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Traces of transposable elements in genome dark matter co-opted by flowering gene regulation networks

Résumé : Transposable elements (TEs) are mobile, repetitive DNA sequences that make the largest contribution to genome bulk. They thus contribute to the so-called “dark matter of the genome”, the part of the genome in which nothing is immediately recognizable as biologically functional. We developed a new method, based on k-mers , to identify degenerate TE sequences. With this new algorithm, we detect up to 10% of the A. thaliana genome as derived from as yet unidentified TEs, bringing the proportion of the genome known to be derived from TEs up to 50%. A significant proportion of these sequences overlapped conserved non-coding sequences identified in crucifers and rosids, and transcription factor binding sites. They are overrepresented in some gene regulation networks, such as the flowering gene network, suggesting a functional role for these sequences that have been conserved for more than 100 million years, since the spread of flowering plants in the Cretaceous.
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Preprints, Working Papers, ...
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https://hal.inrae.fr/hal-02956027
Contributor : Hadi Quesneville <>
Submitted on : Friday, October 2, 2020 - 12:26:51 PM
Last modification on : Wednesday, June 2, 2021 - 4:26:36 PM

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Agnès Baud, Mariène Wan, Danielle Nouaud, Nicolas Francillonne, Dominique Anxolabéhère, et al.. Traces of transposable elements in genome dark matter co-opted by flowering gene regulation networks. 2020. ⟨hal-02956027⟩

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