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

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 ORCID: https://orcid.org/0000-0003-4773-7176, Schuster, Stephan C., Alonso Blanco, Carlos, Roudier, François, Carbonero Zalduegui, Pilar ORCID: https://orcid.org/0000-0002-4949-3577, Paz Ares, Javier, Davis, Seth J., Pecinka, Ales, Quesneville, Hadi, Colot, Vicent, Lysak, Martin A., Weigel, Detlef, 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 https://orcid.org/0000-0003-4773-7176
  • Schuster, Stephan C.
  • Alonso Blanco, Carlos
  • Roudier, François
  • Carbonero Zalduegui, Pilar https://orcid.org/0000-0002-4949-3577
  • 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

Type
Code
Acronym
Leader
Title
FP7
226477
AENEAS
Universita Degli Studie di Padova
Aquired Environmental Epigenetics Advances: from Arabidopsis to maize
Government of Spain
CONSOLIDER CSD 2007-00057
TRANSPLANTA
Francisco Javier Paz Ares
Función y Potencial Biotecnológico de los Factores de Transcripción en plantas
Government of Spain
2007-28317
CONSOLIDER
Unspecified
Unspecified
Government of Spain
BIO2013-45407
Unspecified
Unspecified
Identificación de nuevos genes y mecanismos moleculares implicados en la adaptación al cambio climático en arabidopsis
Government of Spain
BIO2011-30546
Unspecified
Unspecified
Los 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 Spain
BFU2009-11809
Unspecified
Unspecified
Unspecified
FP7
257082
EPIGENESYS
Unspecified
Epigenetics towards systems biology
Government of Spain
JCI-2010-07909
Unspecified
Unspecified
Unspecified
Government of Spain
CSD2007-00057
Unspecified
Unspecified
Unspecified

More information

Item ID: 53821
DC Identifier: https://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 Agronómica, Alimentaria y de Biosistemas
Deposited on: 01 Feb 2019 13:38
Last Modified: 10 Jun 2019 16:50
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