Possible mechanisms responsible for absence of a retrotransposon family on a plant Y chromosome.
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.
Department of Plant Developmental Genetics, Institute of Biophysics ASCR, Kralovopolska 135, Brno, 61200, Czech Republic.|Laboratory of Genome Dynamics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.
Zdenek
Z
Kubat
Department of Plant Developmental Genetics, Institute of Biophysics ASCR, Kralovopolska 135, Brno, 61200, Czech Republic.
Jitka
J
Zluvova
Laboratory of Genome Dynamics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.
Ivan
I
Vogel
Department of Plant Developmental Genetics, Institute of Biophysics ASCR, Kralovopolska 135, Brno, 61200, Czech Republic.
Viera
V
Kovacova
Department of Plant Developmental Genetics, Institute of Biophysics ASCR, Kralovopolska 135, Brno, 61200, Czech Republic.
Tomas
T
Cermak
Department of Plant Developmental Genetics, Institute of Biophysics ASCR, Kralovopolska 135, Brno, 61200, Czech Republic.
Radim
R
Cegan
Department of Plant Developmental Genetics, Institute of Biophysics ASCR, Kralovopolska 135, Brno, 61200, Czech Republic.|Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Sokolovska 6, Olomouc, 77200, Czech Republic.
Roman
R
Hobza
Department of Plant Developmental Genetics, Institute of Biophysics ASCR, Kralovopolska 135, Brno, 61200, Czech Republic.
Boris
B
Vyskot
Department of Plant Developmental Genetics, Institute of Biophysics ASCR, Kralovopolska 135, Brno, 61200, Czech Republic.|Laboratory of Genome Dynamics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.
Eduard
E
Kejnovsky
D001483:Base Sequence; D032461:Chromosomes, Plant; D018744:DNA, Plant; D044127:Epigenesis, Genetic; D019143:Evolution, Molecular; D020868:Gene Silencing; D018745:Genome, Plant; D008969:Molecular Sequence Data; D010802:Phylogeny; D018749:RNA, Plant; D018626:Retroelements; D029751:Silene / Q000235:genetics*; D020079:Terminal Repeat Sequences
D018744:DNA, Plant; D018749:RNA, Plant; D018626:Retroelements
Silene latifolia (white campion); epigenetics; genome size; long terminal repeat (LTR) retrotransposon; plant sex chromosomes; silencing; small RNA