Transposable element annotation in Corydoras fulleri

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Transposable element annotation in Corydoras fulleri

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Bell, E. A., Butler, C. L., Oliveira, C., Marburger, S., Yant, L., & Taylor, M. I. (2021). 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. 18 August 2021

https://doi.org/10.1111/1755-0998.13489
https://onlinelibrary.wiley.com/doi/ful ... 0998.13489
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.
This paper won't be of much interest to most fish keepers, but it's interesting and FUN to see a rare Corydoras (Corydoras(ln1) fulleri) make its way into the scientific literature.

Cheers, Eric
Attachments
TE library type influences TE abundance. (a) the two Corydoras species used in this study (i) Corydoras fulleri and (ii) Corydoras maculifer. (b) Estimated TE abundance is given as percentage of total genome/transcriptome size for the C. fulleri genome and the C. maculifer genome and transcriptome
TE library type influences TE abundance. (a) the two Corydoras species used in this study (i) Corydoras fulleri and (ii) Corydoras maculifer. (b) Estimated TE abundance is given as percentage of total genome/transcriptome size for the C. fulleri genome and the C. maculifer genome and transcriptome
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