title: Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation.
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.
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany.
authors.forename: Eva-Maria
authors.initials: EM
authors.lastname: Willing
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany.
authors.forename: Vimal
authors.initials: V
authors.lastname: Rawat
authors.affiliation: Research group Plant Cytogenomics, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
authors.forename: Terezie
authors.initials: T
authors.lastname: Mandáková
authors.affiliation: INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France.
authors.forename: Florian
authors.initials: F
authors.lastname: Maumus
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany.
authors.forename: Geo Velikkakam
authors.initials: GV
authors.lastname: James
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany.
authors.forename: Karl J V
authors.initials: KJ
authors.lastname: Nordström
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors.forename: Claude
authors.initials: C
authors.lastname: Becker
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.|Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia.
authors.forename: Norman
authors.identifier: http://orcid.org/0000-0002-1178-8409
authors.initials: N
authors.lastname: Warthmann
authors.affiliation: Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 and Institut National de la Santé et de la Recherche Médicale (INSERM) U 1024, Paris, France.
authors.forename: Claudia
authors.initials: C
authors.lastname: Chica
authors.affiliation: Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 and Institut National de la Santé et de la Recherche Médicale (INSERM) U 1024, Paris, France.
authors.forename: Bogna
authors.initials: B
authors.lastname: Szarzynska
authors.affiliation: INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France.
authors.forename: Matthias
authors.initials: M
authors.lastname: Zytnicki
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany.
authors.forename: Maria C
authors.initials: MC
authors.lastname: Albani
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany.
authors.forename: Christiane
authors.initials: C
authors.lastname: Kiefer
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany.
authors.forename: Sara
authors.initials: S
authors.lastname: Bergonzi
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany.
authors.forename: Loren
authors.initials: L
authors.lastname: Castaings
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany.
authors.forename: Julieta L
authors.initials: JL
authors.lastname: Mateos
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany.
authors.forename: Markus C
authors.initials: MC
authors.lastname: Berns
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany.
authors.forename: Nora
authors.initials: N
authors.lastname: Bujdoso
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Piofczyk
authors.affiliation: Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain.
authors.forename: Laura
authors.initials: L
authors.lastname: de Lorenzo
authors.affiliation: Centro de Biotecnología y Genómica de Plantas (UPM-INIA). ETSI agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain.
authors.forename: Cristina
authors.initials: C
authors.lastname: Barrero-Sicilia
authors.affiliation: Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain.
authors.forename: Isabel
authors.initials: I
authors.lastname: Mateos
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Piednoël
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors.forename: Jörg
authors.initials: J
authors.lastname: Hagmann
authors.affiliation: Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 and Institut National de la Santé et de la Recherche Médicale (INSERM) U 1024, Paris, France.
authors.forename: Romy
authors.initials: R
authors.lastname: Chen-Min-Tao
authors.affiliation: Centro de Biotecnología y Genómica de Plantas (UPM-INIA). ETSI agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain.
authors.forename: Raquel
authors.initials: R
authors.lastname: Iglesias-Fernández
authors.affiliation: Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors.forename: Stephan C
authors.initials: SC
authors.lastname: Schuster
authors.affiliation: Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain.
authors.forename: Carlos
authors.initials: C
authors.lastname: Alonso-Blanco
authors.affiliation: Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 and Institut National de la Santé et de la Recherche Médicale (INSERM) U 1024, Paris, France.
authors.forename: François
authors.identifier: http://orcid.org/0000-0002-1757-6386
authors.initials: F
authors.lastname: Roudier
authors.affiliation: Centro de Biotecnología y Genómica de Plantas (UPM-INIA). ETSI agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain.
authors.forename: Pilar
authors.initials: P
authors.lastname: Carbonero
authors.affiliation: Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain.
authors.forename: Javier
authors.initials: J
authors.lastname: Paz-Ares
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany.
authors.forename: Seth J
authors.initials: SJ
authors.lastname: Davis
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany.
authors.forename: Ales
authors.initials: A
authors.lastname: Pecinka
authors.affiliation: INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France.
authors.forename: Hadi
authors.identifier: http://orcid.org/0000-0003-3001-4908
authors.initials: H
authors.lastname: Quesneville
authors.affiliation: Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 and Institut National de la Santé et de la Recherche Médicale (INSERM) U 1024, Paris, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Colot
authors.affiliation: Research group Plant Cytogenomics, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
authors.forename: Martin A
authors.initials: MA
authors.lastname: Lysak
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors.forename: Detlef
authors.initials: D
authors.lastname: Weigel
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany.
authors.forename: George
authors.initials: G
authors.lastname: Coupland
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany.
authors.forename: Korbinian
authors.initials: K
authors.lastname: Schneeberger