Evolutionary study of the 412/mdg1 lineage of the Ty3/gypsy group of LTR retrotransposons in Diptera

LTR-retrotransposons are structurally similar to retroviruses, as they possess the enzymes reverse transcriptase, Ribonuclease H, integrase, proteinase, and the gag gene and are flanked by long terminal repeats (LTRs). The 412/mdg1 lineage, belonging to the Ty3/Gypsy group, consists of the TEs 412, mdg1, stalker, pilgrim, and blood. The 412/mdg1 lineage is distinguished from the others in the gypsy group in that it has small ORFs at the beginning of the TE and is highly similar to the pol ORF among the TEs that make up the lineage. In this study, our aim was to elucidate the evolutionary history of the 412/mdg1 lineage in the 127 dipteran genomes available to date, and the characteristics of the sequences in each genome. We used the canonical TE 412 probe described in Drosophila melanogaster as the query. We found sequences homologous to the 412/mdg1 lineage restricted to the suborder Brachycera. These sequences are widely distributed in drosophilids but are also present in other groups of flies. We note the presence of the 412/mg1 lineage in tsetse flies (Glossina). Furthermore, our results showed an elaborate evolutionary history for the pol ORF in the 412/mdg1 lineage of the LTR-Retrotransposon.

Evolutionary history and classification of Micropia retroelements in Drosophilidae species

Current knowledge indicates TEs have been 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 hypothesis frequently result from studies with model species, and Drosophila detaches as a great model organism to the study of TEs. Micropia belongs to the Ty3/Gypsy group of 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 analyzed its presence in the genome of several species from natural populations and then, based on searches within genomic databases, we retrieved Micropia-like sequences from distinct Drosophilidae species genomes. We expanded the knowledge of Micropia distribution within Drosophila, and detected an array of divergent sequences, which allowed subdividing this retroelement in 20 subfamilies. Even so, a patchy distribution of Micropia sequences within the Drosophilidae phylogeny could be identified combined with incongruences of the species and the Micropia phylogenies. Comparing dS values between Micropia and host nuclear sequences, we found several cases of unexpected high levels of similarity between Micropia sequences found in divergent species. All these findings propose a hypothesis to the evolution of Micropia within Drosophilidae, including several VTTs and HTTs events, associated to ancestral polymorphisms and recurrent Micropia sequences diversification.