Phylogenetic analysis of the superfamily reveals the unexplored diversity of -like elements.

Background: transposons are widespread DNA transposable elements (TEs) that have made important contributions to the evolution of host genomic complexity in metazoans. However, the evolution and diversity of the superfamily remains poorly understood. Following recent developments in genome sequencing and the availability of a wealth of new genomes, TEs have been identified in many new taxa across the eukaryotic tree of life. To date, the majority of studies focussing on / elements have considered only a single host lineage or just a small number of host lineages. Thus, much remains to be learnt about the evolution of TEs by performing analyses that consider elements that originate from across host diversity.

Results: We mined the non-redundant database of NCBI using BLASTp searches, with transposase sequences from a diverse set of reference elements as queries. A total of 5158 elements were retrieved and used to reconstruct evolutionary relationships within the superfamily. The resulting phylogeny is well resolved and includes several new groups of elements. In particular, we identify a new family of plant-genome restricted elements, which we call . We also show that the family is much larger and more diverse than previously appreciated, and we review evidence for a potential revision of its status to become a separate superfamily.

Conclusions: Our study provides an overview of phylogeny and summarises the impressive diversity of TEs among sequenced eukaryotes. TEs are successful in a wide range of eukaryotes, especially unikonts (the taxonomic supergroup containing Amoebozoa, Opisthokonta, Breviatea, and Apusomonadida). In particular, ecdysozoa, and especially arthropods, emerge as important hosts for elements (except the family). Meanwhile, the family, which is by far the largest family, also includes many elements from fungal and chordate genomes. Moreover, there is evidence of the repeated exaptation of elements in vertebrates, including humans, in addition to the well-known example of . Collectively, our findings provide a considerable advancement in understanding of elements, and more generally they suggest that much work remains to improve understanding of the diversity and evolution of DNA TEs.