Tetris is a foldback transposon that provided the building blocks for an emerging satellite DNA of Drosophila virilis

Abstract

Transposable elements (TEs) and satellite DNAs (satDNAs) are abundant components of most eukaryotic genomes studied so far and their impact on evolution has been the focus of several studies. A number of studies linked TEs with satDNAs, but the nature of their evolutionary relationships remains unclear. During in silico analyses of the Drosophila virilis assembled genome, we found a novel DNA transposon we named Tetris based on its modular structure and diversity of rearranged forms. We aimed to characterize Tetris and investigate its role in generating satDNAs. Data mining and sequence analysis showed that Tetris is apparently nonautonomous, with a structure similar to foldback elements, and present in D. virilis and D. americana. Herein, we show that Tetris shares the final portions of its terminal inverted repeats (TIRs) with DAIBAM, a previously described miniature inverted transposable element implicated in the generation of chromosome inversions. Both elements are likely to be mobilized by the same autonomous TE. Tetris TIRs contain approximately 220-bp internal tandem repeats that we have named TIR-220. We also found TIR-220 repeats making up longer (kb-size) satDNA-like arrays. Using bioinformatic, phylogenetic and cytogenomic tools, we demonstrated that Tetris has contributed to shaping the genomes of D. virilis and D. americana, providing internal tandem repeats that served as building blocks for the amplification of satDNA arrays. The β-heterochromatic genomic environment seemed to have favored such amplification. Our results imply for the first time a role for foldback elements in generating satDNAs.

Keywords: fiber-FISH; polytene chromosomes; repetitive DNA; satellite DNA; transposable elements; β-heterochromatin.

Fig. 1.—

Schematic representation of the foldback structure and examples of the main types of variation found in the analyzed Tetris copies. (A) Schematic representation of foldback elements (adapted from Casals et al. 2005). M, middle domain. L and R refer to the left and right extremities of the transposon, respectively. (B) Schematic representation of the structurally complete copies of Tetris found in the Drosophila virilis assembled genome plus one hit from Fosmid 16B18 (accession: GU120717). Arrowheads in opposite orientation and solid black bars on top of the Ctg 17663 scheme represent the primers used to amplify the two fragments used as probes for the FISH experiments. (C) Main types of arrangements found between the Tetris and its TIR-220 repeats in the D. virilis genome, including one partial copy of Tetris next to the short heterochromatic gene RpL15. Green boxes represent Tetris’ TIR. Red boxes indicate the tandem repeats (TIR-220), and the grey boxes represent the Tetris’ TIR-ID.

Fig. 2.—

Schematic comparison between Tetris (Ctg 16378) and DAIBAM (EU280326). Regions with high sequence identity between the elements are shown in green. The DAIBAM region that could not be confidently aligned with Tetris is shown in the striped bar.

Fig. 3.—

NJ tree containing TIR-220 repeats extracted from Drosophila virilis and D. americana assembled genomes. Purple branches with no symbols at the tips represent the bulk of D. virilis amplified copies. Repeats belonging to the three structurally complete copies of Tetris are shown in orange (Ctg 17663), red (Ctg 16378), and green (Ctg 17538) diamonds. Purple triangles represent the three D. virilis TIR-220 repeats obtained by PCR and sequenced in this work. Drosophila americana TIR-220 repeats are shown in black circles and branches. The tree was estimated using the NJ algorithm and the p-distance substitution method.

Fig. 4.—

FISH of TIR-FD (green) and TIR-220 (red) probes hybridized on (A) Drosophila virilis metaphase, (B) D. americana metaphase, and (C) D. virilis polytene chromosomes. Arrows in (A) and (B) indicate the chromosome 6 (the dot chromosome). The chromocenter of the polytene chromosomes is indicated with an asterisk in (C). The “β” indicates the chromosome 2 β-heterochromatin and the number 6 is placed next to the polytene arm corresponding to the chromosome 6. Bars in (A) and (B) correspond to 10 µm, and in (C), to 5 µm.

Fig. 5.—

FISH of TIR-220 and TIR-FD probes onto extended DNA fibers of Drosophila virilis. Long DNA fibers with several Tetris hybridization signals including some expanded TIR-220 arrays are shown in (A) for D. americana and in (B) for D. virilis. Arrowhead in (C) indicates a long array of TIR-220 within Tetris from D. virilis. A representation of the hybridization signals highlighted in (C) is shown in the bottom row. The bars correspond to 10 kb (assuming 10 µm = 29 kb; Schwarzacher and Heslop-Harrison 2000).

Fig. 6.—

Sequence identity between a 37-bp stretch shared by the TIR-FD and TIR-220 domains of Tetris. The nucleotide identity values are given on the right side of the connection lines.