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.

Center for Comparative Genomics and Bioinformatics Pennsylvania State University University Park Pennsylvania 16802 USA

Centro de Biotecnología y Genómica de Plantas ETSI agrónomos Universidad Politécnica de Madrid Campus de Montegancedo Pozuelo de Alarcón 28223 Madrid Spain

Department of Molecular Biology Max Planck Institute for Developmental Biology 72076 Tübingen Germany

Department of Plant Developmental Biology Max Planck Institute for Plant Breeding Research Carl von Linné Weg 10 D 50829 Cologne Germany

Department of Plant Molecular Genetics Centro Nacional de Biotecnología Consejo Superior de Investigaciones Científicas Campus de Cantoblanco 28049 Madrid Spain

INRA UR1164 URGI Research Unit in Genomics Info INRA de Versailles Grignon Route de Saint Cyr Versailles 78026 France

Institut de Biologie de l'Ecole Normale Supérieure U 1024 Paris France

Research group Plant Cytogenomics CEITEC Central European Institute of Technology Masaryk University Brno Czech Republic

Research School of Biology The Australian National University Canberra ACT 0200 Australia

References provided by Crossref.org

Complementing model species with model clades

Repeat Dynamics across Timescales: A Perspective from Sibling Allotetraploid Marsh Orchids (Dactylorhiza majalis s.l.)

Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina

The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic

The Evolution of Chromosome Numbers: Mechanistic Models and Experimental Approaches

Genomic Blocks in Aethionema arabicum Support Arabideae as Next Diverging Clade in Brassicaceae

Genome Evolution in Arabideae Was Marked by Frequent Centromere Repositioning

The large genome size variation in the Hesperis clade was shaped by the prevalent proliferation of DNA repeats and rarer genome downsizing

PERPETUAL FLOWERING2 coordinates the vernalization response and perennial flowering in Arabis alpina

Monophyletic Origin and Evolution of the Largest Crucifer Genomes

Genome Structure of the Heavy Metal Hyperaccumulator Noccaea caerulescens and Its Stability on Metalliferous and Nonmetalliferous Soils