PCI Genomics

Title

Traces of transposable element in genome dark matter co-opted by flowering gene regulation networksuse asterix (*) to get italics

Authors

Agnes Baud, Mariene Wan, Danielle Nouaud, Nicolas Francillonne, Dominique Anxolabehere, Hadi QuesnevillePlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"

Year

2021

Picture

Abstract

<p>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.</p>

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Keywords

Transposable element, Arabidopsis, Bioinformatics, Genome evolution

Methods that require specific expertise (optional)

NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).

Thematic fields

Bioinformatics, Evolutionary genomics, Functional genomics, Plants, Structural genomics, Viruses and transposable elements

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Submission date

2020-04-07 17:12:12

Recommender

Francois Sabot

Reviewers

Anonymous, Josep Casacuberta

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