Evolutionary history of LTR-retrotransposons among 20 Drosophila species

Abstract

BackgroundThe presence of transposable elements (TEs) in genomes is known to explain in part the variations of genome sizes among eukaryotes. Even among closely related species, the variation of TE amount may be striking, as for example between the two sibling species, Drosophila melanogaster and D. simulans. However, not much is known concerning the TE content and dynamics among other Drosophila species. The sequencing of several Drosophila genomes, covering the two subgenus Sophophora and Drosophila, revealed a large variation of the repeat content among these species but no much information is known concerning their precise TE content. The identification of some consensus sequences of TEs from the various sequenced Drosophila species allowed to get an idea concerning their variety in term of diversity of superfamilies but the used classification remains very elusive and ambiguous.ResultsWe choose to focus on LTR-retrotransposons because they represent the most widely represented class of TEs in the Drosophila genomes. In this work, we describe for the first time the phylogenetic relationship of each LTR-retrotransposon family described in 20 Drosophila species, compute their proportion in their respective genomes and identify several new cases of horizontal transfers.ConclusionAll these results allow us to have a clearer view on the evolutionary history of LTR retrotransposons among Drosophila that seems to be mainly driven by vertical transmissions although the implications of horizontal transfers, losses and intra-specific diversification are clearly also at play.Electronic supplementary materialThe online version of this article (doi:10.1186/s13100-017-0090-3) contains supplementary material, which is available to authorized users.

DeviaTE: Assembly‐free analysis and visualization of mobile genetic element composition

“…TE composition varies substantially among and within species (Bargues & Lerat, ; Bergman, Han, Nelson, Bondarenko, & Kozeretska, ), which could have important biological consequences. Variation in TE abundance among populations may be the hallmark of a recent TE invasion (Anxolabéhère, Kidwell, & Periquet, ; Kofler, Hill, Nolte, Betancourt, & Schlötterer, ) and may even drive speciation (Serrato‐Capuchina & Matute, ).…”

Evolutionary history and classification of Micropia retroelements in Drosophilidae species

“…Phylogenetic analyses were performed using the amino acid alignment obtained after resolving all gaps and leaving all nucleotide sequences in frame. Fifty amino acid sequences belonging to each of the five main clades recently established by [15] for the Micropia/Sacco group within Ty3/Gypsy were selected from the alignment provided by the authors. These sequences were included as a “taxonomic framework” to guide conclusions related to new Micropia sequences in our phylogenetic analyses, in which a Copia-like transposable element sequence from D. melanogaster (GenBank access number X01472) was used as outgroup.…”

“…A large fraction of the genomes of most eukaryotes is composed by TEs known as retroelements [12, 13, 14], some of which belong to the LTR order. Phylogenetic analyses of such retroelements reveal an evolutionary history consisting mainly of vertical transmissions and intraspecific diversification [15]. However, autonomous TEs are able to invade naïve genomes through horizontal transposon transfers (HTT), in which they make copies of themselves and evade host defense systems before becoming fully silenced by genomic anti-TE mechanisms [16, 17].…”

“…A growing number of studies have identified HTTs using distinct analysis strategies [15, 16, 23, 24, 25]. For instance, a patchy taxonomic distribution among monophyletic species is expected if TEs are moving horizontally rather than being vertically inherited.…”

“…Until recently, there were only four best-characterized Micropia elements, and these were found in the genomes of D. hydei (named dhMiF2 and dhMiF8) and D. melanogaster (named Dm11 and Dm2) [33, 34, 35]. Recently, complete and probably active Micropia reference sequences were found in the genomes of D. simulans and D. sechellia [15]. Nevertheless, Micropia related sequences are also present in the genomes of several Drosophila and Zaprionus species, showing an irregular pattern of distribution [36, 37, 38, 39, 40, 41].…”