Biology subjects

Gluck-Thaler, E.

Publications and source records attributed to Gluck-Thaler, E..

At least 19 recordsLinked to original sources

bioRxiv2026

Distinct modes of sequence evolution and epigenetic modifications underpin the origins of Starship-mediated variation in Pyricularia fungal plant pathogens

Fungal pathogens display remarkable variation in genome content and organization that directly impacts their survival and host interactions. Although numerous models have been proposed to explain the origins of this variation, they generally fail to explain or predict the mechanisms that generate the genome variation observed in natural populations. Starships are a recently discovered group of giant fungal transposons that carry dozens of genes as cargo and horizontally transfer both within and between species. Here, we identify the features of a newly defined "Starship compartment" in the major fungal plant pathogen Pyricularia oryzae. We test the hypothesis that the Starship compartment makes distinct contributions to fungal genome evolution by explicitly comparing its transferability, mutability, and epigenetic modifications with those of the canonical core and accessory compartments. To enable this, we developed an updated and user-friendly version of the annotation tool stargraph for the comprehensive annotation of Starships and Starship-like regions. Using this approach, we identified two distinct families of Starships and related Starship-like regions in P. oryzae that differ in their activity, impacts on genome organization, modes of sequence evolution, and epigenetic modifications. Elements from the more active family exhibit higher rates of structural variation than all other genomic compartments in the predominantly clonal isolates infecting rice. Both families of Starships encode specific suites of known effector sequences that contribute to plant disease and Starship activity accounts for avirulence gene turnover, which suggests that evolutionary change within the Starship compartment may subsequently impact the evolution of plant-fungal interactions. Starships from the more active family have repeatedly transferred across the Pyricularia genus and tend to be depleted in heterochromatic histone modifications and repeat-induced point mutations. However, contrasting histone modification profiles in this family suggests a genomic conflict between silencing or maintaining Starship activity. Our findings demonstrate that variation in the mode of sequence diversification and epigenetic modification within the Starship compartment underpins the impacts of these giant transposons on fungal genome evolution. We argue for the explicit consideration of not only the Starship compartment but of element-specific dynamics when investigating the evolution of host-fungal interactions.

genomics↗

bioRxiv2025

starbase: A Database and Toolkit for Exploration of Extremely Large Mobile Elements in Fungi

Starships are a recently discovered superfamily of extremely large mobile genetic element (MGE)s in fungi that encode diverse gene sequences, many of unknown function. Starships are widespread throughout filamentous Ascomycetes (Pezizomycotina), but relatively little is known about their fine-grained distributions at lower taxonomic levels. As more and more Starships are discovered, it is increasingly important to more effectively catalog their gene contents and taxonomic distributions to better understand their contributions to fungal evolution. To address this, we developed starbase, a web server and comparative toolkit for exploring Starship diversity and hypothesis generation. The starbase database is constructed from Starships identified from existing studies, as well as an exhaustive de novo survey of Starship sequences within a set of 19 863 publicly available fungal genome assemblies. This database consists of 5 493 Starships, their associated nucleotide sequences, captain gene protein sequences, cargo gene annotations, and other metadata pertaining to the annotation and analysis of Starships in fungal genomes. As a resource, starbase provides new avenues for studying structural variation in fungal genomes. starbase provides several key features for the research community: a centralized repository of curated Starship annotations, a standardized accessioning system enabling consistent referencing of elements across studies, tools for searching existing sequences and classifying novel Starships based on established classification schemes, and a submission portal encouraging community contributions. As Starship identification becomes a routine component of fungal genome annotation, starbase provides a framework for organizing this growing body of data and facilitating comparative analyses across the expanding landscape of fungal genomic diversity.

bioinformatics↗

bioRxiv2025

PAQman: reference-free ensemble evaluation of long-read eukaryotic genome assemblies

Advances in long-read sequencing have made it easier and more cost effective to generate high-quality genome assemblies. However, assessing assembly quality remains a challenge, as existing tools often focus on a few metrics and/or require a reference assembly for comparison. Furthermore, the number of available metrics and associated tools for genome evaluation have expanded in recent years, making it more difficult for researchers to easily use and develop comprehensive pipelines. To address this, we developed the Post-Assembly Quality manager (PAQman), a tool that lowers the barrier to entry for assembly quality assessment by measuring seven reference-free features of genome quality within a single framework: Contiguity, Gene content, Completeness, Accuracy, Correctness, Coverage, and Telomerality. PAQman integrates multiple commonly used tools alongside custom scripts, requiring users to provide only a query genome assembly and its underlying long-read data, while providing a streamlined and consistent framework for quality assessment across datasets. Impact StatementPAQman is an ensemble-based tool for comprehensive, reference-free evaluation of genome assemblies derived from long-read sequencing data. The simultaneous integration of seven quality features enables users to easily assess assembly quality within a standardized, reproducible framework across diverse organisms, while lowering the barrier to entry for biologists analyzing their data.

bioinformatics↗

bioRxiv2025

A large European diversity panel reveals complex azole fungicide resistance gains of a major wheat pathogen

Fungicide resistance in crop pathogens poses severe challenges to sustainable agriculture. Demethylation inhibitors (DMIs) are critical for controlling crop diseases but face rapid resistance gains in the field. Even though the main molecular basis of resistance is well established, field surveys have repeatedly revealed alternative resistance mechanisms. The European continent in particular has seen rapid and heterogeneous gains in azole resistance in the past decades. Here, we establish a large genome panel to dissect the genetic architecture of emerging resistance in the major wheat pathogen Zymoseptoria tritici. The European diversity panel spans 15 sampling years and 27 countries for a total of 1394 sequenced and phenotyped strains. Using two complementary assays to quantify resistance levels of each strain, we captured fine-grained shifts in DMI resistance over space and time. We conducted genome-wide association studies based on a comprehensive set of genotyping approaches for six DMIs. We mapped a total of 21,220 genetic variants and 158 genes linked to resistance. The substantial scope in genetic mechanisms underpinning DMI resistance significantly expands our mechanistic understanding how continent-wide resistance arises in fungal pathogens over time. Diversification of the Cyp51 coding sequence was particularly striking with new resistant haplotypes emerging with complex configurations and geographic patterns. This study provides expansive new insights into fungicide resistance gains of crop pathogens relevant for future resistance management strategies.

microbiology↗

bioRxiv2025

A natural mechanism of eukaryotic horizontal gene transfer

Horizontal gene transfer (HGT) is an important and potentially frequent process impacting the evolutionary trajectory of eukaryotic species. Yet to date, the mechanism of HGT among eukaryotes has remained a mystery. Here, we demonstrate that Starships, a newly discovered group of cargo-mobilizing transposable elements, are active vectors of horizontally transferred DNA among eukaryotic species. We find that multiple Starships simultaneously transfer themselves and their cargo within and between fungal genera separated by upwards of 100 million years of evolution. Transferred Starships are recovered in strains with and without selection for particular Starship-encoded phenotypes. Using whole genome sequencing, we exclude alternative hypotheses such as heterokaryosis, parasex or the random uptake of exogenous DNA by showing that only Starship DNA is precisely transferred. Furthermore, we demonstrate that the introduction of the Hephaestus Starship into a new species increases metal resistance due to the genes carried by this element. Between 18-27% of all Starships in our focal genus, Paecilomyces, have evidence of horizontal transfer under natural conditions, including to other fungal genera, revealing Starship-mediated HGT to be a widespread and frequent phenomenon across filamentous fungi. This study identifies the first active genetic mechanism for HGT between eukaryotic species.

evolutionary biology↗

bioRxiv2024

Variation in a microbial mutualist has cascading consequences for host-parasite interactions

Strains of microbial symbionts often vary in their effect on their host. However, little is known about how the genetic variation in microbial symbiont populations impacts host interactions with other co-colonizing microbes. We investigated how different strains of nitrogen-fixing rhizobial bacteria affect their host plants response to parasitic root-knot nematodes in the legume Medicago truncatula. Using dual RNAseq of the root organs harboring rhizobia or nematodes, we identified genes from plant host, rhizobia, and nematode whose expression differed between parasite-infected and-uninfected plants, and between plants inoculated with different rhizobial strains. At the site of host-parasite interactions (in nematode galls), hundreds of host genes and few nematode genes differed in expression between host plants inoculated with different rhizobia strains. At the site of host-mutualist interactions (in rhizobia nodules), hundreds of host genes and few rhizobial genes responded to parasite infection. The vast majority of parasite-induced changes in host gene expression depended on the resident rhizobia strain. We additionally observed differences in parasite load and in some root architecture traits between plants inoculated with different rhizobia strains, showing that genetic variation in a mutualistic symbiont impacted parasite colonization. The transcriptomic and phenotypic differences we observed suggest that microbial indirect genetic effects play an underappreciated role in their hosts interactions with other co-colonizing microorganisms.

ecology↗

bioRxiv2024

Giant transposons promote strain heterogeneity in a major fungal pathogen

Fungal infections are difficult to prevent and treat in large part due to strain heterogeneity which confounds diagnostic predictability. Yet the genetic mechanisms driving strain-to-strain variation remain poorly understood. Here, we determined the extent to which Starships--giant transposons capable of mobilizing numerous fungal genes--generate genetic and phenotypic variability in the opportunistic human pathogen Aspergillus fumigatus. We analyzed 519 diverse strains, including 11 newly sequenced with long-read technology and multiple isolates of the same reference strain, to reveal 20 distinct Starships that are generating genomic heterogeneity over timescales relevant for experimental reproducibility. Starship-mobilized genes encode diverse functions, including known biofilm-related virulence factors and biosynthetic gene clusters, and many are differentially expressed during infection and antifungal exposure in a strain-specific manner. These findings support a new model of fungal evolution wherein Starships help generate variation in genome structure, gene content and expression among fungal strains. Together, our results demonstrate that Starships are a previously hidden mechanism generating genotypic and, in turn, phenotypic heterogeneity in a major human fungal pathogen. ImportanceNo "one size fits all" option exists for treating fungal infections in large part due to genetic and phenotypic variability among strains. Accounting for strain heterogeneity is thus fundamental for developing efficacious treatments and strategies for safeguarding human health. Here, we report significant progress towards achieving this goal by uncovering a previously hidden mechanism generating heterogeneity in the human fungal pathogen Aspergillus fumigatus: giant transposons called Starships that span dozens of kilobases and mobilize fungal genes as cargo. By conducting a systematic investigation of these unusual transposons in a single fungal species, we demonstrate their contributions to population-level variation at the genome, pangenome and transcriptome levels. The Starship compendium we develop will not only help predict variation introduced by these elements in laboratory experiments but will serve as a foundational resource for determining how Starships impact clinically-relevant phenotypes, such as antifungal resistance and pathogenicity.

microbiology↗

bioRxiv2023

Gene acquisition by giant transposons primes eukaryotes for rapid evolution via horizontal gene transfer

Horizontal gene transfer (HGT) disseminates genetic information between species. The significance of HGT in eukaryotes is not well established, with evidence currently limited to isolated examples, typically absent of a mechanism. It has been proposed that mobile elements might be active agents of HGT in eukaryotes, as they are in prokaryotes. To test this hypothesis, we examined a gene cluster, which putatively contributes to formaldehyde resistance and is found within some members of the Starship superfamily of giant transposons. Remarkably, we found four instances where ssf has been independently acquired by distantly related Starships, and show that each acquisition event coincided with the elements horizontal transfer (at least 9 HGT events in total). Our results demonstrate that acquisition of host-beneficial cargo by Starships primes fungi for rapid and repeated adaptation via HGT, revealing and elevating the role of HGT in eukaryotic biology.

evolutionary biology↗

bioRxiv2023

Systematic identification of cargo-carrying genetic elements reveals new dimensions of eukaryotic diversity

Cargo-carrying mobile elements (CCEs) are genetic entities that transpose diverse protein coding sequences. Although common in bacteria, we know little about the biology of eukaryotic CCEs because no appropriate tools exist for their annotation. For example, Starships are fungal CCEs whose functions are largely unknown because they require time-intensive manual curation. To address this knowledge gap, we developed starfish, a computational workflow for high-throughput eukaryotic CCE annotation. We applied starfish to 2, 899 genomes of 1, 649 fungal species and found that starfish recovers known Starships with >95% precision and accuracy while expanding the number of annotated elements ten-fold. Extant Starship diversity is partitioned into 11 families that differ in their enrichment patterns across fungal classes. Starship cargo changes rapidly such that elements from the same family differ substantially in their functional repertoires, which are predicted to contribute to diverse biological processes such as metabolism. Many elements have convergently evolved to insert into 5S rDNA and AT-rich sequence while others integrate into random locations, revealing both specialist and generalist strategies for persistence. Our work establishes a framework for advancing mobile element biology and provides the means to investigate an emerging dimension of eukaryotic genetic diversity, that of genomes within genomes.

genomics↗

bioRxiv2023

Copy number variation introduced by a massive mobile element underpins global thermal adaptation in a fungal wheat pathogen

Copy number variation (CNV) can drive rapid evolution in changing environments. In microbial pathogens, such adaptation is a key factor underpinning epidemics and colonization of new niches. However, the genomic determinants of such adaptation remain poorly understood. Here, we systematically investigate CNVs in one of the largest to date genome sequencing dataset spanning a worldwide collection of 1109 genomes from the major wheat pathogen Zymoseptoria tritici. We found overall strong purifying selection acting on most CNVs. Genomic defense mechanisms likely accelerated gene loss over episodes of continental colonization. Local adaptation along climatic gradients was facilitated by CNVs affecting secondary metabolite production and gene loss in general. One of the strongest candidates for climatic adaptation is a highly conserved gene of the NAD-dependent Sirtuin family. The Sirtuin CNV locus localizes to an [~]68-kb Starship mobile element unique to the species carrying genes highly expressed during plant infection. The element has likely lost the ability to transpose, demonstrating how the ongoing domestication of cargo-carrying selfish elements can contribute to selectable variation within populations. Our work highlights how standing variation in gene copy numbers at the global scale is a major factor driving climatic and metabolic adaptation in microbial species.

evolutionary biology↗

bioRxiv2023

Endophyte genomes support greater metabolic gene cluster diversity compared with non-endophytes in Trichoderma

Trichoderma is a cosmopolitan genus with diverse lifestyles and nutritional modes, including mycotrophy, saprophytism, and endophytism. Previous research has reported greater metabolic gene repertoires in endophytic fungal species compared to closely-related non-endophytes. However, the extent of this ecological trend and its underlying mechanisms are unclear. Some endophytic fungi may also be mycotrophs and have one or more mycoparasitism mechanisms. Mycotrophic endophytes are prominent in certain genera like Trichoderma, therefore, the mechanisms that enable these fungi to colonize both living plants and fungi may be the result of expanded metabolic gene repertoires. Our objective was to determine what, if any, genomic features are overrepresented in endophytic fungi genomes in order to undercover the genomic underpinning of the fungal endophytic lifestyle. Here we compared metabolic gene cluster and mycoparasitism gene diversity across a dataset of thirty-eight Trichoderma genomes representing the full breadth of environmental Trichodermas diverse lifestyles and nutritional modes. We generated four new Trichoderma endophyticum genomes to improve the sampling of endophytic isolates from this genus. As predicted, endophytic Trichoderma genomes contained, on average, more total biosynthetic and degradative gene clusters than non-endophytic isolates, suggesting that the ability to create/modify a diversity of metabolites potential is beneficial or necessary to the endophytic fungi. Still, once the phylogenetic signal was taken in consideration, no particular class of metabolic gene cluster was independently associated with the Trichoderma endophytic lifestyle. Several mycoparasitism genes, but no chitinase genes, were associated with endophytic Trichoderma genomes. Most genomic differences between Trichoderma lifestyles and nutritional modes are difficult to disentangle from phylogenetic divergences among species, suggesting that Trichoderma genomes maybe particularly well-equipped for lifestyle plasticity. We also consider the role of endophytism in diversifying secondary metabolism after identifying the horizontal transfer of the ergot alkaloid gene cluster to Trichoderma.

genomics↗

bioRxiv2022

Metabolic trait means but not correlations differ among fungal endophytes isolated from the same plant species

Trait evolution depends both on the direct fitness effects of specific traits and on indirect selection arising from genetically correlated traits. Although well established in plants and animals, the role of trait correlations in microbial evolution remains a major open question. Here, we tested whether genetic correlations in a suite of metabolic traits are conserved between two sister lineages of fungal endophytes, and whether phenotypic divergence between lineages occurred in the direction of the multivariate trait combination containing the most genetic variance within lineages i.e., the genetic lines of least resistance. We found that while one lineage grew faster across nearly all substrates, lineages differed in their mean response to specific substrates and in their overall multivariate metabolic trait means. The structure of the genetic variance-covariance (G) matrix was conserved between lineages, yet to our surprise, divergence in metabolic phenotypes between lineages was nearly orthogonal to the major axis of genetic variation within lineages, indicating that divergence did not occur along the genetic lines of least resistance. Our findings suggest that the evolutionary genetics of trait correlations in microorganisms warrant further research, and highlight the extensive functional variation that exists at very fine taxonomic scales in host-associated microbial communities.

evolutionary biology↗

bioRxiv2021

Giant Starship elements mobilize accessory genes in fungal genomes

Accessory genes are variably present among members of a species and are a reservoir of adaptive functions. In bacteria, differences in gene distributions among individuals largely result from mobile elements that acquire and disperse accessory genes as cargo. In contrast, the impact of cargo-carrying elements on eukaryotic evolution remains largely unknown. Here, we show that variation in genome content within multiple fungal species is facilitated by Starships, a novel group of massive mobile elements that are 110 kb long on average, share conserved components, and carry diverse arrays of accessory genes. We identified hundreds of Starship-like regions across every major class of filamentous Ascomycetes, including 28 distinct Starships that range from 27-393 kb and last shared a common ancestor ca. 400 mya. Using new long-read assemblies of the plant pathogen Macrophomina phaseolina, we characterize 4 additional Starships whose past and ongoing activities contribute to standing variation in genome structure and content. One of these elements, Voyager, inserts into 5S rDNA and contains a candidate virulence factor whose increasing copy number has contrasting associations with pathogenic and saprophytic growth, suggesting Voyagers activity underlies an ecological trade-off. We propose that Starships are eukaryotic analogs of bacterial integrative and conjugative elements based on parallels between their conserved components and may therefore represent the first known agents of active gene transfer in eukaryotes. Our results suggest that Starships have shaped the content and structure of fungal genomes for millions of years and reveal a new concerted route for evolution throughout an entire eukaryotic phylum.

genomics↗

bioRxiv2021

Gene age predicts the transcriptional landscape of sexual morphogenesis in multicellular fungi

Multicellularity has been one of the most important innovations in the history of life. The role of regulatory evolution in driving transitions to multicellularity is being increasingly recognized; however, patterns and drivers of transcriptome evolution are poorly known in many clades. We here reveal that allele-specific expression, natural antisense transcripts and developmental gene expression, but not RNA editing or a developmental hourglass act in concert to shape the transcriptome of complex multicellular fruiting bodies of fungi. We find that transcriptional patterns of genes are strongly predicted by their evolutionary age. Young genes showed more expression variation both in time and space, possibly because of weaker evolutionary constraint, calling for partially non-adaptive interpretations of evolutionary changes in the transcriptome of multicellular fungi. Gene age also correlated with function, allowing us to separate fruiting body gene expression related to simple sexual development from that potentially underlying complex morphogenesis. Our study highlighted a transcriptional complexity that provides multiple speeds for transcriptome evolution, but also that constraints associated with gene age shape transcriptomic patterns during transitions to complex multicellularity in fungi.

evolutionary biology↗

bioRxiv2020

Repeated gain and loss of a single gene modulates the evolution of vascular pathogen lifestyles

Vascular pathogens travel long distances through host veins leading to life-threatening, systemic infections. In contrast, non-vascular pathogens remain restricted to infection sites, triggering localized symptom development. The contrasting features of vascular and non-vascular diseases suggest distinct etiologies, but the basis for each remains unclear. Here, we show that the hydrolase CbsA acts as a phenotypic switch between vascular and non-vascular plant pathogenesis. cbsA was enriched in genomes of vascular phytopathogenic bacteria in the Xanthomonadaceae family and absent in most non-vascular species. CbsA expression allowed non-vascular Xanthomonas to cause vascular blight while cbsA mutagenesis resulted in reduction of vascular or enhanced non-vascular symptom development. Phylogenetic hypothesis testing further revealed that cbsA was lost in multiple non-vascular lineages and more recently gained by some vascular subgroups, suggesting that vascular pathogenesis is ancestral. Our results overall demonstrate how the gain and loss of single loci can facilitate the evolution of complex ecological traits.

microbiology↗

bioRxiv2020

The architecture of metabolism maximizes biosynthetic diversity in the largest class of fungi

AbstractO_ST_ABSBackgroundC_ST_ABSEcological diversity in fungi is largely defined by metabolic traits, including the ability to produce secondary or "specialized" metabolites (SMs) that mediate interactions with other organisms. Fungal SM pathways are frequently encoded in biosynthetic gene clusters (BGCs), which facilitate the identification and characterization of metabolic pathways. Variation in BGC composition reflects the diversity of their SM products. Recent studies have documented surprising diversity of BGC repertoires among isolates of the same fungal species, yet little is known about how this population-level variation is inherited across macroevolutionary timescales. ResultsHere, we applied a novel linkage-based algorithm to reveal previously unexplored dimensions of diversity in BGC composition, distribution, and repertoire across 101 species of Dothideomycetes, which are considered to be the most phylogenetically diverse class of fungi and are known to produce many SMs. We predicted both complementary and overlapping sets of clustered genes compared with existing methods and identified novel gene pairs that associate with known secondary metabolite genes. We found that variation in BGC repertoires is due to non-overlapping BGC combinations and that several BGCs have biased ecological distributions, consistent with niche-specific selection. We observed that total BGC diversity scales linearly with increasing repertoire size, suggesting that secondary metabolites have little structural redundancy in individual fungi. ConclusionsWe project that there is substantial unsampled BGC diversity across specific families of Dothideomycetes, which will provide a roadmap for future sampling efforts. Our approach and findings lend new insight into how BGC diversity is generated and maintained across an entire fungal taxonomic class.

genomics↗

bioRxiv2018

Discovery of psychoactive plant and mushroom alkaloids in ancient fungal cicada pathogens

Entomopathogenic fungi routinely kill their hosts before releasing infectious spores, but select species keep insects alive while sporulating, which enhances dispersal. Transcriptomics and metabolomics studies of entomopathogens with post-mortem dissemination from their parasitized hosts have unraveled infection processes and host responses, yet mechanisms underlying active spore transmission by Entomophthoralean fungi in living insects remain elusive. Here we report the discovery, through metabolomics, of the plant-associated amphetamine, cathinone, in four Massospora cicadina-infected periodical cicada populations, and the mushroom-associated tryptamine, psilocybin, in annual cicadas infected with Massospora platypediae or Massospora levispora, which appear to represent a single fungal species. The absence of some fungal enzymes necessary for cathinone and psilocybin biosynthesis along with the inability to detect intermediate metabolites or gene orthologs are consistent with possibly novel biosynthesis pathways in Massospora. The neurogenic activities of these compounds suggest the extended phenotype of Massospora that modifies cicada behavior to maximize dissemination is chemically-induced.

ecology↗

bioRxiv2018

Fungal adaptation to plant defenses through convergent assembly of metabolic modules

The ongoing diversification of plant defense compounds exerts dynamic selection pressures on the microorganisms that colonize plant tissues. Evolutionary processes that generate resistance towards these compounds increase microbial fitness by giving access to plant resources and increasing pathogen virulence. These processes entail sequence-based mechanisms that result in adaptive gene functions, and combinatorial mechanisms that result in novel syntheses of existing gene functions. However, the priority and interactions among these processes in adaptive resistance remains poorly understood. Using a combination of molecular genetic and computational approaches, we investigated the contributions of sequence-based and combinatorial processes to the evolution of fungal metabolic gene clusters encoding stilbene cleavage oxygenases (SCOs), which catalyze the degradation of biphenolic plant defense compounds known as stilbenes into monophenolic molecules. We present phylogenetic evidence of convergent assembly among three distinct types of SCO gene clusters containing alternate combinations of phenolic catabolism. Multiple evolutionary transitions between different cluster types suggest recurrent selection for distinct gene assemblages. By comparison, we found that the substrate specificities of heterologously expressed SCO enzymes encoded in different clusters types were all limited to stilbenes and related molecules with a 4-OH group, and differed modestly in substrate range and activity under the experimental conditions. Together, this work suggests a primary role for genome structural rearrangement, and the importance of enzyme modularity, in promoting fungal metabolic adaptation to plant defense chemistry.

evolutionary biology↗