Chromosome Evolution in Connection with Repetitive Sequences and Epigenetics in Plants

Retrotransposons are specified as DNA replication origins in the gene-poor regions of Arabidopsis heterochromatin

(2017) Zaida Vergara et al.   NUCLEIC ACIDS RESEARCH

TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads

(2017) Petr Novák et al.   NUCLEIC ACIDS RESEARCH

Karyotype diversity and genome size variation in Neotropical Maxillariinae orchids

(2017) A. P. Moraes et al.   PLANT BIOLOGY

Comparative Cytogenetics between Two Important Songbird, Models: The Zebra Finch and the Canary

(2017) Michelly da Silva dos Santos et al.   PLoS One

Transcriptional Regulatory Network of Plant Heat Stress Response

(2017) Naohiko Ohama et al.   TRENDS IN PLANT SCIENCE

Karyotypic Evolution and Chromosomal Organization of Repetitive DNA Sequences in Species of Panaque, Panaqolus, and Scobinancistrus (Siluriformes and Loricariidae) from the Amazon Basin

(2017) Thayana Ayres-Alves et al.   Zebrafish

Translational repression by a miniature inverted-repeat transposable element in the 3′ untranslated region

(2017) Jianqiang Shen et al.   Nature Communications

New Evidence for the Theory of Chromosome Organization by Repetitive Elements (CORE)

(2017) Shao-Jun Tang   Genes

Evolutionary implications of heterochromatin and rDNA in chromosome number and genome size changes during dysploidy: A case study in Reichardia genus

(2017) Sonja Siljak-Yakovlev et al.   PLoS One

Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies

(2016) Camille Sessegolo et al.   Biology Letters

Repeat Composition of CenH3-chromatin and H3K9me2-marked heterochromatin in Sugar Beet (Beta vulgaris)

(2016) Teresa Kowar et al.   BMC PLANT BIOLOGY

Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis

(2016) Aiko Iwata-Otsubo et al.   CHROMOSOME RESEARCH

The histone methyltransferases Set5 and Set1 have overlapping functions in gene silencing and telomere maintenance

(2016) Meagan Jezek et al.   Epigenetics

Regulatory activities of transposable elements: from conflicts to benefits

(2016) Edward B. Chuong et al.   NATURE REVIEWS GENETICS

Molecular, genetic and evolutionary analysis of a paracentric inversion inArabidopsis thaliana

(2016) Paul Fransz et al.   PLANT JOURNAL

Dynamic chromatin changes associated withde novocentromere formation in maize euchromatin

(2016) Handong Su et al.   PLANT JOURNAL

Rapid proliferation and nucleolar organizer targeting centromeric retrotransposons in cotton

(2016) Jinlei Han et al.   PLANT JOURNAL

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

Repetitive sequences and epigenetic modification: inseparable partners play important roles in the evolution of plant sex chromosomes

(2016) Shu-Fen Li et al.   PLANTA

De Novo Annotation of Transposable Elements: Tackling the Fat Genome Issue

(2016) Veronique Jamilloux et al.   PROCEEDINGS OF THE IEEE

Inbreeding drives maize centromere evolution

(2016) Kevin L. Schneider et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Retrotransposon Proliferation Coincident with the Evolution of Dioecy in Asparagus

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

Chromosomal polymorphism in mammals: an evolutionary perspective

(2015) Gauthier Dobigny et al.   BIOLOGICAL REVIEWS

Repetitive sequence analysis and karyotyping reveals centromere-associated DNA sequences in radish (Raphanus sativus L.)

(2015) Qunyan He et al.   BMC PLANT BIOLOGY

Is post-polyploidization diploidization the key to the evolutionary success of angiosperms?

(2015) Steven Dodsworth et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Next-generation sequencing reveals differentially amplified tandem repeats as a major genome component of Northern Europe’s oldest Camellia japonica

(2015) Tony Heitkam et al.   CHROMOSOME RESEARCH

Silencing of active transposable elements in plants

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

Epigenetic variation and environmental change: Fig. 1.

(2015) Peter Meyer   JOURNAL OF EXPERIMENTAL BOTANY

Effect of 5-azaC on the growth, flowering time and sexual phenotype of spinach

(2015) S. F. Li et al.   RUSSIAN JOURNAL OF PLANT PHYSIOLOGY

A transposable element in a NAC gene is associated with drought tolerance in maize seedlings

(2015) Hude Mao et al.   Nature Communications

Sunflower centromeres consist of a centromere-specific LINE and a chromosome-specific tandem repeat

(2015) Kiyotaka Nagaki et al.   Frontiers in Plant Science

Genome-wide DNA methylation profiling by modified reduced representation bisulfite sequencing in Brassica rapa suggests that epigenetic modifications play a key role in polyploid genome evolution

(2015) Xun Chen et al.   Frontiers in Plant Science

Accumulation of interspersed and sex-specific repeats in the non-recombining region of papaya sex chromosomes

(2014) Jong-Kuk Na et al.   BMC GENOMICS

Epigenetic regulation and functional exaptation of transposable elements in higher plants

(2014) Xiekui Cui et al.   CURRENT OPINION IN PLANT BIOLOGY

Rapid Genetic and Epigenetic Alterations under Intergeneric Genomic Shock in Newly Synthesized Chrysanthemum morifolium × Leucanthemum paludosum Hybrids (Asteraceae)

(2014) Haibin Wang et al.   Genome Biology and Evolution

Comparative linkage maps suggest that fission, not polyploidy, underlies near-doubling of chromosome number within monkeyflowers (Mimulus; Phrymaceae)

(2014) L Fishman et al.   HEREDITY

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

(2014) Zdenek Kubat et al.   NEW PHYTOLOGIST

Insight into the Karyotype Evolution of Brachypodium Species Using Comparative Chromosome Barcoding

(2014) Dominika Idziak et al.   PLoS One

Reconstructing the Evolution of Brachypodium Genomes Using Comparative Chromosome Painting

(2014) Alexander Betekhtin et al.   PLoS One

Repetitive Sequences in Plant Nuclear DNA: Types, Distribution, Evolution and Function

(2014) Shweta Mehrotra et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

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

Tissue culture-induced genetic and epigenetic alterations in rice pure-lines, F1 hybrids and polyploids

(2013) Xiaoran Wang et al.   BMC PLANT BIOLOGY

The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin

(2013) Assaf Zemach et al.   CELL

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

The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution

(2013) M C Estep et al.   HEREDITY

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

Formation of a Functional Maize Centromere after Loss of Centromeric Sequences and Gain of Ectopic Sequences

(2013) B. Zhang et al.   PLANT CELL

Expansion of Microsatellites on Evolutionary Young Y Chromosome

(2013) Eduard Kejnovský et al.   PLoS One

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

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

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

(2012) Radim Cegan et al.   PLoS One

Transposable Elements, Epigenetics, and Genome Evolution

(2012) N. V. Fedoroff   SCIENCE

Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons

(2012) Steven R. Eichten et al.   PLoS Genetics

RNA-directed DNA methylation

(2011) Huiming Zhang et al.   CURRENT OPINION IN PLANT BIOLOGY

Distinct DNA methylation patterns associated with active and inactive centromeres of the maize B chromosome

(2011) D.-H. Koo et al.   GENOME RESEARCH

Evolution of the large genome in Capsicum annuum occurred through accumulation of single-type long terminal repeat retrotransposons and their derivatives

(2011) Minkyu Park et al.   PLANT JOURNAL

Organisation of the plant genome in chromosomes

(2011) J. S. Pat Heslop-Harrison et al.   PLANT JOURNAL

Interpretation of karyotype evolution should consider chromosome structural constraints

(2011) Ingo Schubert et al.   TRENDS IN GENETICS

Chromosomal evolution in the plant family Solanaceae

(2010) Feinan Wu et al.   BMC GENOMICS

Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing

(2010) Eva Hřibová et al.   BMC PLANT BIOLOGY

Centromere inactivation and epigenetic modifications of a plant chromosome with three functional centromeres

(2010) Wenli Zhang et al.   CHROMOSOMA

Evolution of chromosome 6 of Solanum species revealed by comparative fluorescence in situ hybridization mapping

(2010) Qunfeng Lou et al.   CHROMOSOMA

Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution

(2010) F. Murat et al.   GENOME RESEARCH

Different scales of Ty1/copia-like retrotransposon proliferation in the genomes of three diploid hybrid sunflower species

(2010) T Kawakami et al.   HEREDITY

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces

(2010) Frédéric Choulet et al.   PLANT CELL

An Integrated Physical, Genetic and Cytogenetic Map of Brachypodium distachyon, a Model System for Grass Research

(2010) Melanie Febrer et al.   PLoS One

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

(2009) R. Keith Slotkin et al.   CELL

Alternative Ac/Ds transposition induces major chromosomal rearrangements in maize

(2009) J. Zhang et al.   GENES & DEVELOPMENT

Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression

(2009) J. D. Hollister et al.   GENOME RESEARCH

A transposon-induced epigenetic change leads to sex determination in melon

(2009) Antoine Martin et al.   NATURE

Reactivation of an Inactive Centromere Reveals Epigenetic and Structural Components for Centromere Specification in Maize

(2009) F. Han et al.   PLANT CELL

Centromere repositioning in cucurbit species: Implication of the genomic impact from centromere activation and inactivation

(2009) Y. Han et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants

(2009) J. S. Hawkins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae

(2009) M. C. Luo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Epigenetic regulation of heterochromatic DNA stability

(2008) Jamy C Peng et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

(2008) R. Bergero et al.   GENETICS

Accumulation of Y-specific satellite DNAs during the evolution of Rumex acetosa sex chromosomes

(2008) Beatrice Mariotti et al.   MOLECULAR GENETICS AND GENOMICS

Epigenetic regulation of centromeric chromatin: old dogs, new tricks?

(2008) Robin C. Allshire et al.   NATURE REVIEWS GENETICS