A benchmark of transposon insertion detection tools using real data
Vendrell Mir, Pol (Centre de Recerca en Agrigenòmica)
Barteri, Fabio (Centre de Recerca en Agrigenòmica)
Merenciano, Miriam (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
González, Josefa (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica)
Castanera, Raúl (Centre de Recerca en Agrigenòmica)

Date:	2019
Abstract:	Background: Transposable elements (TEs) are an important source of genomic variability in eukaryotic genomes. Their activity impacts genome architecture and gene expression and can lead to drastic phenotypic changes. Therefore, identifying TE polymorphisms is key to better understand the link between genotype and phenotype. However, most genotype-to-phenotype analyses have concentrated on single nucleotide polymorphisms as they are easier to reliable detect using short-read data. Many bioinformatic tools have been developed to identify transposon insertions from resequencing data using short reads. Nevertheless, the performance of most of these tools has been tested using simulated insertions, which do not accurately reproduce the complexity of natural insertions. Results: We have overcome this limitation by building a dataset of insertions from the comparison of two high-quality rice genomes, followed by extensive manual curation. This dataset contains validated insertions of two very different types of TEs, LTR-retrotransposons and MITEs. Using this dataset, we have benchmarked the sensitivity and precision of 12 commonly used tools, and our results suggest that in general their sensitivity was previously overestimated when using simulated data. Our results also show that, increasing coverage leads to a better sensitivity but with a cost in precision. Moreover, we found important differences in tool performance, with some tools performing better on a specific type of TEs. We have also used two sets of experimentally validated insertions in Drosophila and humans and show that this trend is maintained in genomes of different size and complexity. Conclusions: We discuss the possible choice of tools depending on the goals of the study and show that the appropriate combination of tools could be an option for most approaches, increasing the sensitivity while maintaining a good precision.
Grants:	Ministerio de Economía y Competitividad AGL2016-78992-R European Commission 647900 Ministerio de Ciencia e Innovación BFU2017-82937-P
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Benchmark ; Transposable elements ; Polymorphism ; Transposon insertion ; Resequencing
Published in:	Mobile DNA, Vol. 10 (December 2019) , art. 53, ISSN 1759-8753

DOI: 10.1186/s13100-019-0197-9
PMID: 31892957

19 p, 3.5 MB

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Research literature > UAB research groups literature > Research Centres and Groups (research output) > Experimental sciences > CRAG (Centre for Research in Agricultural Genomics)
Articles > Research articles
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