In the sci-fi classic The Hitchhiker’s Guide to the Galaxy, interstellar explorers hitch rides aboard ships that take them on wild, unexpected journeys across the cosmos. In a new study from researchers at the University of Kiel, fungal genomes tell a similarly whimsical tale: transposable elements (TEs), sometimes dubbed the “jumping genes” of DNA, are hitching rides of their own.
Metarhizium anisopliae, a parasitic fungus in insects, seems to be playing host to TEs that traverse species lines by catching a lift on enormous mobile genetic elements known, quite literally, as “Starships.” These biological vessels cruise through space and cross evolutionary landscapes, carrying cargo that can rewrite genomes, disrupt normal functions, and even influence how virulent a fungus can be.
Scientists have long known that TEs can jump within genomes, but how they manage to leap between species and organisms has remained elusive. With HiFi long-read sequencing, these researchers were able to explore this question with a new level of clarity. The highly accurate and contiguous reads provided by HiFi sequencing allowed them to assemble complex fungal genomes with resolution sufficient to track mobile elements, characterize their movements, and compare their structure across strains and species.
Transposon-rich Starships linked to genome restructuring
The study centers around two strains of the insect-pathogenic fungus Metarhizium anisopliae, named E6 and NE. Using HiFi sequencing on the Revio system, the researchers generated near-complete assemblies of both genomes, capturing chromosomal structure, repeats, and variation with detail sufficient to enable genome-wide comparison.
Looking closely at the two strains, the authors uncovered stark differences in genome organization between the two, including large structural rearrangements and transposon expansion in the NE strain. Digging deeper, the team discovered that these transposons weren’t native to NE. Instead, they appeared to arrive all at once aboard a single Starship element, a giant transposon known to carry genes involved in adaptation and virulence.
This particular Starship, named s00261, carried 73 transposable elements and after arriving in NE, many of these stowaways had duplicated and spread throughout the genome. Nearly 200 highly similar TE copies were found, many clustered near sites where chromosomes appeared to have broken and rejoined, indicating these mobile elements may have contributed to structural remodeling.
Recurring patterns of horizontal transfer in fungal genomes
Curious whether this was an isolated case or part of a broader pattern, the team expanded their analysis to a database of 618 published fungal Starships. Their survey revealed that 74% of these Starships contain TEs, and 16% contain at least one TE with a perfect copy found elsewhere in the genome. Some Starships carried dozens of identical TE copies, with evidence of transposition bursts following their arrival.
The researchers also identified transposable elements shared between Starships from different species. In one case, a DNA sequence encoding reverse transcriptase, an enzyme typically associated with retrotransposons, was nearly identical in Starships across multiple Aspergillus species. These findings suggest that Starships may serve as both delivery systems and repositories, enabling a two-way shuttle of mobile DNA that bypasses traditional species boundaries.
The presence of identical sequences across diverse fungal taxa supports the view that horizontal transfer of TEs in fungi may occur more frequently than previously assumed. Starships appear to facilitate these exchanges, allowing transposons to travel between genomes and potentially reshape them upon arrival.
How genomic hitchhikers can impact fungal virulence
In M. anisopliae NE, the large number of new transposon passengers appeared to influence genome function. Compared to strain E6, NE exhibited reduced pathogenicity in tick hosts. Additional analysis showed that the production of enzymes associated with early stages of host infection was diminished in NE.
This shift correlated with notable changes in genome structure. Genes involved in virulence had been relocated, placed adjacent to transposon insertions, or were near newly formed chromosome junctions. These disruptions are likely to have altered the regulation of gene expression, contributing to the observed loss in pathogenic function.
Starships as drivers of evolutionary novelty
Across fungal species, Starships appear to be facilitating large-scale redistribution of mobile genetic elements. Their activity can promote genome reshaping and introduce variation that affects adaptation and diversification.
By enabling transposable elements to circulate among genomes, Starships may accelerate evolutionary processes. This mechanism allows fungi to explore new genomic configurations, potentially leading to shifts in ecological strategy, phenotype, or speciation.
How HiFi long-read sequencing enables insight into structural complexity
The identification and characterization of Starship-mediated TE movement relied on the accuracy and completeness of HiFi long reads. HiFi sequencing provided the necessary resolution to assemble repeat-rich regions, trace recent TE duplications, and capture chromosomal context around insertions. These attributes were essential for distinguishing between ancient relics and active, high-fidelity TE copies.
The Revio system enabled the full assembly of repetitive and accessory regions, which are often missed by short-read platforms. Starships and their TE cargo typically reside in the genomic dark matter—highly repetitive, structurally complex regions that demand long reads to resolve. With HiFi sequencing, the authors could sequence these regions with sufficient accuracy to detect structural variants and track subtle variation between strains due to TE-hopping, allowing this genomic hitchhiking story to be told in full.
New insights into genome change across fungal evolution
This study provides compelling evidence that mobile genetic elements can move between fungal species by way of Starships, reshaping genomes and influencing functional traits in the process. Long-read HiFi sequencing played a central role in revealing this mechanism, offering the resolution and continuity needed to observe these events and understand their meaning.
By illuminating how transposons travel, multiply, and interact with their genomic surroundings, this research opens new paths for understanding the forces that shape fungal genomes—and how those forces may ripple outward to affect evolution, adaptation, and host interactions.
From parasitic fungi to the broader fungal tree of life, this study illustrates how genetic stowaways can hitch rides across species on Starships, rewriting genomic routes along the way. Long-read HiFi sequencing allowed researchers to capture these voyages in detail, revealing patterns that might otherwise remain hidden.
As we continue exploring the vast expanse of genomics, HiFi sequencing remains essential in pushing the frontier of discovery.
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