Recent transposition activity of Xenopus T2 family miniature inverted-repeat transposable elements

Multiple massive domestication and recent amplification of Kolobok superfamily transposons in the clawed frog Xenopus

BACKGROUND

DNA transposons are generally destroyed by mutations and have short lifespans in hosts, as they are neutral or harmful to the host and therefore not conserved by natural selection. The clawed frog Xenopus harbors many DNA transposons and certain families, such as T2-MITE, have extremely long lives. These have ancient origins, but have shown recent transposition activity. In addition, certain transposase genes may have been "domesticated" by Xenopus and conserved over long time periods by natural selection. The aim of this study was to elucidate the evolutionary interactions between the host and the long-lived DNA transposon family it contains. Here, we investigated the molecular evolution of the Kolobok DNA transposon superfamily. Kolobok is thought to contribute to T2-MITE transposition.

RESULTS

In the diploid western clawed frog Xenopus tropicalis and the allotetraploid African clawed frog Xenopus laevis, we searched for transposase genes homologous to those in the Kolobok superfamily. To determine the amplification and domestication of these genes, we used molecular phylogenetics and analyses of copy numbers, conserved motifs, orthologous gene synteny, and coding sequence divergence between the orthologs of X. laevis and X. tropicalis, or between those of two distant X. tropicalis lineages. Among 38 X. tropicalis and 24 X. laevis prospective transposase genes, 10 or more in X. tropicalis and 14 or more in X. laevis were apparently domesticated. These genes may have undergone multiple independent domestications from before the divergence of X. laevis and X. tropicalis. In contrast, certain other transposases may have retained catalytic activity required for transposition and could therefore have been recently amplified.

CONCLUSION

Multiple domestication of certain transposases and prolonged conservation of the catalytic activity in others suggest that Kolobok superfamily transposons were involved in complex, mutually beneficial relationships with their Xenopus hosts. Some transposases may serve to activate long-lived T2-MITE subfamilies.

Distribution of the T2-MITE Family Transposons in the Xenopus (Silurana) tropicalis Genome

The T2 family of miniature inverted-repeat transposable elements (T2-MITE) is a prevalent MITE family found in both Xenopus(Silurana) tropicalis and X. laevis. Some subfamilies, particularly T2-A1 and T2-C, may have originated prior to the diversification of the 2 Xenopus lineages and currently include active members in X. tropicalis, whereas another subfamily, T2-E, may have lost its transposition activity even earlier. The distribution of each T2-MITE subfamily in X. tropicalis was investigated and compared to evaluate the evolutionary dynamics of the T2-MITE subfamilies. The subfamilies showed differences in chromosomal distribution, uniformity of insertion density on scaffolds, ratios of upstream to downstream insertions with respect to genes, and their distance from genes. Among these, the T2-C subfamily was interesting because it was frequently inserted upstream and close to genes and because genes with close insertions of this subfamily showed high correlations in spatial expression patterns. This unique distribution and long-lived transposition activity may reflect a mutual relationship evolved between this subfamily and the host.

Insights on genome size evolution from a miniature inverted repeat transposon driving a satellite DNA

The genome size in eukaryotes does not correlate well with the number of genes they contain. We can observe this so-called C-value paradox in amphibian species. By analyzing an amphibian genome we asked how repetitive DNA can impact genome size and architecture. We describe here our discovery of a Tc1/mariner miniature inverted-repeat transposon family present in Xenopus frogs. These transposons named miDNA4 are unique since they contain a satellite DNA motif. We found that miDNA4 measured 331 bp, contained 25 bp long inverted terminal repeat sequences and a sequence motif of 119 bp present as a unique copy or as an array of 2-47 copies. We characterized the structure, dynamics, impact and evolution of the miDNA4 family and its satellite DNA in Xenopus frog genomes. This led us to propose a model for the evolution of these two repeated sequences and how they can synergize to increase genome size.

Mobilization of Stowaway-like MITEs in newly formed allohexaploid wheat species

Transposable elements (TEs) dominate the genetic capacity of most eukaryotes, especially plants, where they can account for up to 90 % of the genome, such as in wheat. The relationship between TEs and their hosts and the role of TEs in organismal biology are poorly understood. In this study, we have applied next generation sequencing, together with a transposon display technique in order to test whether a Stowaway-like MITE, termed Minos, transposes following allopolyploidization events in wheat. We have generated a 454-pyrosequencing database of Minos-specific amplicons (transposon display products) from a newly formed wheat allohexaploid and its parental lines and retrieved hundreds of novel MITE insertions in the allohexaploid. Clear mobilization of Minos was also seen by site-specific PCR analysis and sequence validation. In addition, using real-time qPCR analysis we observed an insignificant change in the relative quantity of Minos from the expected value of merging the two parental genomes, indicating that, despite its activation, no significant burst in Minos copy number can be seen in the newly formed allohexaploid. Interestingly, we found that CCGG sites surrounding Minos underwent massive hypermethylation following the allohexaploidization process. Our data suggest that MITEs have maintained their capacity for activity throughout the evolution of wheat and might be epigenetically deregulated in the first generations following allopolyploidization.

msechBari, a new MITE-like element in Drosophila sechellia related to the Bari transposon

A few occurrences of miniature inverted-repeat transposable elements (MITEs) have been reported in species of the genus Drosophila. Here, we describe msechBari, a MITE-like element in Drosophila sechellia. The element is short, approximately 90 bp in length, AT-rich and occurs in association with, or close to, genes, characteristics that are typical for MITEs. The identification was performed in silico using the sequenced genome of D. sechellia and confirmed in a laboratory strain. This short element is related to the Bari_DM transposon of Drosophila melanogaster, having terminal inverted repeats (TIRs) of a similar length and a high identity with the full-length Bari_DM element. The estimated recent origin of the element and the homogeneity observed between copies found in the genome suggests that msechBari could be active in D. sechellia.