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

10.24072/pcjournal.68 - Peer Community Journal, Volume 2 (2022), article no. e14.

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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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DOI: 10.24072/pcjournal.68
Baud, Agnès 1; Wan, Mariène 1; Nouaud, Danielle 2; Francillonne, Nicolas 3; Anxolabéhère, Dominique 2, 4; Quesneville, Hadi 1, 3

1 Université Paris-Saclay, INRAE, URGI, 78026, Versailles, France
2 IJM, Institut Jacques Monod, CNRS UMR 7592, Université Paris-Diderot, Paris, France
3 Université Paris-Saclay, INRAE, BioinfOmics, Plant bioinformatics facility, 78026, Versailles, France
4 Université Paris-Sorbonne, Paris, France
     author = {Baud, Agn\`es and Wan, Mari\`ene and Nouaud, Danielle and Francillonne, Nicolas and Anxolab\'eh\`ere, Dominique and Quesneville, Hadi},
     title = {Traces of transposable elements in genome dark matter co-opted by flowering gene regulation networks},
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Baud, Agnès; Wan, Mariène; Nouaud, Danielle; Francillonne, Nicolas; Anxolabéhère, Dominique; Quesneville, Hadi. Traces of transposable elements in genome dark matter co-opted by flowering gene regulation networks. Peer Community Journal, Volume 2 (2022), article  no. e14. doi : 10.24072/pcjournal.68.

Peer reviewed and recommended by PCI : 10.24072/pci.genomics.100004

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