Substantial Epigenetic Variation Causing Flower Color Chimerism in the Ornamental Tree Prunus mume Revealed by Single Base Resolution Methylome Detection and Transcriptome Sequencing

The vesicle trafficking regulator PN_SCD1 is demethylated and overexpressed in florets of apomictic Paspalum notatum genotypes

(2018) Marika Bocchini et al.   Scientific Reports

Single-base methylome analysis reveals dynamic epigenomic differences associated with water deficit in apple

(2017) Jidi Xu et al.   PLANT BIOTECHNOLOGY JOURNAL

UFGT: The Key Enzyme Associated with the Petals Variegation in Japanese Apricot

(2017) Xinxin Wu et al.   Frontiers in Plant Science

Dynamic Changes of Genome-Wide DNA Methylation during Soybean Seed Development

(2017) Yong-qiang Charles An et al.   Scientific Reports

Differential methylation analysis for BS-seq data under general experimental design

(2016) Yongseok Park et al.   BIOINFORMATICS

RNA-seq-based evaluation of bicolor tepal pigmentation in Asiatic hybrid lilies (Lilium spp.)

(2016) Kazuma Suzuki et al.   BMC GENOMICS

iTAK: A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases

(2016) Yi Zheng et al.   Molecular Plant

Epigenetic regulation of MdMYB1 is associated with paper bagging-induced red pigmentation of apples

(2016) Songling Bai et al.   PLANTA

Genome-Wide Differences in DNA Methylation Changes in Two Contrasting Rice Genotypes in Response to Drought Conditions

(2016) Wensheng Wang et al.   Frontiers in Plant Science

Multiple R2R3-MYB Transcription Factors Involved in the Regulation of Anthocyanin Accumulation in Peach Flower

(2016) Hui Zhou et al.   Frontiers in Plant Science

Comparative proteomic analysis of floral color variegation in peach

(2015) Yong Zhou et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Transciptome analysis reveals flavonoid biosynthesis regulation and simple sequence repeats in yam (Dioscorea alata L.) tubers

(2015) Zhi-Gang Wu et al.   BMC GENOMICS

Analysis of biochemical compounds and differentially expressed genes of the anthocyanin biosynthetic pathway in variegated peach flowers

(2015) D. Hassani et al.   GENETICS AND MOLECULAR RESEARCH

A small indel mutation in an anthocyanin transporter causes variegated colouration of peach flowers

(2015) Jun Cheng et al.   JOURNAL OF EXPERIMENTAL BOTANY

DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control

(2015) Helene Kretzmer et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypiumspp.)

(2015) Maojun Wang et al.   NEW PHYTOLOGIST

Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates

(2015) Hao Wu et al.   NUCLEIC ACIDS RESEARCH

Molecular genetics of blood-fleshed peach reveals activation of anthocyanin biosynthesis by NAC transcription factors

(2015) Hui Zhou et al.   PLANT JOURNAL

A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean

(2015) Kyung Do Kim et al.   PLANT PHYSIOLOGY

Transcriptome sequencing of purple petal spot region in tree peony reveals differentially expressed anthocyanin structural genes

(2015) Yanzhao Zhang et al.   Frontiers in Plant Science

Relationship of DNA Methylation and Gene Expression in Idiopathic Pulmonary Fibrosis

(2014) Ivana V. Yang et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Transcriptome analysis and transient transformation suggest an ancient duplicated MYB transcription factor as a candidate gene for leaf red coloration in peach

(2014) Ying Zhou et al.   BMC PLANT BIOLOGY

Accessing epigenetic variation in the plant methylome

(2014) K. D. Kim et al.   Briefings in Functional Genomics

Programming and Inheritance of Parental DNA Methylomes in Mammals

(2014) Lu Wang et al.   CELL

Peace, a MYB-like transcription factor, regulates petal pigmentation in flowering peach ‘Genpei’ bearing variegated and fully pigmented flowers

(2014) Chiyomi Uematsu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Transposable elements, a treasure trove to decipher epigenetic variation: insights from Arabidopsis and crop epigenomes

(2014) M. Mirouze et al.   JOURNAL OF EXPERIMENTAL BOTANY

Transposon-mediated mutation of CYP76AD3 affects betalain synthesis and produces variegated flowers in four o’clock (Mirabilis jalapa)

(2014) Mariko Suzuki et al.   JOURNAL OF PLANT PHYSIOLOGY

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data

(2014) Hao Feng et al.   NUCLEIC ACIDS RESEARCH

Transcriptome Analysis of Differentially Expressed Genes Relevant to Variegation in Peach Flowers

(2014) Yingnan Chen et al.   PLoS One

Divergence of Gene Body DNA Methylation and Evolution of Plant Duplicate Genes

(2014) Jun Wang et al.   PLoS One

Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population

(2013) R. J. Schmitz et al.   GENOME RESEARCH

Genome-Wide Analysis of DNA Methylation in Soybean

(2013) Qing-Xin Song et al.   Molecular Plant

Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening

(2013) Silin Zhong et al.   NATURE BIOTECHNOLOGY

PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors

(2013) Jinpu Jin et al.   NUCLEIC ACIDS RESEARCH

Folate Polyglutamylation Is Involved in Chromatin Silencing by Maintaining Global DNA Methylation and Histone H3K9 Dimethylation in Arabidopsis

(2013) H.-R. Zhou et al.   PLANT CELL

The Methylation of the PcMYB10 Promoter Is Associated with Green-Skinned Sport in Max Red Bartlett Pear

(2013) Z. Wang et al.   PLANT PHYSIOLOGY

A Reference Methylome Database and Analysis Pipeline to Facilitate Integrative and Comparative Epigenomics

(2013) Qiang Song et al.   PLoS One

Extensive changes in DNA methylation are associated with expression of mutant huntingtin

(2013) C. W. Ng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

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

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

Introduction of apple ANR genes into tobacco inhibits expression of both CHI and DFR genes in flowers, leading to loss of anthocyanin

(2012) Yuepeng Han et al.   JOURNAL OF EXPERIMENTAL BOTANY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Analysing and interpreting DNA methylation data

(2012) Christoph Bock   NATURE REVIEWS GENETICS

A mutation in the rice chalcone isomerase gene causes the golden hull and internode 1 phenotype

(2012) Lilan Hong et al.   PLANTA

Methylation effect on chalcone synthase gene expression determines anthocyanin pigmentation in floral tissues of two Oncidium orchid cultivars

(2012) Xiao-Jing Liu et al.   PLANTA

A Large Insertion in bHLH Transcription Factor BrTT8 Resulting in Yellow Seed Coat in Brassica rapa

(2012) Xia Li et al.   PLoS One

Transcriptome and methylome interactions in rice hybrids

(2012) Ramakrishna K. Chodavarapu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Photosynthetic response to genome methylation affects the growth of Chinese white poplar

(2012) Kaifeng Ma et al.   Tree Genetics & Genomes

The genome of Prunus mume

(2012) Qixiang Zhang et al.   Nature Communications

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Apple skin patterning is associated with differential expression of MYB10

(2011) Adriana Telias et al.   BMC PLANT BIOLOGY

Structure of the acyl-glucose-dependent anthocyanin 5-O-glucosyltransferase gene in carnations and its disruption by transposable elements in some varieties

(2011) Yuzo Nishizaki et al.   MOLECULAR GENETICS AND GENOMICS

Arabidopsis TT19 Functions as a Carrier to Transport Anthocyanin from the Cytosol to Tonoplasts

(2011) Yi Sun et al.   Molecular Plant

Rapid Separation and Identification of Anthocyanins from Flowers of Viola yedoensis and V. prionantha by High-performance Liquid Chromatography-Photodiode Array Detection-Electrospray Ionisation Mass Spectrometry

(2011) Jie Zhang et al.   PHYTOCHEMICAL ANALYSIS

The Jasmonate-ZIM-Domain Proteins Interact with the WD-Repeat/bHLH/MYB Complexes to Regulate Jasmonate-Mediated Anthocyanin Accumulation and Trichome Initiation inArabidopsis thaliana

(2011) Tiancong Qi et al.   PLANT CELL

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Conservation and divergence of methylation patterning in plants and animals

(2010) S. Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Phenotypic instability and epigenetic variability in a diploid potato of hybrid origin, Solanum ruiz-lealii

(2009) Carlos F Marfil et al.   BMC PLANT BIOLOGY

An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites

(2009) Asuka Miura et al.   EMBO JOURNAL

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts

(2009) Akiko Doi et al.   NATURE GENETICS

PlnTFDB: updated content and new features of the plant transcription factor database

(2009) Paulino Pérez-Rodríguez et al.   NUCLEIC ACIDS RESEARCH

A putative autonomous 20.5 kb-CACTA transposon insertion in an F3'H allele identifies a new CACTA transposon subfamily in Glycine max

(2008) Gracia Zabala et al.   BMC PLANT BIOLOGY

Genome-scale DNA methylation maps of pluripotent and differentiated cells

(2008) Alexander Meissner et al.   NATURE

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation, Histone Methylation, and Gene Expression

(2008) X. Li et al.   PLANT CELL

Evolution and Control of Imprinted FWA Genes in the Genus Arabidopsis

(2008) Ryo Fujimoto et al.   PLoS Genetics