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

Abstract 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...

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Bibliographic Details
Published inbioRxiv
Main Authors Baud, Agnès, Wan, Mariène, Nouaud, Danielle, Francillonne, Nicolas, Anxolabéhère, Dominique, Quesneville, Hadi
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 17.02.2021
Subjects
Binding sites
Flowering
Gene regulation
Genomes
Nucleotide sequence
Transcription factors
Transposons
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Summary:Abstract 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. Competing Interest Statement The authors have declared no competing interest. Footnotes * Cite as: Baud, A., Wan, M., Nouaud, D., Francillonne, N., Anxolabéhère, D. and Quesneville, H. (2021). Traces of transposable elements in genome dark matter co-opted by flowering gene regulation networks. bioRxiv, 547877, ver. 6 peer-reviewed and recommended by PCI Genomics.doi: https://doi.org/10.1101/547877 * Version 6 of this preprint has been reformatted according as recommended by Peer Community In Genomics * https://urgi.versailles.inrae.fr/files/sequence/PubAthaDarkmatterData/PubAthaDarkmatterData.zip
DOI:10.1101/547877