Transposable elements in Drosophila

Mérel, Vincent; Boulesteix, Matthieu; Fablet, Marie; Vieira, Cristina

doi:10.1186/s13100-020-00213-z

Cited by 92 publications

(89 citation statements)

References 258 publications

(305 reference statements)

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“…Despite the fact that various TE families are present in the considered heterochromatic region for each of the four major subclasses, one specific superfamily is often over-represented: Jockey for LINEs, Gypsy for LTR elements, P for DNA transposons, Helitron for RC elements ( Figure 4 ). Importantly, this observation is in agreement with dominating TE superfamilies estimated in whole genomes even for evolutionary distant species, i.e., D. melanogaster and D. virilis [ 68 ].…”

Section: Resultssupporting

confidence: 85%

Evolutionary Dynamics of the Pericentromeric Heterochromatin in Drosophila virilis and Related Species

Rezvykh

Funikov

Protsenko

et al. 2021

Genes

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Pericentromeric heterochromatin in Drosophila generally consists of repetitive DNA, forming the environment associated with gene silencing. Despite the expanding knowledge of the impact of transposable elements (TEs) on the host genome, little is known about the evolution of pericentromeric heterochromatin, its structural composition, and age. During the evolution of the Drosophilidae, hundreds of genes have become embedded within pericentromeric regions yet retained activity. We investigated a pericentromeric heterochromatin fragment found in D. virilis and related species, describing the evolution of genes in this region and the age of TE invasion. Regardless of the heterochromatic environment, the amino acid composition of the genes is under purifying selection. However, the selective pressure affects parts of genes in varying degrees, resulting in expansion of gene introns due to TEs invasion. According to the divergence of TEs, the pericentromeric heterochromatin of the species of virilis group began to form more than 20 million years ago by invasions of retroelements, miniature inverted repeat transposable elements (MITEs), and Helitrons. Importantly, invasions into the heterochromatin continue to occur by TEs that fall under the scope of piRNA silencing. Thus, the pericentromeric heterochromatin, in spite of its ability to induce silencing, has the means for being dynamic, incorporating the regions of active transcription.

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Section: Resultssupporting

confidence: 85%

Evolutionary Dynamics of the Pericentromeric Heterochromatin in Drosophila virilis and Related Species

Rezvykh

Funikov

Protsenko

et al. 2021

Genes

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“…In addition, our analysis only included TEIs that are not found in the reference genome, i.e., TEIs that result from transposition events more recent than the set-up of the actual populations. Altogether, while the TE ancient dynamics are different between D. melanogaster and D. simulans [ 60 ], the present results suggest that D. melanogaster and D. simulans TE landscapes are rather similar when comparing only global variants (i.e., the subset of the most recent insertions). As already proposed [ 25 ], this may reveal that the colonization of D. simulans genome by TEs has now reached a state similar to that of D. melanogaster, although it started more recently.…”

Section: Resultsmentioning

confidence: 66%

A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore

Mohamed

Dang

Ogyama

et al. 2020

Cells

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Transposable elements (TEs) are the main components of genomes. However, due to their repetitive nature, they are very difficult to study using data obtained with short-read sequencing technologies. Here, we describe an efficient pipeline to accurately recover TE insertion (TEI) sites and sequences from long reads obtained by Oxford Nanopore Technology (ONT) sequencing. With this pipeline, we could precisely describe the landscapes of the most recent TEIs in wild-type strains of Drosophila melanogaster and Drosophila simulans. Their comparison suggests that this subset of TE sequences is more similar than previously thought in these two species. The chromosome assemblies obtained using this pipeline also allowed recovering piRNA cluster sequences, which was impossible using short-read sequencing. Finally, we used our pipeline to analyze ONT sequencing data from a D. melanogaster unstable line in which LTR transposition was derepressed for 73 successive generations. We could rely on single reads to identify new insertions with intact target site duplications. Moreover, the detailed analysis of TEIs in the wild-type strains and the unstable line did not support the trap model claiming that piRNA clusters are hotspots of TE insertions.

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“…In agreement with the gene disruption hypothesis and observations in a variety of species (Bartolomé et al 2002; Medstrand et al 2002; Wright et al 2003), we observed a depletion of TE copies in gene-rich regions of the D. suzukii genome. Although it is likely that TEs are strongly selected against in these regions due to their negative effect on gene function or expression (Lee and Karpen 2017; Mérel et al 2020), it is also possible that TE copies are depleted in these regions because they promote ectopic recombination. In agreement with the latter hypothesis, gene-rich regions are also known to display high recombination rate in D. melanogaster (Adams et al 2000) .…”

Section: Discussionmentioning

confidence: 99%

The worldwide invasion ofDrosophila suzukiiis accompanied by a large increase of transposable element load and a small number of putatively adaptive insertions

Mérel

Gibert

Buch

et al. 2020

Preprint

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Transposable Elements (TEs) are ubiquitous and mobile repeated sequences. They are major determinants of host fitness. Here, we portrayed the TE content of the spotted wing fly Drosophila suzukii. Using a recently improved genome assembly, we reconstructed TE sequences de novo, and found that TEs occupy 47% of the genome and are mostly located in gene poor regions. The majority of TE insertions segregate at low frequencies, indicating a recent and probably ongoing TE activity. To explore TE dynamics in the context of biological invasions, we studied variation of TE abundance in genomic data from 16 invasive and six native populations (of D. suzukii). We found a large increase of the TE load in invasive populations correlated with a reduced Watterson estimate of genetic diversity θW a proxy of effective population size. We did not find any correlation between TE contents and bio-climatic variables, indicating a minor effect of environmentally induced TE activity. A genome-wide association study revealed that ca. 5,000 genomic regions are associated with TE abundance. We did not find, however, any evidence in such regions of an enrichment for genes known to interact with TE activity (e.g. transcription factor encoding genes or genes of the piRNA pathway). Finally, the study of TE insertion frequencies revealed 15 putatively adaptive TE insertions, six of them being likely associated with the recent invasion history of the species.

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Transposable elements in Drosophila

Cited by 92 publications

References 258 publications

Evolutionary Dynamics of the Pericentromeric Heterochromatin in Drosophila virilis and Related Species

Evolutionary Dynamics of the Pericentromeric Heterochromatin in Drosophila virilis and Related Species

A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore

The worldwide invasion ofDrosophila suzukiiis accompanied by a large increase of transposable element load and a small number of putatively adaptive insertions

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