A novel repeated sequence DNA originated from a Tc1-like transposon in water green frog Rana esculenta

Identification and characterization of a new family of long satellite DNA, specific of true toads (Anura, Amphibia, Bufonidae)

Amphibians have some of the most variable genome sizes among vertebrates. Genome size variation has been attributed to repetitive and noncoding DNA, including satellite repeats, transposable elements, introns, and nuclear insertions of viral and organelle DNA. In vertebrates, satellite DNAs have been widely described in mammals, but few molecular studies have been carried out in amphibians. Here, we provide a detailed characterization of a new family of satellite DNA, present in all 15 examined species of the family Bufonidae. Southern-blot analysis and PCR reveal that this satellite is formed by monomers of 807 bp, is organized in tandem arrays, and has an AT-content of 57.4%. Phylogenetic analyses show that most clades exhibit species-specific variances, indicating that this satellite DNA has evolved by concerted evolution. The homogenization/fixation process is heterogeneous in Bufonidae, where the genera Bufo and Bufotes do not show species-specific differences, while populations from Rhinella marina exhibit population-specific changes. Additionally, variants of this satellite DNA have been identified in Duttaphrynus melanostictus and R. marina, supporting the 'library hypothesis' (a set, 'library', of satellite DNAs is shared by a species group). Physical mapping in Bufo bufo, Bufo spinosus, Epidalea calamita and Bufotes viridis provides evidence that this repetitive DNA is not dispersed in the karyotype, but accumulated in pericentromeric regions of some chromosomal pairs. This location, together with its presence in the transcriptomes of bufonids, could indicate a role in centromere function or heterochromatin formation and maintenance.

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

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.

The impact of transposable elements on eukaryotic genomes: from genome size increase to genetic adaptation to stressful environments

Transposable elements (TEs) are present in roughly all genomes. These mobile DNA sequences are able to invade genomes and their impact on genome evolution is substantial. The mobility of TEs can induce the appearance of deleterious mutations, gene disruption and chromosome rearrangements, but transposition activity also has positive aspects and the mutational activities of TEs contribute to the genetic diversity of organisms. This short review aims to give a brief overview of the impact TEs may have on animal and plant genome structure and expression, and the relationship between TEs and the stress response of organisms, including insecticide resistance.

Identification of a Tc1-like transposon integration site in the genome of the flounder (Platichthys flesus): a novel use of an inverse PCR method

The inverse PCR method has been developed and applied employed for the identification of the integration sites of the Tc1-like transposons in the genome of the flounder, Platichthys flesus. One Tc1-like insertion instance was recognized and characterized, demonstrating an efficiency of the method for determining of transposon integration sites. The similarity of the sequence flanking transposon (SFT) to reverse transcriptase sequences (RVT) was demonstrated. It is likely that the insertion took place within currently degenerated LINE (long interspersed nuclear elements) retrotransposon.

A new pair of CR1-like LINE and tRNA-derived SINE elements in Podarcis sicula genome

We have identified and characterized a new pair of LINE and SINE elements, called Lucy-1 CR1-like LINE and P.s.1/SINE, respectively, in Podarcis sicula genome. The 3'-tail region in the 3' untranslated region (UTR) of Lucy-1 element is almost identical to the of P.s.1/SINE element. This identity suggests that the P.s.1/SINE element, during evolution, has gained the 3'-end sequence of the Lucy-1 element and has exclusively recruited the enzymatic machinery of its partner CR1 LINE for retroposition. Moreover, the complex molecular organization around Lucy-1 insertion site is discussed and we found that Lucy-1 insertion is associated with the calcium binding transporter gene. Our results confirm that the retrotransposons can be an additional source of genomic diversification and the evolution of the retrotransposable elements can be a vector force shaping genomes by reassorting DNA domains thus forming a new DNA arrangement.