Transposable element annotation in non-model species: The benefits of species-specific repeat libraries using semi-automated EDTA and DeepTE de novo pipelines
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1111/1755-0998.13489 http://hdl.handle.net/11449/222331 |
Resumo: | Transposable elements (TEs) are significant genomic components which can be detected either through sequence homology against existing databases or de novo, with the latter potentially reducing the risk of underestimating TE abundance. Here, we describe the semi-automated generation of a de novo TE library using the newly developed EDTA pipeline and DeepTE classifier in a non-model teleost (Corydoras fulleri). Using both genomic and transcriptomic data, we assess this de novo pipeline's performance across four TE based metrics: (i) abundance, (ii) composition, (iii) fragmentation, and (iv) age distributions. We then compare the results to those found when using a curated teleost library (Danio rerio). We identify quantitative differences in these metrics and highlight how TE library choice can have major impacts on TE-based estimates in non-model species. |
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Repositório Institucional da UNESP |
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spelling |
Transposable element annotation in non-model species: The benefits of species-specific repeat libraries using semi-automated EDTA and DeepTE de novo pipelinesTransposable elements (TEs) are significant genomic components which can be detected either through sequence homology against existing databases or de novo, with the latter potentially reducing the risk of underestimating TE abundance. Here, we describe the semi-automated generation of a de novo TE library using the newly developed EDTA pipeline and DeepTE classifier in a non-model teleost (Corydoras fulleri). Using both genomic and transcriptomic data, we assess this de novo pipeline's performance across four TE based metrics: (i) abundance, (ii) composition, (iii) fragmentation, and (iv) age distributions. We then compare the results to those found when using a curated teleost library (Danio rerio). We identify quantitative differences in these metrics and highlight how TE library choice can have major impacts on TE-based estimates in non-model species.Biotechnology and Biological Sciences Research CouncilH2020 European Research CouncilNatural Environment Research CouncilSchool of Biological Sciences University of East AngliaDepartment of Structural and Functional Biology Institute of Biosciences/UNESP Rua Doutor Antonio Celso Wagner ZaninDepartment of Cell and Developmental Biology John Innes CentreFuture Food Beacon of Excellence and the School of Life Sciences University of NottinghamDepartment of Structural and Functional Biology Institute of Biosciences/UNESP Rua Doutor Antonio Celso Wagner ZaninBiotechnology and Biological Sciences Research Council: BB/P013511/1Biotechnology and Biological Sciences Research Council: BB/R017174/1H2020 European Research Council: ERC-StG 679056 HOTSPOTNatural Environment Research Council: NE/L002582/1University of East AngliaUniversidade Estadual Paulista (UNESP)John Innes CentreUniversity of NottinghamBell, Ellen A.Butler, Christopher L.Oliveira, Claudio [UNESP]Marburger, SarahYant, LeviTaylor, Martin I.2022-04-28T19:44:05Z2022-04-28T19:44:05Z2022-02-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article823-833http://dx.doi.org/10.1111/1755-0998.13489Molecular Ecology Resources, v. 22, n. 2, p. 823-833, 2022.1755-09981755-098Xhttp://hdl.handle.net/11449/22233110.1111/1755-0998.134892-s2.0-85114040631Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengMolecular Ecology Resourcesinfo:eu-repo/semantics/openAccess2022-04-28T19:44:05Zoai:repositorio.unesp.br:11449/222331Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T19:10:53.262376Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Transposable element annotation in non-model species: The benefits of species-specific repeat libraries using semi-automated EDTA and DeepTE de novo pipelines |
title |
Transposable element annotation in non-model species: The benefits of species-specific repeat libraries using semi-automated EDTA and DeepTE de novo pipelines |
spellingShingle |
Transposable element annotation in non-model species: The benefits of species-specific repeat libraries using semi-automated EDTA and DeepTE de novo pipelines Bell, Ellen A. |
title_short |
Transposable element annotation in non-model species: The benefits of species-specific repeat libraries using semi-automated EDTA and DeepTE de novo pipelines |
title_full |
Transposable element annotation in non-model species: The benefits of species-specific repeat libraries using semi-automated EDTA and DeepTE de novo pipelines |
title_fullStr |
Transposable element annotation in non-model species: The benefits of species-specific repeat libraries using semi-automated EDTA and DeepTE de novo pipelines |
title_full_unstemmed |
Transposable element annotation in non-model species: The benefits of species-specific repeat libraries using semi-automated EDTA and DeepTE de novo pipelines |
title_sort |
Transposable element annotation in non-model species: The benefits of species-specific repeat libraries using semi-automated EDTA and DeepTE de novo pipelines |
author |
Bell, Ellen A. |
author_facet |
Bell, Ellen A. Butler, Christopher L. Oliveira, Claudio [UNESP] Marburger, Sarah Yant, Levi Taylor, Martin I. |
author_role |
author |
author2 |
Butler, Christopher L. Oliveira, Claudio [UNESP] Marburger, Sarah Yant, Levi Taylor, Martin I. |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
University of East Anglia Universidade Estadual Paulista (UNESP) John Innes Centre University of Nottingham |
dc.contributor.author.fl_str_mv |
Bell, Ellen A. Butler, Christopher L. Oliveira, Claudio [UNESP] Marburger, Sarah Yant, Levi Taylor, Martin I. |
description |
Transposable elements (TEs) are significant genomic components which can be detected either through sequence homology against existing databases or de novo, with the latter potentially reducing the risk of underestimating TE abundance. Here, we describe the semi-automated generation of a de novo TE library using the newly developed EDTA pipeline and DeepTE classifier in a non-model teleost (Corydoras fulleri). Using both genomic and transcriptomic data, we assess this de novo pipeline's performance across four TE based metrics: (i) abundance, (ii) composition, (iii) fragmentation, and (iv) age distributions. We then compare the results to those found when using a curated teleost library (Danio rerio). We identify quantitative differences in these metrics and highlight how TE library choice can have major impacts on TE-based estimates in non-model species. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-04-28T19:44:05Z 2022-04-28T19:44:05Z 2022-02-01 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1111/1755-0998.13489 Molecular Ecology Resources, v. 22, n. 2, p. 823-833, 2022. 1755-0998 1755-098X http://hdl.handle.net/11449/222331 10.1111/1755-0998.13489 2-s2.0-85114040631 |
url |
http://dx.doi.org/10.1111/1755-0998.13489 http://hdl.handle.net/11449/222331 |
identifier_str_mv |
Molecular Ecology Resources, v. 22, n. 2, p. 823-833, 2022. 1755-0998 1755-098X 10.1111/1755-0998.13489 2-s2.0-85114040631 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Molecular Ecology Resources |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
823-833 |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1808129030070730752 |