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

J 2015

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

WILLING, Eva-Maria, Vimal RAWAT, Terezie MANDÁKOVÁ, Florian MAUMUS, Geo Velikkakam JAMES et. al.

Základní údaje

Originální název

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

Autoři

WILLING, Eva-Maria (276 Německo), Vimal RAWAT (276 Německo), Terezie MANDÁKOVÁ (203 Česká republika, domácí), Florian MAUMUS (250 Francie), Geo Velikkakam JAMES (276 Německo), Karl J. V. NORDSTROM (276 Německo), Claude BECKER (276 Německo), Norman WARTHMANN (276 Německo), Claudia CHICA (250 Francie), Bogna SZARZYNSKA (250 Francie), Matthias ZYTNICKI (250 Francie), Maria C. ALBANI (276 Německo), Christiane KIEFER (276 Německo), Sara BERGONZI (276 Německo), Loren CASTAINGS (276 Německo), Julieta L. MATEOS (276 Německo), Markus C. BERNS (276 Německo), Nora BUJDOSO (276 Německo), Thomas PIOFCZYK (276 Německo), Laura DE LORENZO (724 Španělsko), Cristina BARRERO-SICILIA (724 Španělsko), Isabel MATEOS (724 Španělsko), Mathieu PIEDNOEL (276 Německo), Joerg HAGMANN (276 Německo), Romy CHEN-MIN-TAO (250 Francie), Raquel IGLESIAS-FERNANDEZ (724 Španělsko), Stephan C. SCHUSTER (840 Spojené státy), Carlos ALONSO-BLANCO (724 Španělsko), Francois ROUDIER (724 Španělsko), Pilar CARBONERO (724 Španělsko), Javier PAZ-ARES (724 Španělsko), Seth J. DAVIS (276 Německo), Aleš PEČINKA (203 Česká republika), Hadi QUESNEVILLE (250 Francie), Vincent COLOT (250 Francie), Martin LYSÁK (203 Česká republika, garant, domácí), Detlef WEIGEL (276 Německo), George COUPLAND (276 Německo) a Korbinian SCHNEEBERGER (276 Německo)

Vydání

NATURE PLANTS, LONDON, NATURE PUBLISHING GROUP, 2015, 2055-026X

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Kód RIV

RIV/00216224:14740/15:00081444

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1038/NPLANTS.2014.23

UT WoS

000364389500001

Klíčová slova anglicky

ARABIDOPSIS-THALIANA; PROVIDES INSIGHT; EVOLUTION; LYRATA; DIVERGENCE; SEQUENCE; REVEALS; SIZE

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 5. 4. 2016 13:39, Mgr. Eva Špillingová

Anotace

V originále

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.

Návaznosti

EE2.3.20.0189, projekt VaV

Název: Rozvoj výzkumné excelence v oblasti evoluční cytogenomiky, epigenetiky a buněčné signalizace

EE2.3.30.0037, projekt VaV

Název: Zaměstnáním nejlepších mladých vědců k rozvoji mezinárodní spolupráce

GBP501/12/G090, projekt VaV

Název: Evoluce a funkce komplexních genomů rostlin

Citovat

WILLING, Eva-Maria, Vimal RAWAT, Terezie MANDÁKOVÁ, Florian MAUMUS, Geo Velikkakam JAMES, Karl J. V. NORDSTROM, Claude BECKER, Norman WARTHMANN, Claudia CHICA, Bogna SZARZYNSKA, Matthias ZYTNICKI, Maria C. ALBANI, Christiane KIEFER, Sara BERGONZI, Loren CASTAINGS, Julieta L. MATEOS, Markus C. BERNS, Nora BUJDOSO, Thomas PIOFCZYK, Laura DE LORENZO, Cristina BARRERO-SICILIA, Isabel MATEOS, Mathieu PIEDNOEL, Joerg HAGMANN, Romy CHEN-MIN-TAO, Raquel IGLESIAS-FERNANDEZ, Stephan C. SCHUSTER, Carlos ALONSO-BLANCO, Francois ROUDIER, Pilar CARBONERO, Javier PAZ-ARES, Seth J. DAVIS, Aleš PEČINKA, Hadi QUESNEVILLE, Vincent COLOT, Martin LYSÁK, Detlef WEIGEL, George COUPLAND a Korbinian SCHNEEBERGER. Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. NATURE PLANTS. LONDON: NATURE PUBLISHING GROUP, 2015, roč. 1, č. 2, s. 1-7. ISSN 2055-026X. Dostupné z: https://dx.doi.org/10.1038/NPLANTS.2014.23.

@article{1323753,
   author = {Willing, EvaandMaria and Rawat, Vimal and Mandáková, Terezie and Maumus, Florian and James, Geo Velikkakam and Nordstrom, Karl J. V. and Becker, Claude and Warthmann, Norman and Chica, Claudia and Szarzynska, Bogna and Zytnicki, Matthias and Albani, Maria 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 de Lorenzo, Laura and BarreroandSicilia, Cristina and Mateos, Isabel and Piednoel, Mathieu and Hagmann, Joerg and ChenandMinandTao, Romy and IglesiasandFernandez, Raquel and Schuster, Stephan C. and AlonsoandBlanco, Carlos and Roudier, Francois and Carbonero, Pilar and PazandAres, Javier and Davis, Seth J. and Pečinka, Aleš and Quesneville, Hadi and Colot, Vincent and Lysák, Martin and Weigel, Detlef and Coupland, George and Schneeberger, Korbinian},
   article_location = {LONDON},
   article_number = {2},
   doi = {http://dx.doi.org/10.1038/NPLANTS.2014.23},
   keywords = {ARABIDOPSIS-THALIANA; PROVIDES INSIGHT; EVOLUTION; LYRATA; DIVERGENCE; SEQUENCE; REVEALS; SIZE},
   language = {eng},
   issn = {2055-026X},
   journal = {NATURE PLANTS},
   title = {Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation},
   url = {http://www.nature.com/articles/nplants201423},
   volume = {1},
   year = {2015}
}

TY  - JOUR
ID  - 1323753
AU  - Willing, Eva-Maria - Rawat, Vimal - Mandáková, Terezie - Maumus, Florian - James, Geo Velikkakam - Nordstrom, 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 - Piednoel, Mathieu - Hagmann, Joerg - Chen-Min-Tao, Romy - Iglesias-Fernandez, Raquel - Schuster, Stephan C. - Alonso-Blanco, Carlos - Roudier, Francois - Carbonero, Pilar - Paz-Ares, Javier - Davis, Seth J. - Pečinka, Aleš - Quesneville, Hadi - Colot, Vincent - Lysák, Martin - Weigel, Detlef - Coupland, George - Schneeberger, Korbinian
PY  - 2015
TI  - Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation
JF  - NATURE PLANTS
VL  - 1
IS  - 2
SP  - 1-7
EP  - 1-7
PB  - NATURE PUBLISHING GROUP
SN  - 2055026X
KW  - ARABIDOPSIS-THALIANA
KW  - PROVIDES INSIGHT
KW  - EVOLUTION
KW  - LYRATA
KW  - DIVERGENCE
KW  - SEQUENCE
KW  - REVEALS
KW  - SIZE
UR  - http://www.nature.com/articles/nplants201423
L2  - http://www.nature.com/articles/nplants201423
N2  - 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.
ER  -

WILLING, Eva-Maria, Vimal RAWAT, Terezie MANDÁKOVÁ, Florian MAUMUS, Geo Velikkakam JAMES, Karl J. V. NORDSTROM, Claude BECKER, Norman WARTHMANN, Claudia CHICA, Bogna SZARZYNSKA, Matthias ZYTNICKI, Maria C. ALBANI, Christiane KIEFER, Sara BERGONZI, Loren CASTAINGS, Julieta L. MATEOS, Markus C. BERNS, Nora BUJDOSO, Thomas PIOFCZYK, Laura DE LORENZO, Cristina BARRERO-SICILIA, Isabel MATEOS, Mathieu PIEDNOEL, Joerg HAGMANN, Romy CHEN-MIN-TAO, Raquel IGLESIAS-FERNANDEZ, Stephan C. SCHUSTER, Carlos ALONSO-BLANCO, Francois ROUDIER, Pilar CARBONERO, Javier PAZ-ARES, Seth J. DAVIS, Aleš PEČINKA, Hadi QUESNEVILLE, Vincent COLOT, Martin LYSÁK, Detlef WEIGEL, George COUPLAND a Korbinian SCHNEEBERGER. Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. \textit{NATURE PLANTS}. LONDON: NATURE PUBLISHING GROUP, 2015, roč.~1, č.~2, s.~1-7. ISSN~2055-026X. Dostupné z: https://dx.doi.org/10.1038/NPLANTS.2014.23.

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