Evolutionary history and classification of Micropia retroelements in Drosophilidae species

Abstract

Transposable elements (TEs) have the main role in shaping the evolution of genomes and host species, contributing to the creation of new genes and promoting rearrangements frequently associated with new regulatory networks. Support for these hypotheses frequently results from studies with model species, and Drosophila provides a great model organism to the study of TEs. Micropia belongs to the Ty3/Gypsy group of long terminal repeats (LTR) retroelements and comprises one of the least studied Drosophila transposable elements. In this study, we assessed the evolutionary history of Micropia within Drosophilidae, while trying to assist in the classification of this TE. At first, we performed searches of Micropia presence in the genome of natural populations from several species. Then, based on searches within online genomic databases, we retrieved Micropia-like sequences from the genomes of distinct Drosophilidae species. We expanded the knowledge of Micropia distribution within Drosophila species. The Micropia retroelements we detected consist of an array of divergent sequences, which we subdivided into 20 subfamilies. Even so, a patchy distribution of Micropia sequences within the Drosophilidae phylogeny could be identified, with incongruences between the species phylogeny and the Micropia phylogeny. Comparing the pairwise synonymous distance (dS) values between Micropia and three host nuclear sequences, we found several cases of unexpectedly high levels of similarity between Micropia sequences in divergent species. All these findings provide a hypothesis to the evolution of Micropia within Drosophilidae, which include several events of vertical and horizontal transposon transmission, associated with ancestral polymorphisms and recurrent Micropia sequences diversification.

Horizontal Transposon Transfer and Their Ecological Drivers: The Case of Flower-breeding Drosophila

“…Among LTR elements, Gypsy was recovered as the most abundant TE in all species of the bromeliae group and also in D. incompta ( Fonseca et al 2019 ). The LTR-Gypsy superfamily is widely distributed and conserved within Drosophila , especially within the Sophophora subgenus, indicating an old diversification associated with numerous recent HT events ( Herédia et al 2007 ; Loreto et al 2008 ; Cordeiro et al 2019 ). This study shows that it is also the most abundant TE in different FBD species of the Siphlodora subgenus.…”