The slowdown of Y chromosome expansion in dioecious Silene latifolia due to DNA loss and male-specific silencing of retrotransposons

tRNA-derived small RNAs target transposable element transcripts

(2017) German Martinez et al.   NUCLEIC ACIDS RESEARCH

The First Rule of Plant Transposable Element Silencing: Location, Location, Location

(2016) Meredith J. Sigman et al.   PLANT CELL

Analysis of transposable elements and organellar DNA in male and female genomes of a species with a huge Y chromosome reveals distinct Y centromeres

(2016) Aretuza Sousa et al.   PLANT JOURNAL

Retrotransposon Proliferation Coincident with the Evolution of Dioecy in Asparagus

(2016) Alex Harkess et al.   G3-Genes Genomes Genetics

Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia

(2015) N Blavet et al.   BMC GENOMICS

Impact of repetitive DNA on sex chromosome evolution in plants

(2015) Roman Hobza et al.   CHROMOSOME RESEARCH

Gene Loss from a Plant Sex Chromosome System

(2015) Roberta Bergero et al.   CURRENT BIOLOGY

Silencing of active transposable elements in plants

(2015) Dalen Fultz et al.   CURRENT OPINION IN PLANT BIOLOGY

RAD mapping reveals an evolving, polymorphic and fuzzy boundary of a plant pseudoautosomal region

(2015) S. Qiu et al.   MOLECULAR ECOLOGY

RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome

(2015) Qing Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid Y degeneration and dosage compensation in plant sex chromosomes

(2015) Alexander S. T. Papadopulos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Identification of a Novel Retrotransposon with Sex Chromosome-Specific Distribution in Silene latifolia

(2014) Tereza Kralova et al.   CYTOGENETIC AND GENOME RESEARCH

miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis

(2014) Kate M. Creasey et al.   NATURE

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

(2014) Zdenek Kubat et al.   NEW PHYTOLOGIST

Accessible DNA and Relative Depletion of H3K9me2 at Maize Loci Undergoing RNA-Directed DNA Methylation

(2014) Jonathan I. Gent et al.   PLANT CELL

Three Groups of Transposable Elements with Contrasting Copy Number Dynamics and Host Responses in the Maize (Zea mays ssp. mays) Genome

(2014) Concepcion M. Diez et al.   PLoS Genetics

RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

(2013) P. Novak et al.   BIOINFORMATICS

Strong Accumulation of Chloroplast DNA in the Y Chromosomes of Rumex acetosa and Silene latifolia

(2013) P. Steflova et al.   CYTOGENETIC AND GENOME RESEARCH

Parent-of-origin control of transgenerational retrotransposon proliferation in Arabidopsis

(2013) Jon Reinders et al.   EMBO REPORTS

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

(2013) Pavlina Steflova et al.   Genome Biology and Evolution

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Expansion of Microsatellites on Evolutionary Young Y Chromosome

(2013) Eduard Kejnovský et al.   PLoS One

Rapid Degeneration of Noncoding DNA Regions Surrounding SlAP3X/Y After Recombination Suppression in the Dioecious Plant Silene latifolia

(2013) Kotaro Ishii et al.   G3-Genes Genomes Genetics

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA

(2012) Joseph P. Calarco et al.   CELL

CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize

(2012) J. I. Gent et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Genomic Diversity in Two Related Plant Species with and without Sex Chromosomes - Silene latifolia and S. vulgaris

(2012) Radim Cegan et al.   PLoS One

Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes

(2012) C. A. Ibarra et al.   SCIENCE

Plant Y Chromosome Degeneration Is Retarded by Haploid Purifying Selection

(2011) Margarita V. Chibalina et al.   CURRENT BIOLOGY

Sex Chromosome Evolution Revealed by Physical Mapping of SlAP3X/Y in the Dioecious Plant Silene latifolia

(2011) Rie Nishiyama et al.   CYTOLOGIA

DOES LOCAL ADAPTATION CAUSE HIGH POPULATION DIFFERENTIATION OF SILENE LATIFOLIA Y CHROMOSOMES?

(2011) Graham Muir et al.   EVOLUTION

Next Generation Sequencing-Based Analysis of Repetitive DNA in the Model Dioceous Plant Silene latifolia

(2011) Jiří Macas et al.   PLoS One

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data

(2010) Petr Novák et al.   BMC BIOINFORMATICS

Structure and evolution of Apetala3, a sex-linked gene in Silene latifolia

(2010) Radim Cegan et al.   BMC PLANT BIOLOGY

Nucleotide diversity in Silene latifolia autosomal and sex-linked genes

(2010) S. Qiu et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

(2009) R. Keith Slotkin et al.   CELL

Extensive Demethylation of Repetitive Elements During Seed Development Underlies Gene Imprinting

(2009) M. Gehring et al.   SCIENCE

Genome-Wide Demethylation of Arabidopsis Endosperm

(2009) T.-F. Hsieh et al.   SCIENCE

Survey of repetitive sequences in Silene latifolia with respect to their distribution on sex chromosomes

(2008) Tomas Cermak et al.   CHROMOSOME RESEARCH

Evidence for Degeneration of the Y Chromosome in the Dioecious Plant Silene latifolia

(2008) Gabriel A.B. Marais et al.   CURRENT BIOLOGY

Recent Spread of a Retrotransposon in the Silene latifolia Genome, Apart From the Y Chromosome

(2008) D. A. Filatov et al.   GENETICS

Active Miniature Transposons From a Plant Genome and Its Nonrecombining Y Chromosome

(2008) R. Bergero et al.   GENETICS

Microsatellite accumulation on the Y chromosome in Silene latifolia

(2008) Zdenek Kubat et al.   GENOME