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. ORCID: https://orcid.org/0000-0001-7427-6331, Butler, Christopher L., Oliveira, Claudio, Marburger, Sarah, Yant, Levi and Taylor, Martin I. ORCID: https://orcid.org/0000-0002-3858-0712 (2022) Transposable element annotation in non-model species ‐ the benefits of species‐specific repeat libraries using semi-automated EDTA and DeepTE de novo pipelines. Molecular Ecology Resources, 22 (2). pp. 823-833. ISSN 1755-098X

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Abstract

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.

Item Type:	Article
Additional Information:	Funding information: Natural Environment Research Council. Grant Number: NE/L002582/1; Biotechnology and Biological Science Research Council. Grant Numbers: BB/R017174/1, BB/P013511/1; European Research Council. Grant Number: ERC-StG 679056 HOTSPOT
Faculty \ School:	Faculty of Science > School of Biological Sciences
UEA Research Groups:	Faculty of Science > Research Groups > Organisms and the Environment Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation
Related URLs:	https://onlinelibrary.wiley.com/doi/10.1...
Depositing User:	LivePure Connector
Date Deposited:	25 Aug 2021 09:54
Last Modified:	03 Nov 2024 00:49
URI:	https://ueaeprints.uea.ac.uk/id/eprint/81200
DOI:	10.1111/1755-0998.13489

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