Altered chromatin conformation and transcriptional regulation in watermelon following genome doubling

Chromatin Organization in Early Land Plants Reveals an Ancestral Association between H3K27me3, Transposons, and Constitutive Heterochromatin

(2020) Sean A. Montgomery et al.   CURRENT BIOLOGY

The role of 3D chromatin domains in gene regulation: a multi-facetted view on genome organization

(2020) Daniel M Ibrahim et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Gene Balance Predicts Transcriptional Responses Immediately Following Ploidy Change in Arabidopsis thaliana

(2020) Michael J. Song et al.   PLANT CELL

TADCompare: An R Package for Differential and Temporal Analysis of Topologically Associated Domains

(2020) Kellen G. Cresswell et al.   Frontiers in Genetics

Gene body demethylation increases expression and is associated with self-pruning during grape genome duplication

(2020) Luming Zou et al.   Horticulture Research

Chromosome doubling mediates superior drought tolerance in Lycium ruthenicum via abscisic acid signaling

(2020) Shupei Rao et al.   Horticulture Research

Tissue‐specific Hi‐C analyses of rice, foxtail millet and maize suggest non‐canonical function of plant chromatin domains

(2019) Pengfei Dong et al.   Journal of Integrative Plant Biology

Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection

(2019) Shan Wu et al.   PLANT BIOTECHNOLOGY JOURNAL

The effects of Arabidopsis genome duplication on the chromatin organization and transcriptional regulation

(2019) Hui Zhang et al.   NUCLEIC ACIDS RESEARCH

Terpene Synthases as Metabolic Gatekeepers in the Evolution of Plant Terpenoid Chemical Diversity

(2019) Prema S. Karunanithi et al.   Frontiers in Plant Science

Autopolyploidization in switchgrass alters phenotype and flowering time via epigenetic and transcription regulation

(2019) Haidong Yan et al.   JOURNAL OF EXPERIMENTAL BOTANY

Efficient Characterization of Tetraploid Watermelon

(2019) Na Zhang et al.   Plants-Basel

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization

(2018) Joachim Wolff et al.   NUCLEIC ACIDS RESEARCH

Genome-wide Hi-C analysis reveals extensive hierarchical chromatin interactions in rice

(2018) Qianli Dong et al.   PLANT JOURNAL

Identification and expression analyses of WRKY genes reveal their involvement in growth and abiotic stress response in watermelon (Citrullus lanatus)

(2018) Xiaozhen Yang et al.   PLoS One

Effect of constitutive expression of Arabidopsis CLAVATA3 on cell growth and possible role of cytokinins in leaf size control in transgenic tobacco plants

(2018) Bulat Kuluev et al.   JOURNAL OF PLANT PHYSIOLOGY

Polyploidy, the Nucleotype, and Novelty: The Impact of Genome Doubling on the Biology of the Cell

(2018) Jeff J. Doyle et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Genome duplication improves the resistance of watermelon root to salt stress

(2018) Hongju Zhu et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Global impacts of chromosomal imbalance on gene expression in Arabidopsis and other taxa

(2018) Jie Hou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

3D Chromatin Architecture of Large Plant Genomes Determined by Local A/B Compartments

(2017) Pengfei Dong et al.   Molecular Plant

Pure polyploidy: Closing the gaps in autopolyploid research

(2017) Jonathan P. Spoelhof et al.   Journal of Systematics and Evolution

Effect of ploidy level on expression of lycopene biosynthesis genes and accumulation of phytohormones during watermelon (Citrullus lanatus) fruit development and ripening

(2017) Jun-ling DOU et al.   Journal of Integrative Agriculture

Genome-wide expression analysis of salt-stressed diploid and autotetraploid Paulownia tomentosa

(2017) Zhenli Zhao et al.   PLoS One

Expression-level support for gene dosage sensitivity in threeGlycinesubgenusGlycinepolyploids and their diploid progenitors

(2016) Jeremy E. Coate et al.   NEW PHYTOLOGIST

A GBS-SNP-based linkage map and quantitative trait loci (QTL) associated with resistance to Fusarium oxysporum f. sp. niveum race 2 identified in Citrullus lanatus var. citroides

(2016) Sandra E. Branham et al.   THEORETICAL AND APPLIED GENETICS

Global Expressions Landscape of NAC Transcription Factor Family and Their Responses to Abiotic Stresses in Citrullus lanatus

(2016) Xiaolong Lv et al.   Scientific Reports

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Whole genome duplications in plants: an overview fromArabidopsis

(2015) Juan Carlos del Pozo et al.   JOURNAL OF EXPERIMENTAL BOTANY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Comparative Transcriptome Analysis of Cultivated and Wild Watermelon during Fruit Development

(2015) Shaogui Guo et al.   PLoS One

Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression

(2015) Jie Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

genomation: a toolkit to summarize, annotate and visualize genomic intervals

(2014) A. Akalin et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Differential gene expression and alternative splicing between diploid and tetraploid watermelon

(2014) Thangasamy Saminathan et al.   JOURNAL OF EXPERIMENTAL BOTANY

Hi-C Analysis in Arabidopsis Identifies the KNOT, a Structure with Similarities to the flamenco Locus of Drosophila

(2014) Stefan Grob et al.   MOLECULAR CELL

Genome-wide Hi-C Analyses in Wild-Type and Mutants Reveal High-Resolution Chromatin Interactions in Arabidopsis

(2014) Suhua Feng et al.   MOLECULAR CELL

Deciphering the molecular bases for drought tolerance inArabidopsisautotetraploids

(2014) JUAN C. DEL POZO et al.   PLANT CELL AND ENVIRONMENT

Evolution of physiological responses to salt stress in hexaploid wheat

(2014) C. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome duplication improves rice root resistance to salt stress

(2014) Yi Tu et al.   Rice

A positive regulatory role of the watermelon ClWRKY70 gene for disease resistance in transgenic Arabidopsis thaliana

(2012) S. M. Cho et al.   BIOLOGIA PLANTARUM

Phenotypic and epigenetic changes occurred during the autopolyploidization ofAegilops tauschii

(2012) Z. Zeng et al.   CEREAL RESEARCH COMMUNICATIONS

Autopolyploidy differentially influences body size in plants, but facilitates enhanced accumulation of secondary metabolites, causing increased cytosine methylation

(2012) Umesh C. Lavania et al.   PLANT JOURNAL

Gene balance hypothesis: Connecting issues of dosage sensitivity across biological disciplines

(2012) J. A. Birchler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

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

(2011) Felix Krueger et al.   BIOINFORMATICS

DNA cytosine methylation in plant development

(2010) Meishan Zhang et al.   Journal of Genetics and Genomics

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

Impact of natural genetic variation on the transcriptome of autotetraploidArabidopsis thaliana

(2010) Zheng Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE