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Section: Genomics
Topic: Genetics/Genomics, Plant biology, Evolution

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

Baud, Agnès1; Wan, Mariène1; Nouaud, Danielle2; Francillonne, Nicolas3 ; Anxolabéhère, Dominique2, 4; Quesneville, Hadi3, 1  
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

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

Get full text PDF Peer reviewed and recommended by PCI

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.

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

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
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
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     title = {Traces of transposable elements in genome dark matter co-opted by flowering gene regulation networks},
     journal = {Peer Community Journal},
     eid = {e14},
     publisher = {Peer Community In},
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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. https://peercommunityjournal.org/articles/10.24072/pcjournal.68/

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

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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