Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation

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Authors

WILLING Eva-Maria RAWAT Vimal MANDÁKOVÁ Terezie MAUMUS Florian JAMES Geo Velikkakam NORDSTROM Karl J. V. BECKER Claude WARTHMANN Norman CHICA Claudia SZARZYNSKA Bogna ZYTNICKI Matthias ALBANI Maria C. KIEFER Christiane BERGONZI Sara CASTAINGS Loren MATEOS Julieta L. BERNS Markus C. BUJDOSO Nora PIOFCZYK Thomas DE LORENZO Laura BARRERO-SICILIA Cristina MATEOS Isabel PIEDNOEL Mathieu HAGMANN Joerg CHEN-MIN-TAO Romy IGLESIAS-FERNANDEZ Raquel SCHUSTER Stephan C. ALONSO-BLANCO Carlos ROUDIER Francois CARBONERO Pilar PAZ-ARES Javier DAVIS Seth J. PEČINKA Aleš QUESNEVILLE Hadi COLOT Vincent LYSÁK Martin WEIGEL Detlef COUPLAND George SCHNEEBERGER Korbinian

Year of publication 2015
Type Article in Periodical
Magazine / Source NATURE PLANTS
MU Faculty or unit

Central European Institute of Technology

Citation
Web http://www.nature.com/articles/nplants201423
Doi http://dx.doi.org/10.1038/NPLANTS.2014.23
Field Botany
Keywords ARABIDOPSIS-THALIANA; PROVIDES INSIGHT; EVOLUTION; LYRATA; DIVERGENCE; SEQUENCE; REVEALS; SIZE
Description Despite evolutionary conserved mechanisms to silence transposable element activity, there are drastic differences in the abundance of transposable elements even among closely related plant species. We conducted a de novo assembly for the 375 Mb genome of the perennial model plant, Arabis alpina. Analysing this genome revealed long-lasting and recent transposable element activity predominately driven by Gypsy long terminal repeat retrotransposons, which extended the low-recombining pericentromeres and transformed large formerly euchromatic regions into repeat-rich pericentromeric regions. This reduced capacity for long terminal repeat retrotransposon silencing and removal in A. alpina co-occurs with unexpectedly low levels of DNA methylation. Most remarkably, the striking reduction of symmetrical CG and CHG methylation suggests weakened DNA methylation maintenance in A. alpina compared with Arabidopsis thaliana. Phylogenetic analyses indicate a highly dynamic evolution of some components of methylation maintenance machinery that might be related to the unique methylation in A. alpina.
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