Drosophila telomeric retrotransposons derived from an ancestral element that was recruited to replace telomerase

Abstract

Drosophila telomeres do not have arrays of simple telomerase-generated G-rich repeats. Instead, Drosophila maintains its telomeres by occasional transposition of specific non-long terminal repeat (non-LTR) retrotransposons to chromosome ends. The genus Drosophila provides a superb model system for comparative telomere analysis. Here we present an evolutionary study of Drosophila telomeric elements to ascertain the significance of telomeric retrotransposons (TRs) in the maintenance of Drosophila telomeres. PCR and in silico surveys in the sibling species of Drosophila melanogaster and in more distantly related species show that multiple TRs maintain telomeres in Drosophila. In addition to TRs with two open reading frames (ORFs) capable of autonomous transposition, there are deleted telomeric retrotransposons that have lost their ORF2, which we refer to as half telomeric-retrotransposons (HTRs). The phylogenetic relationship among these telomeric elements is congruent with the phylogeny of the species, suggesting that they have been vertically inherited from a common ancestor. Our results suggest that an existing non-LTR retrotransposon was recruited to perform the cellular function of telomere maintenance.

Figure 1.

TAHRE elements in the D. melanogaster species subgroup. (A) Dot-matrix comparisons of the nucleotide sequence of each TAHRE (Dsec\TAHRE scaffold 182, 15703-7717; Dyak\TAHRE and Dere\TAHRE are listed in Supplemental Fig. S12) with its corresponding HeT-A (Dsec\HeT-A scaffold 182, 7716-2747; Dyak\HeT-A AF043258; Dere\HeT-A scaffold 4836, 38316–32346). The three-frame ORF maps of TAHRE elements are indicated (the tall tick marks correspond to stop codons; the short tick marks correspond to methionines; the ORFs are the long stretches without tall tick marks). (B) Diagram of scaffold 182 from D. sechellia. The color code for the TRs is indicated in the box below. (C) FISH of TAHRE-ORF2 probes to polytene chromosomes of D. simulans and D. yakuba. Hybridization signals are shown in green on the chromosomes counterstained with DAPI (blue).

Figure 2.

Diagrams of scaffolds containing head-to-tail arrays of telomeric retrotransposons from D. ananassae, D. persimilis, D. mojavensis, D. virilis, and D. grimshawi. The putative origin of each scaffold appears between brackets. The color code for TRs, HTRs, TAS, and euchromatin is indicated in boxes. In the euchromatin regions a distal gene is indicated. Ns indicates the presence of unsequenced regions.

Figure 3.

Dot-matrix analysis of TRs with HTRs. Dot-matrix comparisons of the nucleotide sequence of Dana\TR2A: Dana\HTR2A, Dper\TR1A: Dper\HTR1A, Dper\TR3A: Dper\HTR3A, Dper\TR3B: Dper\HTR3B, Dmoj\TR1Ab: Dmoj\HTR1Ab, Dmoj\TR1D: Dmoj\HTR1D, Dmoj\TR1C: Dmoj\HTR1C, Dmoj\TR1E: Dmoj\HTR1E. The three-frame ORF maps are indicated.

Figure 4.

Diagrams of the structure of TRs and HTRs. Diagrams are approximately to scale. The 5′UTR regions appear in yellow, the ORF1 in green, the ORF2 in orange, and the 3′UTR in magenta. The three zinc knuckles domain in ORF1 and the RT domain in ORF2 are indicated. The polyglutamines appear as a single “Q” and the polyasparagines as a single “N.” The presence of repeats in the 3′UTR regions is also indicated.

Figure 5.

Phylogenetic relationships of TRs based on their RT domains. The tree was inferred using the neighbor-joining method. Bootstrap values are given as percentage numbers. The color code for TRs is indicated. TART and TAHRE have not been renamed to keep their historical names.

Figure 6.

Phylogenetic relationships of TRs and HTRs based on their ORF1 domains. The tree was inferred using the neighbor-joining method. Bootstrap values are given as percentage numbers. The color code for TRs and HTRs is indicated. TART, TAHRE, and HeT-A have not been renamed to keep their historical names.