Starship giant transposable elements cluster by host taxonomy using kmer-based phylogenetics

Starships are a recently established superfamily of giant cargo-mobilising transposable elements in the fungal subphylum Pezizomyotina (phylum Ascomycota). To date, Starship elements have been identified up to ∼700 Kbp in length and carrying hundreds of accessory genes, which can confer both beneficial and deleterious traits to the host genome. Classification of Starship elements has been centred on the tyrosine recombinase gene that mobilises the element, termed the captain. We contribute a new perspective to Starship classification by using an alignment-free kmer-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 Gaeumannomyces species as a case study, we found that kmer-based relationships correspond with similarity of cargo gene content. Our results suggest that Starship-mediated horizontal transfer events are frequent between species within the same genus but are less prevalent across larger host evolutionary distances. This novel application of a kmer-based phylogenetics approach overcomes the issue of how to represent and compare highly variable Starships elements as a whole, and in effect shifts the perspective from a captain to a cargo-centred concept of Starship identity.

SUMMARY We applied a kmer-based phylogenetic classification approach to giant Starship cargo-mobilising elements from species across the Pezizomycotina (Ascomycota, Fungi). We found Starship elements to frequently cluster according to host taxonomy, suggesting horizontal transfer of elements is less common across larger evolutionary distances. Kmer-based phylogenetics approaches show promise for both element classification and to inform our understanding of the evolution of Starships and other giant cargo-mobilising elements.