Starship giant transposable elements cluster by host taxonomy using k-mer-based phylogenetics.

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.