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

EVA-MARIA WILLING; VIMAL RAWAT; TEREZIE MANDÁKOVÁ; FLORIAN MAUMUS; GEO VELIKKAKAM JAMES; KARL J.V. NORDSTRÖM; CLAUDE BECKER; NORMAN WARTHMANN; CLAUDIA CHICA; BOGNA SZARZYNSKA; MATTHIAS ZYTNICKI; MARIA C. ALBANI; CHRISTIANE KIEFER; SARA BERGONZI; LOREN CASTAINGS; JULIETA L, MATEOS; MARKUS C. BERNS; NORA BUJDOSO; THOMAS PIOFCZYK; LAURA DE LORENZO; CRISTINA BARRERO-SICILIA; ISABEL MATEOS; MATHIEU PIEDNOËL; JÖRG HAGMANN; ROMY CHEN-MIN-TAO; RAQUEL IGLESIAS-FERNÁNDEZ; STEPHAN C. SCHUSTER; CARLOS ALONSO-BLANCO; FRANÇOIS ROUDIER; PILAR CARBONERO; JAVIER PAZ-ARES; SETH J. DAVIES; ALES PECINKA; HADI QUESNEVILLE; VINCENT COLOT; MARTIN A. LYSAK; DETLEF WEIGEL; GEORGE COUPLAND; KORBINIAN SCHNEEBERGER

Nature Plants

Nature Publishing Group

Año: 2015 vol. 1

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 lowr ecombining 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.