A benchmark of transposon insertion detection tools using real data

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 betwee...

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Autores: Vendrell Mir, Pol|||0000-0002-5695-5880, Barteri, Fabio, Merenciano, Miriam, González, Josefa|||0000-0001-9824-027X, Casacuberta, Josep M.|||0000-0002-5609-4152, Castanera, Raúl|||0000-0002-3772-7727
Tipo de recurso: artículo
Fecha de publicación:2019
País:España
Institución:Universitat Autònoma de Barcelona
Repositorio:Dipòsit Digital de Documents de la UAB
Idioma:inglés
OAI Identifier:oai:ddd.uab.cat:221109
Acceso en línea:https://ddd.uab.cat/record/221109
https://dx.doi.org/urn:doi:10.1186/s13100-019-0197-9
Access Level:acceso abierto
Palabra clave:Benchmark
Transposable elements
Polymorphism
Transposon insertion
Resequencing
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spelling A benchmark of transposon insertion detection tools using real dataVendrell Mir, Pol|||0000-0002-5695-5880Barteri, FabioMerenciano, MiriamGonzález, Josefa|||0000-0001-9824-027XCasacuberta, Josep M.|||0000-0002-5609-4152Castanera, Raúl|||0000-0002-3772-7727BenchmarkTransposable elementsPolymorphismTransposon insertionResequencingBackground: 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. 22019-01-0120192019-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/221109https://dx.doi.org/urn:doi:10.1186/s13100-019-0197-9reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengAgencia Estatal de Investigación https://doi.org/10.13039/501100011033 AGL2016-78992-REuropean Commission https://doi.org/10.13039/501100000780 647900Agencia Estatal de Investigación https://doi.org/10.13039/501100011033 BFU2017-82937-Popen accesshttp://purl.org/coar/access_right/c_abf2Aquest 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.https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:2211092026-06-06T12:50:31Z
dc.title.none.fl_str_mv A benchmark of transposon insertion detection tools using real data
title A benchmark of transposon insertion detection tools using real data
spellingShingle A benchmark of transposon insertion detection tools using real data
Vendrell Mir, Pol|||0000-0002-5695-5880
Benchmark
Transposable elements
Polymorphism
Transposon insertion
Resequencing
title_short A benchmark of transposon insertion detection tools using real data
title_full A benchmark of transposon insertion detection tools using real data
title_fullStr A benchmark of transposon insertion detection tools using real data
title_full_unstemmed A benchmark of transposon insertion detection tools using real data
title_sort A benchmark of transposon insertion detection tools using real data
dc.creator.none.fl_str_mv Vendrell Mir, Pol|||0000-0002-5695-5880
Barteri, Fabio
Merenciano, Miriam
González, Josefa|||0000-0001-9824-027X
Casacuberta, Josep M.|||0000-0002-5609-4152
Castanera, Raúl|||0000-0002-3772-7727
author Vendrell Mir, Pol|||0000-0002-5695-5880
author_facet Vendrell Mir, Pol|||0000-0002-5695-5880
Barteri, Fabio
Merenciano, Miriam
González, Josefa|||0000-0001-9824-027X
Casacuberta, Josep M.|||0000-0002-5609-4152
Castanera, Raúl|||0000-0002-3772-7727
author_role author
author2 Barteri, Fabio
Merenciano, Miriam
González, Josefa|||0000-0001-9824-027X
Casacuberta, Josep M.|||0000-0002-5609-4152
Castanera, Raúl|||0000-0002-3772-7727
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Benchmark
Transposable elements
Polymorphism
Transposon insertion
Resequencing
topic Benchmark
Transposable elements
Polymorphism
Transposon insertion
Resequencing
description 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.
publishDate 2019
dc.date.none.fl_str_mv 2
2019-01-01
2019
2019-01-01
dc.type.none.fl_str_mv Article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://ddd.uab.cat/record/221109
https://dx.doi.org/urn:doi:10.1186/s13100-019-0197-9
url https://ddd.uab.cat/record/221109
https://dx.doi.org/urn:doi:10.1186/s13100-019-0197-9
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv Agencia Estatal de Investigación https://doi.org/10.13039/501100011033 AGL2016-78992-R
European Commission https://doi.org/10.13039/501100000780 647900
Agencia Estatal de Investigación https://doi.org/10.13039/501100011033 BFU2017-82937-P
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Dipòsit Digital de Documents de la UAB
instname:Universitat Autònoma de Barcelona
instname_str Universitat Autònoma de Barcelona
reponame_str Dipòsit Digital de Documents de la UAB
collection Dipòsit Digital de Documents de la UAB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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