Polymorphism of canonical and noncanonical gypsy sequences in different species of Drosophila melanogaster subgroup: possible evolutionary relations

Abstract

Mobile genetic elements constitute a substantial part of eukaryotic genome and play an important role in its organization and functioning. Co-evolution of retrotransposons and their hosts resulted in the establishment of control systems employing mechanisms of RNA interference that seem to be impossible to evade. However, "active" copies of endogenous retrovirus gypsy escape cellular control in some cases, while its evolutionary elder "inactive" variants do not. To clarify the evolutionary relationship between "active" and "inactive" gypsy we combined two approaches: the analysis of gypsy sequences, isolated from G32 Drosophila melanogaster strain and from different Drosophila species of the melanogaster subgroup, as well as the study of databases, available on the Internet. No signs of "intermediate" (between "active" and "inactive") gypsy form were found in GenBank, and four full-size G32 gypsy copies demonstrated a convergence that presumably involves gene conversion. No "active" gypsy were revealed among PCR generated gypsy ORF3 sequences from the various Drosophila species indicating that "active" gypsy appeared in some population of D. melanogaster and then started to spread out. Analysis of sequences flanking gypsy variants in G32 revealed their predominantly heterochromatic location. Discrepancy between the structure of actual gypsy sites in G32 and corresponding sequences in database might indicate significant inter-strain heterochromatin diversity.

Drosophila errantiviruses

“…Extensive data concerning the distribution and polymorphism of errantiviruses in different Drosophila strains and species is accumulated 110 , 111 , 46 , 112 . Moreover, there is a growing amount of data indicating the significant rate of horizontal transfer of errantiviruses between evolutionary distant Drosophila species 113 , 114 .…”

Evolutionary dynamics of the LTR retrotransposons roo and rooA inferred from twelve complete Drosophila genomes

“…The median estimated time since insertion for the elements is shown in Table 1 (column 4 and 7 for roo and rooA elements, respectively) for each genome, and the full age distribution is shown in Figure 2 for roo and rooA in red and blue bars, respectively. These insertion times have to be considered with caution, because it is possible that transposable elements may experience gene conversion [24,25], which compromise this molecular clock. (For instance, the LTR sequences of D. ananassae are identical despite high divergence in their coding regions, a disagreement that might be explained by gene conversion of the LTR sequences.)…”

Amplification of “defective” retrotransposon gtwin in D. melanogaster strain carrying large complex chromosomal aberration

“…On the contrary to gypsy, which is present in G32 in a few copy number and all of them, except one, are located in heterochromatin (Salenko et al 2008), gtwin is abundant in euchromatic regions. Usually silent transposable elements are substantially eliminated from euchromatin, but not heterochromatin (Fontanillas et al 2007;Fablet et al 2007).…”

“…The model explaining the formation of cellular immunity to TE activity suggests the following events: introduction of novel-to-the-host transposable element (Ludwig and Loreto 2007) followed by its active transpositions and alterations until it enters heterochromatic piRNA cluster resulting in its silencing by RNAi pathways Bergman et al 2006;Kotnova et al 2007;Salenko et al 2008).…”