Transposable elements hitchhike on Starships across fungal genomes

Horizontal transfer (HT) of transposable elements (TEs) is a widespread phenomenon in eukaryotes and is often associated with bursts of TE activity. This process profoundly influences genome evolution by introducing novel genetic material and driving genetic variation. However, the precise mechanisms facilitating these transfers remain largely uncharacterized. Here, we report a recent TE burst in the insect-pathogenic fungus Metarhizium anisopliae . Our analysis reveals that the actively transposing TEs were introduced via hitchhiking on a so-called Starship—a class of large, themselves horizontally transferable transposons found within the fungal subphylum Pezizomycotina . This particular Starship carried 73 TEs, 43 of which exhibited increased copy numbers in the recipient genome, including 508 perfect copies. This expansion triggered extensive structural reshuffling across all chromosomes and led to the formation of a novel chromosome. Remarkably, this structural reorganization was associated with a dramatic phenotypic shift: the loss of pathogenicity. Expanding our analysis to other fungi, we found that Starship-mediated horizontal transfer of TEs is a general phenomenon. A majority (74%) of 618 published Starships also harbor TEs, which can constitute up to 72% of their content. Moreover, Starships serve as sources of actively transposing TEs: 16% of Starships carried at least one TE with a perfect copy found elsewhere in the genome, and identical TEs were observed on Starships from different species. Collectively, our results establish Starships as major vectors of horizontal TE transfer within Pezizomycotina and further highlight their profound impact on recipient fungal genomes through TE piggybacking.