PMID- 24456522
OWN - NLM
STAT- MEDLINE
DCOM- 20141103
LR  - 20220409
IS  - 1469-8137 (Electronic)
IS  - 0028-646X (Linking)
VI  - 202
IP  - 2
DP  - 2014 Apr
TI  - Possible mechanisms responsible for absence of a retrotransposon family on a 
      plant Y chromosome.
PG  - 662-678
LID - 10.1111/nph.12669 [doi]
AB  - 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.
CI  - (c) 2014 The Authors. New Phytologist (c) 2014 New Phytologist Trust.
FAU - Kubat, Zdenek
AU  - Kubat Z
AD  - Department of Plant Developmental Genetics, Institute of Biophysics ASCR, 
      Kralovopolska 135, Brno, 61200, Czech Republic.
AD  - Laboratory of Genome Dynamics, CEITEC - Central European Institute of Technology, 
      Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.
FAU - Zluvova, Jitka
AU  - Zluvova J
AD  - Department of Plant Developmental Genetics, Institute of Biophysics ASCR, 
      Kralovopolska 135, Brno, 61200, Czech Republic.
FAU - Vogel, Ivan
AU  - Vogel I
AD  - Laboratory of Genome Dynamics, CEITEC - Central European Institute of Technology, 
      Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.
FAU - Kovacova, Viera
AU  - Kovacova V
AD  - Department of Plant Developmental Genetics, Institute of Biophysics ASCR, 
      Kralovopolska 135, Brno, 61200, Czech Republic.
FAU - Cermak, Tomas
AU  - Cermak T
AD  - Department of Plant Developmental Genetics, Institute of Biophysics ASCR, 
      Kralovopolska 135, Brno, 61200, Czech Republic.
FAU - Cegan, Radim
AU  - Cegan R
AD  - Department of Plant Developmental Genetics, Institute of Biophysics ASCR, 
      Kralovopolska 135, Brno, 61200, Czech Republic.
FAU - Hobza, Roman
AU  - Hobza R
AD  - Department of Plant Developmental Genetics, Institute of Biophysics ASCR, 
      Kralovopolska 135, Brno, 61200, Czech Republic.
AD  - Institute of Experimental Botany, Centre of the Region Hana for Biotechnological 
      and Agricultural Research, Sokolovska 6, Olomouc, 77200, Czech Republic.
FAU - Vyskot, Boris
AU  - Vyskot B
AD  - Department of Plant Developmental Genetics, Institute of Biophysics ASCR, 
      Kralovopolska 135, Brno, 61200, Czech Republic.
FAU - Kejnovsky, Eduard
AU  - Kejnovsky E
AD  - Department of Plant Developmental Genetics, Institute of Biophysics ASCR, 
      Kralovopolska 135, Brno, 61200, Czech Republic.
AD  - Laboratory of Genome Dynamics, CEITEC - Central European Institute of Technology, 
      Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20140123
PL  - England
TA  - New Phytol
JT  - The New phytologist
JID - 9882884
RN  - 0 (DNA, Plant)
RN  - 0 (RNA, Plant)
RN  - 0 (Retroelements)
SB  - IM
MH  - Base Sequence
MH  - *Chromosomes, Plant
MH  - *DNA, Plant
MH  - Epigenesis, Genetic
MH  - *Evolution, Molecular
MH  - Gene Silencing
MH  - *Genome, Plant
MH  - Molecular Sequence Data
MH  - Phylogeny
MH  - RNA, Plant
MH  - *Retroelements
MH  - Silene/*genetics
MH  - *Terminal Repeat Sequences
OTO - NOTNLM
OT  - Silene latifolia (white campion)
OT  - epigenetics
OT  - genome size
OT  - long terminal repeat (LTR) retrotransposon
OT  - plant sex chromosomes
OT  - silencing
OT  - small RNA
EDAT- 2014/01/25 06:00
MHDA- 2014/11/05 06:00
CRDT- 2014/01/25 06:00
PHST- 2013/09/13 00:00 [received]
PHST- 2013/11/25 00:00 [accepted]
PHST- 2014/01/25 06:00 [entrez]
PHST- 2014/01/25 06:00 [pubmed]
PHST- 2014/11/05 06:00 [medline]
AID - 10.1111/nph.12669 [doi]
PST - ppublish
SO  - New Phytol. 2014 Apr;202(2):662-678. doi: 10.1111/nph.12669. Epub 2014 Jan 23.