Contrasting Patterns of Transposable Element and Satellite
Distribution on Sex Chromosomes (XY1Y2) in the Dioecious Plant
Rumex acetosa

J 2013

Contrasting Patterns of Transposable Element and Satellite Distribution on Sex Chromosomes (XY1Y2) in the Dioecious Plant Rumex acetosa

ŠTEFLOVÁ, Pavlína, Viktor TOKAN, Ivan VOGEL, Matej LEXA, Jiří MACAS et. al.

Basic information

Original name

Contrasting Patterns of Transposable Element and Satellite Distribution on Sex Chromosomes (XY1Y2) in the Dioecious Plant Rumex acetosa

Authors

ŠTEFLOVÁ, Pavlína (203 Czech Republic, belonging to the institution), Viktor TOKAN (203 Czech Republic), Ivan VOGEL (703 Slovakia, belonging to the institution), Matej LEXA (703 Slovakia, belonging to the institution), Jiří MACAS (203 Czech Republic), Petr NOVAK (203 Czech Republic), Roman HOBZA (203 Czech Republic), Boris VYSKOT (203 Czech Republic) and Eduard KEJNOVSKÝ (203 Czech Republic, guarantor, belonging to the institution)

Edition

GENOME BIOLOGY AND EVOLUTION, Oxford, UK, Oxford Univ Press, 2013, 1759-6653

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10601 Cell biology

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 4.532

RIV identification code

RIV/00216224:14740/13:00068595

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1093/gbe/evt049

UT WoS

000318557200013

Keywords in English

sex chromosomes; sorrel (Rumex acetosa); transposable elements; satellites

Abstract

V originále

Rumex acetosa is a dioecious plant with the XY1Y2 sex chromosome system. Both Y chromosomes are heterochromatic and are thought to be degenerated.We performed low-pass 454 sequencing and similarity-based clustering of male and female genomic 454 reads to identify and characterize major groups of R. acetosa repetitive DNA. We found that Copia and Gypsy retrotransposons dominated, followed by DNA transposons and nonlong terminal repeat retrotransposons. CRM and Tat/Ogre retrotransposons dominated the Gypsy superfamily, whereas Maximus/Sireviruses were most abundant among Copia retrotransposons. Only one Gypsy subfamily had accumulated on Y1 and Y2 chromosomes,whereas many retrotransposons were ubiquitous on autosomes and the X chromosome, but absent on Y1 and Y2 chromosomes, and otherswere depleted fromthe X chromosome. One group of CRM Gypsywas specifically localized to centromeres.Wealso found thatmajority of previously described satellites (RAYSI, RAYSII, RAYSIII, andRAE180) are accumulatedontheYchromosomeswherewe identifiedYchromosome-specific variant ofRAE180.Wediscovered two novel satellites-RA160 satellite dominating on the X chromosome and RA690 localized mostly on the Y1 chromosome. The expression pattern obtained from IlluminaRNAsequencing showedthat the expression of transposable elements is similar in leaves of both sexes and that satellites are also expressed. Contrasting patterns of transposable elements (TEs) and satellite localization on sex chromosomes in R. acetosa,where not only accumulation but also depletion of repetitiveDNAwas observed, suggest that a plethora of evolutionary processes can shape sex chromosomes.

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

EE2.3.20.0045, research and development project

Name: Podpora profesního růstu a mezinárodní integrace výzkumných týmů v oblasti molekulární medicíny

Files attached

Steflova_13_GBE.pdf

Request the author's version of the file

Citovat

ŠTEFLOVÁ, Pavlína, Viktor TOKAN, Ivan VOGEL, Matej LEXA, Jiří MACAS, Petr NOVAK, Roman HOBZA, Boris VYSKOT and Eduard KEJNOVSKÝ. Contrasting Patterns of Transposable Element and Satellite Distribution on Sex Chromosomes (XY1Y2) in the Dioecious Plant Rumex acetosa. GENOME BIOLOGY AND EVOLUTION. Oxford, UK: Oxford Univ Press, 2013, vol. 5, No 4, p. 769-782. ISSN 1759-6653. Available from: https://dx.doi.org/10.1093/gbe/evt049.

@article{1112012,
   author = {Šteflová, Pavlína and Tokan, Viktor and Vogel, Ivan and Lexa, Matej and Macas, Jiří and Novak, Petr and Hobza, Roman and Vyskot, Boris and Kejnovský, Eduard},
   article_location = {Oxford, UK},
   article_number = {4},
   doi = {http://dx.doi.org/10.1093/gbe/evt049},
   keywords = {sex chromosomes; sorrel (Rumex acetosa); transposable elements; satellites},
   language = {eng},
   issn = {1759-6653},
   journal = {GENOME BIOLOGY AND EVOLUTION},
   title = {Contrasting Patterns of Transposable Element and Satellite Distribution on Sex Chromosomes (XY1Y2) in the Dioecious Plant Rumex acetosa},
   url = {http://gbe.oxfordjournals.org/content/5/4/769.full.pdf+html},
   volume = {5},
   year = {2013}
}

TY  - JOUR
ID  - 1112012
AU  - Šteflová, Pavlína - Tokan, Viktor - Vogel, Ivan - Lexa, Matej - Macas, Jiří - Novak, Petr - Hobza, Roman - Vyskot, Boris - Kejnovský, Eduard
PY  - 2013
TI  - Contrasting Patterns of Transposable Element and Satellite Distribution on Sex Chromosomes (XY1Y2) in the Dioecious Plant Rumex acetosa
JF  - GENOME BIOLOGY AND EVOLUTION
VL  - 5
IS  - 4
SP  - 769-782
EP  - 769-782
PB  - Oxford Univ Press
SN  - 17596653
KW  - sex chromosomes
KW  - sorrel (Rumex acetosa)
KW  - transposable elements
KW  - satellites
UR  - http://gbe.oxfordjournals.org/content/5/4/769.full.pdf+html
L2  - http://gbe.oxfordjournals.org/content/5/4/769.full.pdf+html
N2  - Rumex acetosa is a dioecious plant with the XY1Y2 sex chromosome system. Both Y chromosomes are heterochromatic and are thought to be degenerated.We performed low-pass 454 sequencing and similarity-based clustering of male and female genomic 454 reads to identify and characterize major groups of R. acetosa repetitive DNA. We found that Copia and Gypsy retrotransposons dominated, followed by DNA transposons and nonlong terminal repeat retrotransposons. CRM and Tat/Ogre retrotransposons dominated the Gypsy superfamily, whereas Maximus/Sireviruses were most abundant among Copia retrotransposons. Only one Gypsy subfamily had accumulated on Y1 and Y2 chromosomes,whereas many retrotransposons were ubiquitous on autosomes and the X chromosome, but absent on Y1 and Y2 chromosomes, and otherswere depleted fromthe X chromosome. One group of CRM Gypsywas specifically localized to centromeres.Wealso found thatmajority of previously described satellites (RAYSI, RAYSII, RAYSIII, andRAE180) are accumulatedontheYchromosomeswherewe identifiedYchromosome-specific variant ofRAE180.Wediscovered two novel satellites-RA160 satellite dominating on the X chromosome and RA690 localized mostly on the Y1 chromosome. The expression pattern obtained from IlluminaRNAsequencing showedthat the expression of transposable elements is similar in leaves of both sexes and that satellites are also expressed. Contrasting patterns of transposable elements (TEs) and satellite localization on sex chromosomes in R. acetosa,where not only accumulation but also depletion of repetitiveDNAwas observed, suggest that a plethora of evolutionary processes can shape sex chromosomes.
ER  -

ŠTEFLOVÁ, Pavlína, Viktor TOKAN, Ivan VOGEL, Matej LEXA, Jiří MACAS, Petr NOVAK, Roman HOBZA, Boris VYSKOT and Eduard KEJNOVSKÝ. Contrasting Patterns of Transposable Element and Satellite Distribution on Sex Chromosomes (XY1Y2) in the Dioecious Plant Rumex acetosa. \textit{GENOME BIOLOGY AND EVOLUTION}. Oxford, UK: Oxford Univ Press, 2013, vol.~5, No~4, p.~769-782. ISSN~1759-6653. Available from: https://dx.doi.org/10.1093/gbe/evt049.

Detailed Information on Publication Record