DeviaTE: Assembly‐free analysis and visualization of mobile genetic element composition

Weilguny, Lukas; Kofler, Robert

doi:10.1111/1755-0998.13030

Cited by 31 publications

(65 citation statements)

References 64 publications

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“…The key idea is that the expected TE landscape can be directly derived from the Illumina raw reads using our novel tool, DeviaTE (Weilguny and Kofler, 2019). Briefly, DeviaTE aligns Illumina reads to the consensus sequences of TEs and provides estimates of the abundance (rpm) and diversity (SNPs and IDs counts) of each TE family (for example, see supplementary fig.…”

Section: Resultsmentioning

confidence: 99%

Generating high quality assemblies for genomic analysis of transposable elements

Wierzbicki

Schwarz

Cannalonga

et al. 2020

Preprint

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The advent of long-read sequencing holds great promise for research on transposable elements (TEs). Long reads may finally allow us to obtain reliable assemblies of repetitive regions, and thus shed light on many open questions in TE biology, such as the evolution of piRNA clusters, i.e., the master loci controlling TE activity. Currently, many different assembly strategies exist and it is not clear how to obtain the most suitable assemblies for TE research. In fact, it is not even clear how to best identify suitable assemblies as classic quality metrics such as BUSCO and NG50 are ignorant of TEs. To address these problems, we introduce four novel quality metrics that assess i) how well piRNA clusters are assembled (CUSCO) and ii) to which extent an assembly captures the TE landscape of an organism (TE abundance, SNPs and internal deletions). Using these novel metrics, we evaluate the effect of assemblers, polishing, read length, coverage, residual polymorphisms, and finally, identify suitable assembly strategies. Using an optimized approach, we provide high-quality assemblies for the two Drosophila melanogaster strains Canton-S and Pi2. Around 80% of the piRNA clusters were contiguously assembled in these two strains. Such high-quality assemblies will provide novel insights into the biology of TEs. It is, for example, an open question of whether piRNA clusters contain abundant presence/absence polymorphism of TE insertions, as expected when piRNA clusters are responsible for stopping TE invasions. A comparison of the sequences of our assembled piRNA clusters reveals that such polymorphisms are indeed abundantly found in clusters.

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Section: Resultsmentioning

confidence: 99%

Generating high quality assemblies for genomic analysis of transposable elements

Wierzbicki

Schwarz

Cannalonga

et al. 2020

Preprint

Self Cite

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“…Our approach requires estimates of the abundance of IDs for TE families and samples (usually populations) of interest. For this purpose we previously developed a novel tool, DeviaTE [Weilguny and Kofler, 2019]. Briefly, DeviaTE aligns reads of a sample to consensus sequences of TEs (e.g.…”

Section: Resultsmentioning

confidence: 99%

“…the P-element) using a local alignment algorithm, reconstructs the breakpoints of IDs from the partial alignment of reads, and finally infers the frequency of IDs by relating the number of reads supporting an ID to the total coverage of the TE ( Fig. 1A; [Weilguny and Kofler, 2019]). This approach is indifferent to the genomic insertion sites of TEs.…”

Section: Resultsmentioning

confidence: 99%

“…Reads were mapped with bwasw and sorted with samtools ]. Subsequently, the position and the frequency of IDs was estimated with DeviaTE [Weilguny and Kofler, 2019]. A custom script (dm-deviate.py) was used to estimate the genetic distance among samples.…”

Section: Analysis Of Datamentioning

confidence: 99%

“…The frequency of ID and FL insertions can be estimated from the coverage of the TE and the abundance of the split-reads, e.g. using our novel tool DeviaTE (right panel) [Weilguny and Kofler, 2019]. B) Example of an ID fingerprint for the P-element in a D. melanogaster population collected 2018 from Eutawville [data from Bergland et al, 2014].…”

Section: Introductionmentioning

confidence: 99%

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Reconstructing the invasion route of DNA transposons using extant population samples

Weilguny¹,

Vlachos²,

Selvaraju³

et al. 2019

Preprint

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Reconstructing invasion routes of transposable elements (TEs), so far, required capturing an ongoing invasion with population samples from different geographic regions and time points. Here, we propose a more accessible approach. Abundantly occurring internal deletions of DNA transposons allow to trace the direction as well as the path of an invasion, even hundreds of generations after the spread of a TE. We validated this hypothesis with computer simulations and by accurately reproducing the route of the P-element invasion in Drosophila melanogaster. Finally, we used our method to shed light on the controversial hobo invasion in D. melanogaster . Our approach solely requires sequenced samples from extant populations and sequences of TEs of interest. Hence, DNA transposons in a wide range of model and non-model organisms may be analyzed. Our approach will further our understanding of TE dynamics, migration patterns, and the ecology of species.

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Assembly-Free Detection and Quantification of Transposable Elements with dnaPipeTE

Goubert

2022

Transposable Elements

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DeviaTE: Assembly‐free analysis and visualization of mobile genetic element composition

Cited by 31 publications

References 64 publications

Generating high quality assemblies for genomic analysis of transposable elements

Generating high quality assemblies for genomic analysis of transposable elements

Reconstructing the invasion route of DNA transposons using extant population samples

Assembly-Free Detection and Quantification of Transposable Elements with dnaPipeTE

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