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International,  ACL (papers with reading comittee)

Mobile DNA, 2019, 10 (1) : 1-17.

05 Sep 2019   Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes

Legrand, S. ; Caron, T. ; Maumus, F. ; Schvartzman, S. ; Quadrana, L. ; Durand, E. ; Gallina, S. ; Pauwels, M. ; Mazoyer, C. ; Huyghe, L. ; Colot, V. ; Hanikenne, M. ; Castric, V.

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_Legrand_Mobile DNA.pdf

Creation date: 30 Sep 2019