搜索结果：Starships

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 toward 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.

There is increasing evidence that mobile genetic elements can drive the emergence of pathogenic fungal species by moving virulence genes horizontally. The 14 kbp ToxhAT transposon was shown to move the necrotrophic effector, ToxA, horizontally between wheat pathogens, namely Parastagonospora nodorum, Pyrenophora tritici-repentis, and Bipolaris sorokiniana. All three species utilize the ToxA protein to infect wheat. Previous work found ToxhAT in distinct chromosomal positions in two B. sorokiniana isolates, indicating that the transposon remains active in this species. Here, we confirm the movement of ToxhAT using long-read sequencing of eight new and one previously published B. sorokiniana isolates. One event of independent transposition of ToxhAT was observed, and target site duplications of "TA" were identified, confirming that this is an active transposon in this species that likely falls into the Tc1/Mariner transposon family. We propose renaming this non-autonomous transposon to ToxTA. Whole genome analysis revealed that ToxTA is a passenger embedded in a much larger, conserved 170-196 kbp mobile genetic element. This element, termed Sanctuary, belongs to the newly described Starship transposon superfamily. This classification is based on the presence of direct repeats, empty insertion sites, a putative tyrosine recombinase gene, and other features of Starship transposons. We also show that ToxTA has been independently acquired by two different Starships, Sanctuary and Horizon, which share little to no sequence identity, outside of ToxTA. This classification makes Horizon and Sanctuary part of a growing number of Starships involved in the horizontal gene transfer of adaptive genetic material between fungal species.IMPORTANCEThe work presented here expands our understanding of a novel group of mobile genetic elements called Starships that facilitate the horizontal exchange of numerous genes between fungal pathogens. Our analysis shows that Sanctuary and ToxTA are both active transposons within the Bipolaris sorokiniana genome. We also show that the smaller ToxTA transposon has been independently acquired by two different Starships, namely Sanctuary in B. sorokiniana and Horizon in Pyrenophora tritici-repentis and Parastagonospora nodorum. Outside of ToxTA, these two Starships share no sequence identity. The acquisition of ToxTA by two different mobile elements in three different fungal wheat pathogens demonstrates how horizontal transposon transfer is driving the evolution of virulence in these important wheat pathogens.

Starships form a recently discovered superfamily of giant transposons in Pezizomycotina fungi, implicated in mediating horizontal transfer of diverse cargo genes between fungal genomes. Their elusive nature has long obscured their significance, and their impact on genome evolution remains poorly understood. Here, we reveal a surprising abundance and diversity of Starships in the phytopathogenic fungus Verticillium dahliae. Remarkably, Starships dominate the plastic genomic compartments involved in host colonization, carry multiple virulence-associated genes, and exhibit genetic and epigenetic characteristics associated with adaptive genome evolution. Phylogenetic analyses suggest extensive horizontal transfer of Starships between Verticillium species and, strikingly, from distantly related Fusarium fungi. Finally, homology searches and phylogenetic analyses suggest that a Starship contributed to de novo virulence gene formation. Our findings illuminate the profound influence of Starship dynamics on fungal genome evolution and the development of virulence.

New outbreaks of fungal diseases are an ongoing threat to global agriculture. One known mechanism generating novel diseases is the horizontal transfer of genes between fungal species. Yet we have little understanding of how such transfers are mediated. Here, we raise the possibility that Starships, a recently discovered superfamily of giant transposable elements, might be responsible. To support this hypothesis, we discuss three potential cases where Starships may have mediated disease outbreaks. These are ToxA in wheat pathogens, genes underlying Glomerella leaf spot on apple trees, and the defoliating gene cluster of Verticillium dahliae on cotton. In the Verticillium example, we provide strong evidence for a Starship-mediated mechanism: disease-promoting genes reside in closely related Starships across distantly related species. We aim to spark interest in Starships' roles in fungal pathogens and how this knowledge could inform disease management strategies.

Defoliating (D) strains of the vascular wilt fungus Verticillium dahliae cause severe yield losses in cotton and olive, but the genetic basis of this pathotype remained unknown. Using comparative genomics, functional genetics, structural analysis, and phylogenomics, we identify a D-pathotype-specific genomic region encoding two duplicated secreted effector genes. Simultaneous deletion of both copies abolishes pathogenicity and defoliation in cotton and olive, and affects virulence in Nicotiana benthamiana and Arabidopsis thaliana. Expression of the effector in non-defoliating strains induces cotton defoliation, and purified protein causes wilting and leaf drop. Structural analyses reveal a previously uncharacterized protein fold conserved across Verticillium and Fusarium species, with evidence of functional diversification and host specificity. Phylogenomic and genomic context analyses indicate repeated horizontal transfer mediated by giant transposable elements known as Starships. Together, these findings identify the D effector as a central determinant of defoliation and virulence and show how Starship-mediated gene transfer drives emergence of an agriculturally important fungal trait.

Starships are a recently established superfamily of giant cargo-mobilizing transposable elements in the fungal subphylum Pezizomyotina (phylum Ascomycota). To date, Starship elements have been identified up to ∼700 kbp in length and carry hundreds of accessory genes, which can confer both beneficial and deleterious traits to the host genome. Classification of Starship elements is centered on the tyrosine recombinase gene that mobilizes the element, termed the captain. We contribute a new perspective to Starship relatedness by using an alignment-free k-mer-based phylogenetic tree-building method, which can infer relationships between elements in their entirety, including both active and degraded elements and irrespective of high variability in element length and cargo content. In doing so we found that relationships between entire Starships differed from those inferred from captain genes and revealed patterns of element relatedness corresponding to host taxonomy. Using Starships from root/soil-dwelling Gaeumannomyces species as a case study, we found that k-mer -based relationships correspond with the similarity of cargo gene content. Our results provide insights into the prevalence of Starship-mediated horizontal transfer events. This novel application of a k-mer -based phylogenetics approach overcomes the issue of how to represent and compare highly variable Starship elements as a whole, and in effect shifts the perspective from a captain to a cargo-centered concept of Starship identity.

Transposable elements drive genomic changes and are mobilized by specific nucleases. Among them are tyrosine recombinases (YRs), which mediate DNA cleavage and rejoining. YR-encoding elements, such as DIRS, Ngaro, Crypton, and Starships, occur in diverse eukaryotes and display characteristic terminal repeat structures that enable their mobility. Their activity in fungi results in large-scale chromosomal rearrangements, horizontal gene transfer, and the movement of genes for pathogenicity, symbiosis, and secondary metabolism. Other YR-elements underwent domestication giving rise to ZMYM transcriptional regulators in animals. We identify and characterize the fungal members of the CryptonA lineage of tyrosine recombinase-encoding transposons, which we name Glomhoppers. These elements encode a DUF3504 domain that retains the conserved catalytic residues characteristic of active YRs. In contrast, many domesticated animal DUF3504 homologs lack key catalytic residues, whereas active CryptonA transposon-derived DUF3504 elements have also been reported in animals. Structural modeling suggested the presence of a putative DNA-binding groove, and phylogenetic analyses placed Glomhoppers as a well-supported subclade within the CryptonA lineage, together with domesticated ZMYM-like derivatives. Across 72 Glomeromycota genomes, ~ 1,800 Glomhopper copies were identified, representing a subset of DUF3504-containing loci, mostly truncated or intronized, but ~ 25% lacked introns and maintained intact catalytic motifs, consistent with potential mobility. Genomic context analysis revealed their frequent localization within highly repetitive compartments, often alongside other transposon families. Expression data indicated that intronless variants respond to stress, reaching several-fold higher expression levels than intron-containing forms, especially in Gigaspora species. This is consistent with the possibility that a subset of Glomhoppers remains transcriptionally active and potentially mobilizable, although direct evidence of transposition is lacking. Our findings establish Glomhoppers as a novel subfamily of DUF3504-encoding CryptonAs. The lineage-specific distribution, intron variation, and stress-responsive expression of Glomhoppers suggest divergent evolutionary trajectories, potentially including both mobility and domestication. These elements expand the known diversity of YR transposons and highlight DUF3504 as a candidate domain for further functional and evolutionary studies.

The virulence gene ToxA has been proposed to be horizontally transferred between three fungal wheat pathogens (Parastagonospora nodorum, Pyrenophora tritici-repentis, and Bipolaris sorokiniana) as part of a conserved ~14 kb ToxhAT transposon. Here, our analysis of 2137 fungal species-representative assemblies revealed that the ToxA gene is an isolate of Alternaria ventricosa and shows a remarkable 99.5% similarity to those found in B. sorokiniana and P. tritici-repentis. Analysis of the regions flanking ToxA within A. ventricosa revealed that it was embedded within a 14 kb genomic element nearly identical to the corresponding ToxhAT regions in B. sorokiniana, P. nodorum, and P. tritici-repentis. Comparative analysis further showed that ToxhAT in A. ventricosa resides within a larger mobile genetic element, which we identified as a member of the Starship transposon superfamily, named Frontier. Our analysis demonstrated that ToxhAT has been independently captured by three distinct Starships-Frontier, Sanctuary, and Horizon-which, despite having minimal sequence similarity outside of ToxhAT, facilitate its mobilization. These findings place Frontier, Sanctuary, and Horizon within a growing class of Starships implicated in the horizontal transfer of adaptive genes among fungal species. Moreover, we identified three distinct HGT events involving ToxA across these four fungal species, reinforcing the hypothesis of a single evolutionary origin for the ToxhAT transposon. These findings underscore the pivotal role of transposon-mediated HGT in the adaptive evolution of eukaryotic pathogens, offering new insights into how transposons facilitate genetic exchange and shape host-pathogen interactions in fungi.

Horizontal gene transfer (HGT) disseminates genetic information between species and is a powerful mechanism of adaptation. Yet, we know little about its underlying drivers in eukaryotes. Giant Starship transposons have been implicated as agents of fungal HGT, providing an unprecedented opportunity to reveal the evolutionary parameters behind this process. Here, we characterize the ssf gene cluster, which contributes to formaldehyde resistance, and use it to demonstrate how mobile element evolution shapes fungal adaptation. We found that ssf clusters have been acquired by various distantly related Starships, which each exhibit multiple instances of horizontal transfer across fungal species (at least nine events, including between different taxonomic orders). Many ssf clusters have subsequently integrated into their host's genome, illustrating how Starships shape the evolutionary trajectory of fungal hosts beyond any single transfer. Our results demonstrate the key role Starships play in mediating rapid and repeated adaptation via HGT, elevating the importance of mobile element evolution in eukaryotic biology.

The genomic diversity of many fungal species is augmented by accessory chromosomes, which are variably present in individual strains. These genomic regions evolve rapidly, accumulating genes important in pathogenicity but also harbor a significant number of transposable elements. This duality suggests a trade-off: accessory chromosomes provide infection-related benefits while otherwise being deleterious due to their highly repetitive nature and contributions to genomic instability. Despite this, accessory chromosomes often appear to be stably maintained even when strains are grown on media, with no plant host. Previously, we had observed that genes homologous to meiotic drive toxin/antidote proteins from Podospora anserina (Spoks) are abundant on accessory chromosomes in various Fusarium species. Using a functionality screen in yeast, we demonstrate that some of these homologs have active toxin and antidote properties. We propose that these selfish genes could maintain accessory chromosomes during vegetative growth and may influence their spread via parasexual cycles. Finally, as Spok genes are found on the newly described transposable element superfamily Starships, we also present a model for how these transposable elements could play a role in forming accessory chromosomes and regions. These results illuminate a mysterious facet of fungal biology, a key step towards describing the origin, spread, and maintenance of pathogenicity in many fungal species.

Recombination suppression can evolve in sex or mating-type chromosomes, or in 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 to be partially physically linked to the mating-type (MAT) locus based on segregation analyses. Using hundreds of available C. parasitica genomes and generating new high-quality genome assemblies, we show that a ca. 1.2 Mb genomic region proximal to the mating-type locus lacks recombination, with the segregation of two highly differentiated haplotypes in balanced proportions in invasive populations. High-quality genome assemblies further revealed an inversion in one of the haplotypes in the invaded range. The two haplotypes were estimated to have diverged 1.5 million years ago, and each harboured specific genes, some of which likely belonging to Starships. These are large transposable elements, mobilized by tyrosine recombinases, able to move accessory genes, and involved in adaptation in multiple fungi. The MAT-proximal region carried genes upregulated under virus infection or vegetative incompatibility reaction. In the native range, the MAT-proximal region also appeared to have a different evolutionary history than the rest of the genome. In all continents, the MAT-Proximal region was enriched in nonsynonymous substitutions, in gene presence/absence polymorphism, in tyrosine recombinases and in transposable elements. This study thus sheds light on a case of a large nonrecombining region partially linked to a mating compatibility locus, likely maintained by balancing selection on differentiated haplotypes, possibly involved in adaptation in a devastating tree pathogen.

Gaeumannomyces tritici is responsible for take-all disease, one of the most important wheat root threats worldwide. High-quality annotated genome resources are sorely lacking for this pathogen, as well as for the closely related antagonist and potential wheat take-all biocontrol agent, G. hyphopodioides. As such, we know very little about the genetic basis of the interactions in this host-pathogen-antagonist system. Using PacBio HiFi sequencing technology we have generated nine near-complete assemblies, including two different virulence lineages for G. tritici and the first assemblies for G. hyphopodioides and G. avenae (oat take-all). Genomic signatures support the presence of two distinct virulence lineages in G. tritici (types A and B), with A strains potentially employing a mechanism to prevent gene copy-number expansions. The CAZyme repertoire was highly conserved across Gaeumannomyces, while candidate secreted effector proteins and biosynthetic gene clusters showed more variability and may distinguish pathogenic and non-pathogenic lineages. A transition from self-sterility (heterothallism) to self-fertility (homothallism) may also be a key innovation implicated in lifestyle. We did not find evidence for transposable element and effector gene compartmentalisation in the genus, however the presence of Starship giant transposable elements may contribute to genomic plasticity in the genus. Our results depict Gaeumannomyces as an ideal system to explore interactions within the rhizosphere, the nuances of intraspecific virulence, interspecific antagonism, and fungal lifestyle evolution. The foundational genomic resources provided here will enable the development of diagnostics and surveillance of understudied but agriculturally important fungal pathogens.

Cargo-mobilizing mobile elements (CMEs) are genetic entities that faithfully transpose diverse protein coding sequences. Although common in bacteria, we know little about eukaryotic CMEs because no appropriate tools exist for their annotation. For example, Starships are giant fungal CMEs 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 CME annotation. We applied starfish to 2 899 genomes of 1 649 fungal species and found that starfish recovers known Starships with 95% combined precision and recall 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.

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 newly discovered 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 to 393 kb and last shared a common ancestor ca. 400 Ma. Using new long-read assemblies of the plant pathogen Macrophomina phaseolina, we characterize four additional Starships whose 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 Voyager's 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 dedicated 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.

To date, most reports of horizontal gene transfer (HGT) in fungi rely on genome sequence data and are therefore an indirect measure of HGT after the event has occurred. However, a novel group of class II-like transposons known as Starships may soon alter this status quo. Starships are giant transposable elements that carry dozens of genes, some of which are host-beneficial, and are linked to many recent HGT events in the fungal kingdom. These transposons remain active and mobile in many fungal genomes and their transposition has recently been shown to be driven by a conserved tyrosine-recombinase called 'Captain'. This perspective explores some of the remaining unanswered questions about how these Starship transposons move, both within a genome and between different species. We seek to outline several experimental approaches that can be used to identify the genes essential for Starship-mediated HGT and draw links to other recently discovered giant transposons outside of the fungal kingdom.