Identification of Bari Transposons in 23 Sequenced Drosophila Genomes Reveals Novel Structural Variants, MITEs and Horizontal Transfer

Abstract

Bari elements are members of the Tc1-mariner superfamily of DNA transposons, originally discovered in Drosophila melanogaster, and subsequently identified in silico in 11 sequenced Drosophila genomes and as experimentally isolated in four non-sequenced Drosophila species. Bari-like elements have been also studied for their mobility both in vivo and in vitro. We analyzed 23 Drosophila genomes and carried out a detailed characterization of the Bari elements identified, including those from the heterochromatic Bari1 cluster in D. melanogaster. We have annotated 401 copies of Bari elements classified either as putatively autonomous or inactive according to the structure of the terminal sequences and the presence of a complete transposase-coding region. Analyses of the integration sites revealed that Bari transposase prefers AT-rich sequences in which the TA target is cleaved and duplicated. Furthermore evaluation of transposon’s co-occurrence near the integration sites of Bari elements showed a non-random distribution of other transposable elements. We also unveil the existence of a putatively autonomous Bari1 variant characterized by two identical long Terminal Inverted Repeats, in D. rhopaloa. In addition, we detected MITEs related to Bari transposons in 9 species. Phylogenetic analyses based on transposase gene and the terminal sequences confirmed that Bari-like elements are distributed into three subfamilies. A few inconsistencies in Bari phylogenetic tree with respect to the Drosophila species tree could be explained by the occurrence of horizontal transfer events as also suggested by the results of dS analyses. This study further clarifies the Bari transposon’s evolutionary dynamics and increases our understanding on the Tc1-mariner elements’ biology.

“What You Need, Baby, I Got It”: Transposable Elements as Suppliers of Cis-Operating Sequences in Drosophila

“…Afterwards, few additional transposon families, mainly residing in the heterochromatin or absent in the reference strain, were discovered and characterized [29][30][31]. This set of information has been complemented with the genome sequencing of 69 additional species of the Drosophila genus https://www.ncbi.nlm.nih.gov/genome/?term=drosophila-last (accessed on 24 December 2019) and the TE characterization in non-model Drosophila species, leading to the possibility to perform large comparative and evolutionary studies [32][33][34][35]. Figure 1A summarizes the main structural features of the TE types in the genome.…”

“…Furthermore, the promoters of elements belonging to the Bari family [34] have been recently tested for their ability to drive a reporter gene expression in expression vectors [81,82]. While the promoter of LTR retrotransposons such as copia, ZAM and Tirant strongly supported the reporter transcription, the promoter of two DNA transposons, Bari1 and Bari3, turned out to be weak promoters [81].…”

“…One of them has a peculiar feature. The Bari1 cluster maps in the h39 region of the second chromosome of D. melanogaster, adjacent to the XbaI repeat that identify the Responder (Rsp) locus [34]. While apparently devoid of functional significance, this region has been proven to be important for some fitness-related performance of the species [113].…”

Double insertion of transposable elements provides a substrate for the evolution of satellite DNA

“…ConTExt successfully identified the two known TEderived satellites in D. melanogaster, which we further investigated to understand the dynamics of established satellites. One satellite is comprised of tandemly arrayed copies of the 1.7-kb DNA transposon Bari1 and is located in two blocks, with the majority of copies in the pericentromeric heterochromatin of the right arm of Chromosome 2 (Caizzi et al 1993;Marsano et al 2003;Palazzo et al 2016). The second block is nested in a Stalker4 element on an unmapped scaffold (JSAE01000184) suggested to reside in the X or Y heterochromatin based on the presence of rDNA and R-elements (Palazzo et al 2016).…”

Transposable elements inDrosophila

“…MITEs are short TIR transposons, generally less than 500 bp in length, that do not encode a functional transposase and often lack coding regions entirely 33 . Numerous Bari -like MITEs have been detected in 9 Drosophila species, and are suspected to have originated from internal deletions in Bari elements 36 . Many of these Bari -like MITEs in Drosophila have been amplified in their respective genomes 36 .…”