Drosophila Euchromatic LTR Retrotransposons are Much Younger Than the Host Species in Which They Reside

Abstract

The recent release of the complete euchromatic genome sequence of Drosophila melanogaster offers a unique opportunity to explore the evolutionary history of transposable elements (TEs) within the genome of a higher eukaryote. In this report, we describe the annotation and phylogenetic comparison of 178 full-length long terminal repeat (LTR) retrotransposons from the sequenced component of the D. melanogaster genome. We report the characterization of 17 LTR retrotransposon families described previously and five newly discovered element families. Phylogenetically, these families can be divided into three distinct lineages that consist of members from the canonical Copia and Gypsy groups as well as a newly discovered third group containing BEL, mazi, and roo elements. Each family consists of members with average pairwise identities Ն99% at the nucleotide level, indicating they may be the products of recent transposition events. Consistent with the recent transposition hypothesis, we found that 70% (125/178) of the elements (across all families) have identical intra-element LTRs. Using the synonymous substitution rate that has been calculated previously for Drosophila (.016 substitutions per site per million years) and the intra-element LTR divergence calculated here, the average age of the remaining 30% (53/178) of the elements was found to be 137,000 ±89,000 yr. Collectively, these results indicate that many full-length LTR retrotransposons present in the D. melanogaster genome have transposed well after this species diverged from its closest relative Drosophila simulans, 2.3 ± .3 million years ago.

Molecular Spectrum of Spontaneous de Novo Mutations in Male and Female Germline Cells of Drosophila melanogaster

“…The insertion was $5 kb long, which is comparable to the full length of the Transpac element (5249 bp; AF222049). Duplication of the four-nucleotide target sequence, 59-ATAT-39, was observed at the boundary, which is also consistent with the previous study (Bowen and McDonald 2001).…”

“…We determined the sequences surrounding the insertion site and found the insertion of a retrotransposon, Transpac, in exon 3 (supplemental Figure 1). Transpac is a member of the gypsy group of LTR retrotransposons in Drosophila (Bowen and Mcdonald 2001). The insertion was $5 kb long, which is comparable to the full length of the Transpac element (5249 bp; AF222049).…”

The Evolutionary History of Drosophila buzzatii. XXXVI. Molecular Structural Analysis of Osvaldo Retrotransposon Insertions in Colonizing Populations Unveils Drift Effects in Founder Events

“…Second, the age estimation of these insertions, ranging between 0.2 (A4 LTR and B9 RT regions) and 1.5 MY (A4 complete sequence), is much older than the age (300 years) of colonization (Fontdevila 1989), reinforcing the conclusion that the occupancy profile is due to genetic drift. It is important to note that even if these insertions are older than the colonization event, they are young in evolutionary time and these age estimates support Bowen and Mcdonald's (2001) conclusion that Drosophila euchromatic LTR retrotransposons are evolutionarily young. Third, if independent transpositions occur, it is difficult to explain the identical sequences of the 2F4a and 5A4b insertions across populations, unless only one Osvaldo copy is active…”

“…Drosophila contains at least 23 families of LTR retrotransposons and retroviruses and 11 families of non-LTR retrotransposons, representing 5-10% of the Drosophila genome (Bowen and Mcdonald 2001;Kaminker et al 2002;Lerat et al 2003).…”

Tropical Africa as a cradle for horizontal transfers of transposable elements between species of the genera Drosophila and Zaprionus

“…One noteworthy approach is to analyze the TE rate of the synonymous substitution (Ks or Ds) and that of nuclear genes. [14][15][16][41][42][43][44][45][46][47] This approach allows the HT event to be dated using the rationale that if the TEs are evolving vertically and the lack of congruence in the phylogeny is a consequence of differential subfamily distribution in the species analyzed, the Ks values of the TE sequences and those of the nuclear gene(s) should be equivalent. However, if the Ks of the TE are significantly lower than that of the nuclear gene, the lower Ks values can be explained by a small divergence time of the TE copies between the species as a consequence of HT.…”