Crop Pathogen

O_LIMany pathogens evolved compartmentalized genomes with conserved core and variable accessory regions which carry effector genes mediating virulence. The fungal plant pathogen Fusarium oxysporum has such accessory regions often spanning entire chromosomes. The presence of specific accessory regions influences the host range, and horizontal transfer of some accessory regions can modify the pathogenicity of the receiving strain. However, understanding how these accessory regions evolve in strains that infect the same host remains limited. C_LIO_LIHere, we define the pan-genome of 69 diverse Fusarium strains that cause Fusarium wilt of banana, a significant constraint to global banana production. In this diverse panel of Fusarium strains infecting banana, we analyzed the diversity and evolution of the accessory regions. C_LIO_LIAccessory regions in Fusarium strains infecting the same banana cultivar are highly diverse, and we could not identify any shared genomic regions and in planta induced effectors. We demonstrate that segmental duplications drive the evolution of accessory regions. Furthermore, we show that recent segmental duplications and aneuploidy occur specifically in accessory chromosomes and cause the expansion of accessory regions in F. oxysporum. C_LIO_LITaken together we conclude that extensive recent duplications drive the evolution of accessory regions in Fusarium, which contribute to the evolution of virulence. C_LI

genomics↗

bioRxiv2023

Lifestyle transitions in basidiomycetous fungi are reflected by tRNA composition and translation efficiency of metabolic genes

Fungi are ubiquitous and inhabit every known terrestrial habitat. Pathogenic fungi are highly diverse, and recent years have seen an uprise in the emergence of new pathogens on crops, animals and humans. The order Trichosporonales (Tremellomycetes, Agaricomycotina, Basidiomycota) harbours saprobic and a few opportunistic human pathogenic species. These emerging pathogens cause superficial skin irritations, as well as invasive life-threatening infections. Yet, little is known about their evolution, ecology, virulence mechanisms and transition to pathogenic lifestyles. In this study we aimed to determine genomic signatures associated with lifestyle transitions, virulence and host/substrate specialization among 30 Trichosporonales species from a total of 41 genome sequences. We used comparative analyses of genome content, including gene functional categories, repetitive element content and tRNA composition among saprotrophic and reported opportunistic human pathogens. A genome-scale phylogenetic reconstruction revealed that even though the different genera are monophyletic, opportunistic pathogenic species are present in distantly-related clades. Statistical analyses showed that differences in genome structure among species did not correlate with predicted lifestyles. Intriguingly, we found that tRNA content varied widely across species (from 51 to 1455 manually curated tRNA genes). The expansion was independent from the phylogenetic structure. Opportunistic pathogenic species showed an overall increased efficiency in the translation of genes associated with host colonization (i.e. lipid metabolism), while exclusively saprotrophic species showed an increase translation efficiency for genes associated with a saprotrophic lifestyle (i.e. carbohydrate metabolism). This pattern was consistent among distantly-related saprotrophic and pathogenic Cryptococcus species (order Tremellales). In conclusion, our analyses link genomic information with ecology and fungal lifestyles across an entire order. We find evidence for an evolutionary scenario where distinct habitats select for an optimized translation of genes involved in successful proliferation in the respective habitat. We predict that lifestyles are not strictly defined by gene repertoires, but also by expression profiles in fungal pathogens.

genomics↗

bioRxiv2023

Improved gene annotation of the fungal wheat pathogen Zymoseptoria tritici based on combined Iso-Seq and RNA-Seq evidence

Despite large omics datasets, the establishment of a reliable gene annotation is still challenging for eukaryotic genomes. Here, we used the reference genome of the major fungal wheat pathogen Zymoseptoria tritici (isolate IPO323) as a case study to develop methods to improve eukaryotic gene prediction. Four previous IPO323 annotations identified 10,933 to 13,260 gene models, but only one third of these coding sequences (CDS) have identical structures. To resolve these discrepancies and improve gene models, we generated full-length transcripts using long-read sequencing. This dataset was used together with other evidence (RNA-Seq transcripts and protein sequences) to generate novel ab initio gene models. The selection of the best structure among novel and existing gene models was performed according to transcript and protein evidence using InGenAnnot, a novel bioinformatics suite. Overall, 13,414 re-annotated gene models (RGMs) were predicted, including 671 new genes among which 53 encoded effector candidates. This process corrected many of the errors (15%) observed in previous gene models (coding sequence fusions, false introns, missing exons). While fungal genomes have poor annotations of untranslated regions (UTRs), our Iso-Seq long-read sequences outlined 5 and 3UTRs for 73% of the RGMs. Alternative transcripts were identified for 13% of RGMs, mostly due to intron retention (75%), likely corresponding to unprocessed pre-mRNAs. A total of 353 genes displayed alternative transcripts with combinations of previously predicted or novel exons. Long non-coding transcripts (lncRNAs) and double-stranded RNAs from two fungal viruses were also identified. Most lncRNAs corresponded to antisense transcripts of genes (52%). lncRNAs that were up or down regulated during infection were enriched in antisense transcripts (70%), suggesting their involvement in the control of gene expression. Our results showed that combining different ab initio gene predictions and evidence-driven curation using InGenAnnot improved the quality of gene annotations of a compact eukaryotic genome. Our analysis also provided new insights into the transcriptional landscape of Z. tritici, helping develop an increasingly complex picture of its biology.

genomics↗

bioRxiv2019

Higher stochasticity of microbiota composition in seedlings of domesticated wheat compared to wild wheat

Plants constitute an ecological niche for microbial communities that colonize different plant tissues and explore the plant habitat for reproduction and dispersal. The association of microbiota and plant may be altered by ecological and evolutionary changes in the host population. Seedborne microbiota, expected to be largely vertically-transferred, have the potential to co-adapt with their host over generations. Reduced host diversity because of strong directional selection and polyploidization during plant domestication and cultivation may have impacted the assembly and transmission of seed-associated microbiota. Nonetheless, the effect of plant domestication on the diversity of their associated microbes is poorly understood. Here we show that microbial communities in domesticated wheat, Triticum aestivum, are less diverse but more inconsistent among individual plants compared to the wild wheat species, T. dicoccoides. We found that diversity of microbes in seeds overall is low, but comparable in different wheat species, independent of their genetic and geographic origin. However, the diversity of seedborne microbiota that colonize the roots and leaves of the young seedling is significantly reduced in domesticated wheat genotypes. Moreover, we observe a higher variability between replicates of T. aestivum suggesting a stronger effect of chance events in microbial colonization and assembly. We also propagated wild and domesticated wheat in two different soils and found that different factors govern the assembly of soil-derived and seedborne microbial communities. Overall, our results demonstrate that the role of stochastic processes in seedborne microbial community assembly is larger in domesticated wheat compared to the wild wheat. We suggest that the directional selection on the plant host and polyploidization events during domestication may have decreased the degree of wheat-microbiota interactions and consequently led to a decreased stable core microbiota.

microbiology↗

bioRxiv2019

Local adaptation drives the diversification of effectors in the fungal wheat pathogen Parastagonospora nodorum in the United States

Filamentous fungi rapidly evolve in response to environmental selection pressures, exemplified by their genomic plasticity. Parastagonospora nodorum, a fungal pathogen of wheat and causal agent of septoria nodorum blotch, responds to selection pressure exerted by its host, influencing the gain, loss, or functional diversification of putative effector genes. Whole genome resequencing of 197 P. nodorum isolates collected from spring, durum, and winter wheat production regions of the United States enabled the examination of effector diversity and genomic regions under selection specific to geographically discrete populations. A total of 1,026,859 quality SNPs/InDels were identified within the natural population. Implementation of GWAS identified novel loci, as well as SnToxA and SnTox3 as major factors in disease. Genes displaying presence/absence variation and predicted effector genes, as well as genes localized on an accessory chromosome, had significantly higher pN/pS ratios, indicating a greater level of diversifying selection. Population structure analyses indicated two major P. nodorum populations corresponding to the Upper Midwest (Population 1) and Southern/Eastern United States (Population 2). Prevalence of SnToxA varied greatly between the two populations which correlated with presence of the host sensitivity gene Tsn1. Additionally, 12 and 5 candidate effector genes were observed to be diversifying among isolates from Population 1 and Population 2, respectively, but under purifying or neutral selection in the opposite population. Selective sweep analysis revealed 10 and 19 regions of positive selection from Population 1 and Population 2, respectively, with 92 genes underlying population-specific selective sweeps. Also, genes exhibiting presence/absence variation were significantly closer to transposable elements. Taken together, these results indicate that P. nodorum is rapidly adapting to distinct selection pressures unique to spring and winter wheat production regions by various routes of genomic diversification, potentially facilitated through transposable element activity.\n\nAuthor SummaryParastagonospora nodorum is an economically important pathogen of wheat, employing proteinaceous effector molecules to cause disease. Recognition of effectors by host susceptibility genes often leads to the elicitation of programmed cell death. However, little is known on the correlation between effector diversity and the spatial distribution of host resistance/susceptibility or the genomic mechanisms of diversification. This research presents the genome resequencing of 197 P. nodorum isolates collected from spring, winter, and durum wheat production regions of the United States, enabling the investigation of genome dynamics and evolution. Results illustrate local adaptation to host resistance or susceptibility, as evidenced by population-specific evolution of predicted effector genes and positively selected selective sweeps. Predicted effector genes, genes exhibiting presence/absence variation, and genes residing on an accessory chromosome, were found to be diversifying more rapidly. Additionally, transposable elements were predicted to play a role in the maintenance or elimination of genes. A GWAS approach identified the previously reported SnToxA and SnTox3 as well as novel virulence candidates, as major elicitors of disease on winter wheat. These results highlight the flexibility of the P. nodorum genome in response to population-specific selection pressures and illustrates the utility of whole genome resequencing for the identification of putative virulence mechanisms.

evolutionary biology↗

bioRxiv2019

Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms

BackgroundThe interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution and development of both players. These interdependencies inspired a new view of multicellular organisms as \"metaorganisms\". The goal of the Collaborative Research Center \"Origin and Function of Metaorganisms\" is to understand why and how microbial communities form long-term associations with hosts from diverse taxonomic groups, ranging from sponges to humans in addition to plants.\n\nMethodsIn order to optimize the choice of analysis procedures, which may differ according to the host organism and question at hand, we systematically compared the two main technical approaches for profiling microbial communities, 16S rRNA gene amplicon- and metagenomic shotgun sequencing across our panel of ten host taxa. This includes two commonly used 16S rRNA gene regions and two amplification procedures, thus totaling five different microbial profiles per host sample.\n\nConclusionWhile 16S rRNA gene-based analyses are subject to much skepticism, we demonstrate that many aspects of bacterial community characterization are consistent across methods and that metagenomic shotgun results are largely dependent on the employed pipeline. The resulting insight facilitates the selection of appropriate methods across a wide range of host taxa. Finally, by contrasting taxonomic and functional profiles and performing phylogenetic analysis, we provide important and novel insight into broad evolutionary patterns among metaorganisms, whereby the transition of animals from an aquatic to a terrestrial habitat marks a major event in the evolution of host-associated microbial composition.

microbiology↗