Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation
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Author
Willing, Eva Maria
Rawat, Vimal
Mandáková, Terezie
Maumus, Florian
James, Geo Velikkakam
Nordström, 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
Piednoël, Mathieu
Hagmann, Jörg
Chen-Min-Tao, Romy
Iglesias-Fernández, Raquel
Schuster, Stephan C.
Alonso-Blanco, Carlos
Roudier, François
Carbonero, Pilar
Paz-Ares, Javier
Davis, Seth J.
Pecinka, Ales
Quesneville, Hadi
Colot, Vincent
Lysak, Martin A.
Weigel, Detlef
Coupland, George
Schneeberger, Korbinian
Attention
2299/19655
Abstract
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.