Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes

[en] Background: Transposable elements (TEs) are genomic parasites with major impacts on host genome architecture and host adaptation. A proper evaluation of their evolutionary significance has been hampered by the paucity of short scale phylogenetic comparisons between closely related species. Here, we characterized the dynamics of TE accumulation at the micro-evolutionary scale by comparing two closely related plant species, Arabidopsis lyrata and A. halleri. Results: Joint genome annotation in these two outcrossing species confirmed that both contain two distinct populations of TEs with either 'recent' or 'old' insertion histories. Identification of rare segregating insertions suggests that diverse TE families contribute to the ongoing dynamics of TE accumulation in the two species. Orthologous TE fragments (i.e. those that have been maintained in both species), tend to be located closer to genes than those that are retained in one species only. Compared to non-orthologous TE insertions, those that are orthologous tend to produce fewer short interfering RNAs, are less heavily methylated when found within or adjacent to genes and these tend to have lower expression levels. These findings suggest that long-term retention of TE insertions reflects their frequent acquisition of adaptive roles and/or the deleterious effects of removing nearly neutral TE insertions when they are close to genes. Conclusion: Our results indicate a rapid evolutionary dynamics of the TE landscape in these two outcrossing species, with an important input of a diverse set of new insertions with variable propensity to resist deletion. © 2019 The Author(s).

Disciplines :

Genetics & genetic processes

Author, co-author :

Legrand, S; Univ. Lille, CNRS, UMR-Evo-Eco-Paleo, Lille, F-59000, France

Caron, T; Univ. Lille, CNRS, UMR-Evo-Eco-Paleo, Lille, F-59000, France

Maumus, S; URGI, INRA, Université Paris-Saclay, Versailles, 78026, France

Schvartzman, S; Université de Liège - ULiège > Département des sciences de la vie > Génomique fonctionnelle et imagerie moléculaire végétale

Quadrana, L; IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, PSL Research University, Paris, F-75005, France

Durand, E; Univ. Lille, CNRS, UMR-Evo-Eco-Paleo, Lille, F-59000, France

Gallina, S; Univ. Lille, CNRS, UMR-Evo-Eco-Paleo, Lille, F-59000, France

Pauwels, M; Univ. Lille, CNRS, UMR-Evo-Eco-Paleo, Lille, F-59000, France

Mazoyer, C; Univ. Lille, CNRS, UMR-Evo-Eco-Paleo, Lille, F-59000, France

Huyghe, L; Univ. Lille, CNRS, UMR-Evo-Eco-Paleo, Lille, F-59000, France

More authors (3 more)

Language :

English

Title :

Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes

Publication date :

2019

Journal title :

Mobile DNA

ISSN :

1759-8753

Publisher :

BioMed Central, United Kingdom

Volume :

Pages :

Peer reviewed :

Peer Reviewed verified by ORBi

Name of the research project :

ANR-18-CE02-0020-01; PDR-T.0206.13; Novelis: 648321

Funders :

CNRS - Centre National de la Recherche Scientifique
ANR - Agence Nationale de la Recherche
FEDER - Fonds Europ�en de D�veloppement R�gional
F.R.S.-FNRS - Fonds de la Recherche Scientifique
R�gion Hauts-de-France
ERC - European Research Council
ULi�ge - Universit� de Li�ge

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