Conserved motifs and dynamic aspects of the terminal inverted repeat organization within Bari-like transposons

Abstract

In this work the structural variations of Terminal Inverted Repeats (TIR) of Bari like transposons in Drosophila species has been studied. The aim is to try and assess the relevance of different variants in the evolutionary distribution of Bari elements. Bari is a member of the widespread Tc1 superfamily of transposable elements that has colonized most species of the Drosophila genus. We previously reported the structure of two related elements that differ in their TIR organization: Bari1 harbouring 26-bp TIR (short TIRs) and Bari2 with about 250-bp TIR (long TIIR). While elements with short TIRs are complete and potentially autonomous, long ones are invariably composed of defective copies. The results show that in D. pseudobscura, D. persimilis and D. mojavensis, there is a third class of Bari elements, Bari3, that exhibit a long TIR structure and are not defective. Phylogenetic relationships among reconstructed transposases are consistent with the three subfamilies sharing a common origin. However, the final TIR organization into long or short structure is not related by descent but appears to be lineage-specific. Furthermore, we show that, independently of origin and organization, within the 250-bp terminal sequences there are three regions that are conserved in both sequence and position suggesting they are under functional constraint.

Structural and sequence diversity of the transposon Galileo in the Drosophila willistoni genome

“…The presence of Galileo subfamilies within the same genome seems to be the rule rather than the exception, as was previously found in D. buzzatii (subfamilies G, K, and N), D. virilis (subfamilies A and B), and D. mojavensis (subfamilies C, D, E, F, and X) [6–8]. Furthermore, the coexistence of different subfamilies, subgroups, or variants of TEs was reported in studies of Bari [37] and G ypsy [38] in Drosophila , P in Anopheles gambiae and Drosophila [39, 40], and mariner in insects and humans [41, 42], among others.…”

The Drosophila mojavensis Bari3 transposon: distribution and functional characterization

“…Three related Bari sub-families ( Bari1 , Bari2 and Bari3 ), differing in their structural organization and their potential transposition ability, are known to exist in different Drosophila species [13,14]. While elements related to Bari1 and Bari3 can be either potentially autonomous or not, elements related to Bari2 are all non-autonomous [13,14].…”

“…While elements related to Bari1 and Bari3 can be either potentially autonomous or not, elements related to Bari2 are all non-autonomous [13,14]. Bari -like elements belong to the IR-DR group of the Tc1 lineage, comprising elements with terminal ends of about 250 bp in length.…”

“…It has been identified in the genome of the emerging species D. mojavensis, but homologous sequences can be also identified in the sequenced genomes of the phylogenetically distant species D. pseudoobscura , D. persimilis and D. willistoni [14]. Its structural characteristics, that is, long TIRs with three DRs bracketing a transposase coding region, allowed the determination of the evolutionary dynamics acting on the transposon termini [14]. Furthermore, at least ten identical copies of this element can be detected in the sequenced genome D. mojavensis , suggesting its very recent transposition activity.…”

“…Furthermore, at least ten identical copies of this element can be detected in the sequenced genome D. mojavensis , suggesting its very recent transposition activity. Previous studies concerning the phylogenetic distribution of the Bari -like elements have disclosed inconsistencies with the species phylogeny that have demonstrated [27] or postulated [14] ancient horizontal gene transfer events.…”