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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; Butler, Christopher L; Oliveira, Claudio; Marburger, Sarah; Yant, Levi; Taylor, Martin I.
Affiliation
  • Bell EA; School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK.
  • Butler CL; School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK.
  • Oliveira C; Department of Structural and Functional Biology, Institute of Biosciences/UNESP, Rua Professor Doutor Antonio Celso Wagner Zanin, Botucatu, São Paulo, Brazil.
  • Marburger S; Department of Cell and Developmental Biology, John Innes Centre, Norwich, Norfolk, UK.
  • Yant L; Future Food Beacon of Excellence and the School of Life Sciences, University of Nottingham, Nottingham, UK.
  • Taylor MI; School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK.
Mol Ecol Resour ; 22(2): 823-833, 2022 Feb.
Article in En | MEDLINE | ID: mdl-34407282
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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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: DNA Transposable Elements / Genomics Language: En Journal: Mol Ecol Resour Year: 2022 Document type: Article Country of publication: Reino Unido

Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: DNA Transposable Elements / Genomics Language: En Journal: Mol Ecol Resour Year: 2022 Document type: Article Country of publication: Reino Unido