Evolutionary history and classification of Micropia retroelements in Drosophilidae species

Abstract

25Current knowledge indicates TEs have been shaping the evolution of genomes and host 26 species, contributing to the creation of new genes and promoting rearrangements 27 frequently associated with new regulatory networks. Support for these hypothesis 28 frequently result from studies with model species, and Drosophila detaches as a great 29 model organism to the study of TEs. Micropia belongs to the Ty3/Gypsy group of LTR 30 retroelements, and comprises one of the least studied Drosophila transposable elements. 31 In this study, we assessed the evolutionary history of Micropia within Drosophilidae, 32 while trying to assist in the classification of this TE. At first, we analyzed its presence in 33 the genome of several species from natural populations and then, based on searches 34 within genomic databases, we retrieved Micropia-like sequences from distinct 35 Drosophilidae species genomes. We expanded the knowledge of Micropia distribution 36 within Drosophila, and detected an array of divergent sequences, which allowed 37 subdividing this retroelement in 20 subfamilies. Even so, a patchy distribution of 38 Micropia sequences within the Drosophilidae phylogeny could be identified combined 39 with incongruences of the species and the Micropia phylogenies. Comparing dS values 40 between Micropia and host nuclear sequences, we found several cases of unexpected 41 high levels of similarity between Micropia sequences found in divergent species. All 42 these findings propose a hypothesis to the evolution of Micropia within Drosophilidae, 43 including several VTTs and HTTs events, associated to ancestral polymorphisms and 44 recurrent Micropia sequences diversification.45 46 Key words: transposable elements diversification; LTR retrotransposon subfamilies; 47 cardini group; repleta group; melanogaster group; horizontal transposon transfer; 48 vertical transposon transfer 50Since Barbara McClintock publication of maize genes moving around the 51 genome, transposable elements (TEs) went from junk to pivotal characters in the control 52 and evolution of genomes. The discovery of unexpected high amounts of TEs in the 53 genome of distinct species has pointed out toward functions of TEs on these genomes 54 [1, 2, 3]. In fact, current knowledge indicates TEs have been shaping the evolution of 55 genomes and host species [4], contributing to the creation of new genes [5, 6] and 56 promoting rearrangements frequently associated with new regulatory networks [7, 8 9]. 57More than this, there is even evidence that TEs may assist in the control of embryonic 58 development [9, 10] and genomic plasticity [11]. 59A large fraction of the genomes of most eukaryotes is composed by TEs known 60 as retroelements [12, 13, 14], some of which belong to the LTR order. Phylogenetic 61 analyses of such retroelements reveal an evolutionary history consisting mainly of 62 vertical transmissions and intraspecific diversification [15]. However, autonomous TEs 63 are able to invade naïve genomes through horizontal transposon ...