The ongoing invasion of the endogenous retrovirus Kuruka in natural Drosophila melanogaster populations

Abstract

Transposable elements (TEs) are mobile DNA sequences that can proliferate within host genomes, occasionally capable of crossing species boundaries via horizontal transfer (HT). Here, we report the discovery and characterization of Kuruka, a recently invading TE in natural D. melanogaster populations. Kuruka encodes an envelope protein and belongs to the gypsy/gypsy superfamily, also called insect endogenous retroviruses. Analysis of over 1000 D. melanogaster genomes revealed that Kuruka first appeared in sub-Saharan Africa in 2010. Kuruka had spread to Asia, Europe and America in 2017–2019, and is still actively invading Europe and Oceania as of 2021. Phylogenomic analyses suggest that Kuruka entered in D. melanogaster via a recent HT from an Afrotropical Drosophila species, most likely D. erecta. This provides an example of recent TE transfer between an Afrotropical donor species and D. melanogaster. In D. erecta, Kuruka has a single genomic insertion, which is located within flamenco, a master regulator of TE activity. The presence of an active host defense (piRNAs) suggests that Kuruka is silenced in D. erecta. By capturing an invasion still in progress, our study sheds light on the processes that govern the emergence, establishment, and spread of TEs across species boundaries. Transposable elements are mobile DNA sequences that can copy themselves and spread between species. This study finds that Kuruka, a retrovirus-like transposon, invaded Drosophila melanogaster within the last decade and is still spreading worldwide.