The Little Transib That Could -- and Could Not: Contrasting Invasion Outcomes within a Novel DDE DNA Transposon Lineage

Abstract

Transposable-element (TE) abundance can vary substantially among populations, yet population-specific differences in TE content remain incompletely characterized. Here, we compared known TE families across long-read genome assemblies representing geographically and historically distinct Drosophila melanogaster populations. Several genomes showed pronounced strain-specific expansions, including an exceptional increase in copies of the element historically annotated as Hopper in A6-Wild5B. Investigation of this expansion revealed a previously uncharacterized full-length autonomous element encoding a 648-amino-acid transposase. We named this element Nozomi and its non-autonomous derivative Kodama, corresponding to the published Hopper consensus. Protein-sequence, phylogenetic and structural analyses placed Nozomi within the Transib superfamily and showed close correspondence between the predicted Nozomi transposome and the experimentally determined Helicoverpa zea Transib strand-transfer complex. Autonomous Nozomi copies were restricted to a small number of D. melanogaster genomes, where they were associated with extensive but separate expansions of Kodama. All Kodama elements carried the same precise 1,380-bp internal deletion, with breakpoint microhomology suggesting an alternative end-joining-related origin. Comparative searches identified a broader group of related Transib elements with contrasting invasion histories. Unlike the restricted Nozomi distribution, Hayabusa showed minimal sequence divergence, limited structural decay and broad distribution across the Drosophila suzukii and montium groups, consistent with a recent, highly successful horizontal invasion. Thus, closely related Transib elements can follow markedly different trajectories after horizontal acquisition: Nozomi remained restricted while driving local amplification of a shorter non-autonomous derivative, whereas Hayabusa spread broadly across species.