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

Willing, Eva María and Rawat, Vimal and Mandákova, Terezie and Maumus, Florian and James, Geo Velikkaham and Nordström, Karl J.V. and Becker, Claude and Warthmann, Norman and Chica, Claudia and Szarzynska, Bogna and Zythniki, Bogna and Albani, María C. and Kiefer, Christiane and Bergonzi, Sara and Castaings, Loren and Mateos, Julieta L. and Berns, Markus C. and Bujdoso, Nora and Piofczyk, Thomas and Lorenzo, Laura de and Barrero Sicilia, Cristina and Mateos, Isabel and Piednöel, Mathieu and Hagmann, Jörg and Chen-Min-Tao, Romy and Iglesias Fernández, Raquel and Schuster, Stephan C. and Alonso Blanco, Carlos and Roudier, François and Carbonero Zalduegui, Pilar and Paz Ares, Javier and Davis, Seth J. and Pecinka, Ales and Quesneville, Hadi and Colot, Vicent and Lysak, Martin A. and Weigel, Detlef and Coupland, George and Schneeberger, Korbinian (2015). Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. "Nature Plants", v. 1 (n. 2); pp. 1-7. ISSN 2055-026X. https://doi.org/10.1038/NPLANTS.2014.23.

Description

Title: Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation
Author/s:
  • Willing, Eva María
  • Rawat, Vimal
  • Mandákova, Terezie
  • Maumus, Florian
  • James, Geo Velikkaham
  • Nordström, Karl J.V.
  • Becker, Claude
  • Warthmann, Norman
  • Chica, Claudia
  • Szarzynska, Bogna
  • Zythniki, Bogna
  • Albani, María C.
  • Kiefer, Christiane
  • Bergonzi, Sara
  • Castaings, Loren
  • Mateos, Julieta L.
  • Berns, Markus C.
  • Bujdoso, Nora
  • Piofczyk, Thomas
  • Lorenzo, Laura de
  • Barrero Sicilia, Cristina
  • Mateos, Isabel
  • Piednöel, Mathieu
  • Hagmann, Jörg
  • Chen-Min-Tao, Romy
  • Iglesias Fernández, Raquel
  • Schuster, Stephan C.
  • Alonso Blanco, Carlos
  • Roudier, François
  • Carbonero Zalduegui, Pilar
  • Paz Ares, Javier
  • Davis, Seth J.
  • Pecinka, Ales
  • Quesneville, Hadi
  • Colot, Vicent
  • Lysak, Martin A.
  • Weigel, Detlef
  • Coupland, George
  • Schneeberger, Korbinian
Item Type: Article
Título de Revista/Publicación: Nature Plants
Date: February 2015
ISSN: 2055-026X
Volume: 1
Subjects:
Faculty: E.T.S. de Ingeniería Agronómica, Alimentaria y de Biosistemas (UPM)
Department: Biotecnología - Biología Vegetal
Creative Commons Licenses: Recognition - No derivative works - Non commercial

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Abstract

Despite evolutionary conserved mechanisms to silence trans-posable 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 trans-posable 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.

Funding Projects

TypeCodeAcronymLeaderTitle
FP7226477AENEASUniversita Degli Studie di PadovaAquired Environmental Epigenetics Advances: from Arabidopsis to maize
Government of SpainCONSOLIDER CSD 2007-00057TRANSPLANTAFrancisco Javier Paz AresFunción y Potencial Biotecnológico de los Factores de Transcripción en plantas
Government of Spain2007-28317CONSOLIDERUnspecifiedUnspecified
Government of SpainBIO2013-45407UnspecifiedUnspecifiedIdentificación de nuevos genes y mecanismos moleculares implicados en la adaptación al cambio climático en arabidopsis
Government of SpainBIO2011-30546UnspecifiedUnspecifiedLos represores Della y factores PIF: integradores de señales hormonales con un papel central en la adaptación de las plantas a condiciones ambientales adversas
Government of SpainBFU2009-11809UnspecifiedUnspecifiedUnspecified
FP7257082EPIGENESYSUnspecifiedEpigenetics towards systems biology
Government of SpainJCI-2010-07909UnspecifiedUnspecifiedUnspecified
Government of SpainCSD2007-00057UnspecifiedUnspecifiedUnspecified

More information

Item ID: 53821
DC Identifier: http://oa.upm.es/53821/
OAI Identifier: oai:oa.upm.es:53821
DOI: 10.1038/NPLANTS.2014.23
Official URL: https://www.nature.com/articles/nplants201423
Deposited by: Biblioteca ETSI Agrónomos
Deposited on: 01 Feb 2019 13:38
Last Modified: 10 Jun 2019 16:50
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