Possible mechanisms responsible for absence of a
retrotransposon family on a plant Y chromosome

J 2014

Possible mechanisms responsible for absence of a retrotransposon family on a plant Y chromosome

KUBÁT, Zdeněk, Jitka ŽLUVOVÁ, Ivan VOGEL, Viera KOVÁČOVÁ, Tomáš ČERMÁK et. al.

Basic information

Original name

Possible mechanisms responsible for absence of a retrotransposon family on a plant Y chromosome

Authors

KUBÁT, Zdeněk (203 Czech Republic, belonging to the institution), Jitka ŽLUVOVÁ (203 Czech Republic), Ivan VOGEL (703 Slovakia, belonging to the institution), Viera KOVÁČOVÁ (203 Czech Republic), Tomáš ČERMÁK (203 Czech Republic), Radim CEGAN (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

New Phytologist, HOBOKEN, WILEY-BLACKWELL, 2014, 0028-646X

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

Genetics and molecular biology

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 7.672

RIV identification code

RIV/00216224:14740/14:00079376

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1111/nph.12669

UT WoS

000333060500035

Keywords in English

epigenetics; genome size; long terminal repeat (LTR) retrotransposon; plant sex chromosomes; silencing; Silene latifolia (white campion); small RNA

Abstract

V originále

Some transposable elements (TEs) show extraordinary variance in abundance along sex chromosomes but the mechanisms responsible for this variance are unknown. Here, we studied Ogre long terminal repeat (LTR) retrotransposons in Silene latifolia, a dioecious plant with evolutionarily young heteromorphic sex chromosomes. Ogre elements are ubiquitous in the S.latifolia genome but surprisingly absent on the Y chromosome. Bacterial artificial chromosome (BAC) library analysis and fluorescence in situ hybridization (FISH) were used to determine Ogre structure and chromosomal localization. Next generation sequencing (NGS) data were analysed to assess the transcription level and abundance of small RNAs. Methylation of Ogres was determined by bisulphite sequencing. Phylogenetic analysis was used to determine mobilization time and selection forces acting on Ogre elements. We characterized three Ogre families ubiquitous in the S.latifolia genome. One family is nearly absent on the Y chromosome despite all the families having similar structures and spreading mechanisms. We showed that Ogre retrotransposons evolved before sex chromosomes appeared but were mobilized after formation of the Y chromosome. Our data suggest that the absence of one Ogre family on the Y chromosome may be caused by 24-nucleotide (24-nt) small RNA-mediated silencing leading to female-specific spreading. Our findings highlight epigenetic silencing mechanisms as potentially crucial factors in sex-specific spreading of some TEs, but other possible mechanisms are also discussed.

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

Citovat

KUBÁT, Zdeněk, Jitka ŽLUVOVÁ, Ivan VOGEL, Viera KOVÁČOVÁ, Tomáš ČERMÁK, Radim CEGAN, Roman HOBZA, Boris VYSKOT and Eduard KEJNOVSKÝ. Possible mechanisms responsible for absence of a retrotransposon family on a plant Y chromosome. New Phytologist. HOBOKEN: WILEY-BLACKWELL, 2014, vol. 202, No 2, p. 662-678. ISSN 0028-646X. Available from: https://dx.doi.org/10.1111/nph.12669.

@article{1229105,
   author = {Kubát, Zdeněk and Žluvová, Jitka and Vogel, Ivan and Kováčová, Viera and Čermák, Tomáš and Cegan, Radim and Hobza, Roman and Vyskot, Boris and Kejnovský, Eduard},
   article_location = {HOBOKEN},
   article_number = {2},
   doi = {http://dx.doi.org/10.1111/nph.12669},
   keywords = {epigenetics; genome size; long terminal repeat (LTR) retrotransposon; plant sex chromosomes; silencing; Silene latifolia (white campion); small RNA},
   language = {eng},
   issn = {0028-646X},
   journal = {New Phytologist},
   title = {Possible mechanisms responsible for absence of a retrotransposon family on a plant Y chromosome},
   url = {http://onlinelibrary.wiley.com/doi/10.1111/nph.12669/epdf},
   volume = {202},
   year = {2014}
}

TY  - JOUR
ID  - 1229105
AU  - Kubát, Zdeněk - Žluvová, Jitka - Vogel, Ivan - Kováčová, Viera - Čermák, Tomáš - Cegan, Radim - Hobza, Roman - Vyskot, Boris - Kejnovský, Eduard
PY  - 2014
TI  - Possible mechanisms responsible for absence of a retrotransposon family on a plant Y chromosome
JF  - New Phytologist
VL  - 202
IS  - 2
SP  - 662-678
EP  - 662-678
PB  - WILEY-BLACKWELL
SN  - 0028646X
KW  - epigenetics
KW  - genome size
KW  - long terminal repeat (LTR) retrotransposon
KW  - plant sex chromosomes
KW  - silencing
KW  - Silene latifolia (white campion)
KW  - small RNA
UR  - http://onlinelibrary.wiley.com/doi/10.1111/nph.12669/epdf
L2  - http://onlinelibrary.wiley.com/doi/10.1111/nph.12669/epdf
N2  - Some transposable elements (TEs) show extraordinary variance in abundance along sex chromosomes but the mechanisms responsible for this variance are unknown. Here, we studied Ogre long terminal repeat (LTR) retrotransposons in Silene latifolia, a dioecious plant with evolutionarily young heteromorphic sex chromosomes. Ogre elements are ubiquitous in the S.latifolia genome but surprisingly absent on the Y chromosome. Bacterial artificial chromosome (BAC) library analysis and fluorescence in situ hybridization (FISH) were used to determine Ogre structure and chromosomal localization. Next generation sequencing (NGS) data were analysed to assess the transcription level and abundance of small RNAs. Methylation of Ogres was determined by bisulphite sequencing. Phylogenetic analysis was used to determine mobilization time and selection forces acting on Ogre elements. We characterized three Ogre families ubiquitous in the S.latifolia genome. One family is nearly absent on the Y chromosome despite all the families having similar structures and spreading mechanisms. We showed that Ogre retrotransposons evolved before sex chromosomes appeared but were mobilized after formation of the Y chromosome. Our data suggest that the absence of one Ogre family on the Y chromosome may be caused by 24-nucleotide (24-nt) small RNA-mediated silencing leading to female-specific spreading. Our findings highlight epigenetic silencing mechanisms as potentially crucial factors in sex-specific spreading of some TEs, but other possible mechanisms are also discussed.
ER  -

KUBÁT, Zdeněk, Jitka ŽLUVOVÁ, Ivan VOGEL, Viera KOVÁČOVÁ, Tomáš ČERMÁK, Radim CEGAN, Roman HOBZA, Boris VYSKOT and Eduard KEJNOVSKÝ. Possible mechanisms responsible for absence of a retrotransposon family on a plant Y chromosome. \textit{New Phytologist}. HOBOKEN: WILEY-BLACKWELL, 2014, vol.~202, No~2, p.~662-678. ISSN~0028-646X. Available from: https://dx.doi.org/10.1111/nph.12669.

Detailed Information on Publication Record