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

Transposable elements are mobile DNA sequences capable of proliferating within host genomes, occasionally capable of crossing species boundaries via horizontal transfer (HT). Here, we report the discovery and characterization of Kuruka, a newly invading endogenous retrovirus in natural D. melanogaster populations. Kuruka encodes an envelope protein and belongs to the gypsy /gypsy superfamily. Analysis of over 1000 D. melanogaster genomes revealed that Kuruka first appeared in sub-Saharan Africa in 2010. By 2017-2019 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 is the first case of a recent HT from an Afrotropical donor species to 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. Our findings establish Kuruka as a valuable model for studying the early stages of TE invasions and the dynamics of genome defense in real time.