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.

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.

Citation

Bell, E. A., Butler, C. L., Oliveira, C., Marburger, S., Yant, L., & Taylor, M. I. (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), 823-833. https://doi.org/10.1111/1755-0998.13489

• Journal Article Type: Article
• Acceptance Date: Aug 12, 2021
• Online Publication Date: Sep 2, 2021
• Publication Date: 2022-02
• Deposit Date: Sep 24, 2021
• Publicly Available Date: Sep 28, 2021
• Journal: Molecular Ecology Resources
• Print ISSN: 1755-098X
• Electronic ISSN: 1755-0998
• Publisher: Wiley
• Peer Reviewed: Peer Reviewed
• Volume: 22
• Issue: 2
• Pages: 823-833
• DOI: https://doi.org/10.1111/1755-0998.13489
• Keywords: Genetics; Ecology, Evolution, Behavior and Systematics; Biotechnology
• Public URL: https://nottingham-repository.worktribe.com/output/6192964
• Publisher URL: https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13489