Transposable element annotation in non-model species: The benefits of species-specific repeat libraries using semi-automated EDTA and DeepTE de novo pipelines

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MetadadosDescriçãoIdioma
Autor(es): dc.contributorUniversity of East Anglia-
Autor(es): dc.contributorUniversidade Estadual Paulista (UNESP)-
Autor(es): dc.contributorJohn Innes Centre-
Autor(es): dc.contributorUniversity of Nottingham-
Autor(es): dc.creatorBell, Ellen A.-
Autor(es): dc.creatorButler, Christopher L.-
Autor(es): dc.creatorOliveira, Claudio [UNESP]-
Autor(es): dc.creatorMarburger, Sarah-
Autor(es): dc.creatorYant, Levi-
Autor(es): dc.creatorTaylor, Martin I.-
Data de aceite: dc.date.accessioned2022-08-04T22:12:10Z-
Data de disponibilização: dc.date.available2022-08-04T22:12:10Z-
Data de envio: dc.date.issued2022-04-28-
Data de envio: dc.date.issued2022-04-28-
Data de envio: dc.date.issued2022-01-31-
Fonte completa do material: dc.identifierhttp://dx.doi.org/10.1111/1755-0998.13489-
Fonte completa do material: dc.identifierhttp://hdl.handle.net/11449/222331-
Fonte: dc.identifier.urihttp://educapes.capes.gov.br/handle/11449/222331-
Descrição: dc.descriptionTransposable 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.-
Descrição: dc.descriptionBiotechnology and Biological Sciences Research Council-
Descrição: dc.descriptionH2020 European Research Council-
Descrição: dc.descriptionNatural Environment Research Council-
Descrição: dc.descriptionSchool of Biological Sciences University of East Anglia-
Descrição: dc.descriptionDepartment of Structural and Functional Biology Institute of Biosciences/UNESP Rua Doutor Antonio Celso Wagner Zanin-
Descrição: dc.descriptionDepartment of Cell and Developmental Biology John Innes Centre-
Descrição: dc.descriptionFuture Food Beacon of Excellence and the School of Life Sciences University of Nottingham-
Descrição: dc.descriptionDepartment of Structural and Functional Biology Institute of Biosciences/UNESP Rua Doutor Antonio Celso Wagner Zanin-
Descrição: dc.descriptionBiotechnology and Biological Sciences Research Council: BB/P013511/1-
Descrição: dc.descriptionBiotechnology and Biological Sciences Research Council: BB/R017174/1-
Descrição: dc.descriptionH2020 European Research Council: ERC-StG 679056 HOTSPOT-
Descrição: dc.descriptionNatural Environment Research Council: NE/L002582/1-
Formato: dc.format823-833-
Idioma: dc.languageen-
Relação: dc.relationMolecular Ecology Resources-
???dc.source???: dc.sourceScopus-
Título: dc.titleTransposable element annotation in non-model species: The benefits of species-specific repeat libraries using semi-automated EDTA and DeepTE de novo pipelines-
Tipo de arquivo: dc.typelivro digital-
Aparece nas coleções:Repositório Institucional - Unesp

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