Journal
MOBILE DNA
Volume 10, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s13100-019-0171-6
Keywords
Transposable elements; Arabidopsis; Genome evolution; Comparative genomics
Categories
Funding
- European Research Council (NOVEL project) [648321]
- Region Hauts-de-France (MICRO2 project, Program projet emergent)
- Agence Nationale de la Recherche (TE-MoMa project) [ANR-18-CE02-0020-01]
- Fonds de la Recherche Scientifique-FNRS [PDR-T.0206.13]
- University of Liege [SFRD-12/03]
- ANR ELO-CANTH [ANR-12-JSV7-0010]
- Region Hauts-de-France
- Ministere de l'Enseignement Superieur et de la Recherche (CPER Climibio)
- European Fund for Regional Economic Development
- European Research Council (ERC) [648321] Funding Source: European Research Council (ERC)
- Agence Nationale de la Recherche (ANR) [ANR-18-CE02-0020] Funding Source: Agence Nationale de la Recherche (ANR)
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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.
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