Allele‐specific expression and chromatin accessibility contribute to heterosis in tea plants ( Camellia sinensis )

Architecture and Dynamics of the Wounding-Induced Gene Regulatory Network During the Oolong Tea Manufacturing Process (Camellia sinensis)

(2022) Yucheng Zheng et al.   Frontiers in Plant Science

Changes in Non-Volatile and Volatile Metabolites Associated with Heterosis in Tea Plants (Camellia sinensis)

(2022) Pengjie Wang et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Genomes of single‐ and double‐petal jasmines ( Jasminum sambac ) provide insights into their divergence time and structural variations

(2022) Pengjie Wang et al.   PLANT BIOTECHNOLOGY JOURNAL

Arabidopsis cryptochrome 2 forms photobodies with TCP22 under blue light and regulates the circadian clock

(2022) Weiliang Mo et al.   Nature Communications

How does tea (Camellia sinensis) produce specialized metabolites which determine its unique quality and function: a review

(2021) Yinyin Liao et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

Biological pathway expression complementation contributes to biomass heterosis in Arabidopsis

(2021) Wenwen Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic basis of high aroma and stress tolerance in the oolong tea cultivar genome

(2021) Pengjie Wang et al.   Horticulture Research

Chromatin accessibility and translational landscapes of tea plants under chilling stress

(2021) Pengjie Wang et al.   Horticulture Research

Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis

(2021) Xingtan Zhang et al.   NATURE GENETICS

Insight into the cellular and physiological regulatory modulations of Class‐I TCP9 to enhance drought and salinity stress tolerance in cowpea

(2021) Sagarika Mishra et al.   PHYSIOLOGIA PLANTARUM

Genome-wide analysis of ARF transcription factors reveals HcARF5 expression profile associated with the biosynthesis of β-ocimene synthase in Hedychium coronarium

(2021) Farhat Abbas et al.   PLANT CELL REPORTS

Open chromatin in grapevine marks candidate CREs and with other chromatin features correlates with gene expression

(2021) Rachel Schwope et al.   PLANT JOURNAL

Suberin plasticity to developmental and exogenous cues is regulated by a set of MYB transcription factors

(2021) Vinay Shukla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Genome Doubling Event Reshapes Rice Morphology and Products by Modulating Chromatin Signatures and Gene Expression Profiling

(2021) Chao Zhou et al.   Rice

Transcriptome Reveals Allele Contribution to Heterosis in Maize

(2021) Jianzhong Wu et al.   Frontiers in Plant Science

Identification of Co-Expressed Genes Related to Theacrine Synthesis in Tea Flowers at Different Developmental Stages

(2021) Xiaomin Chen et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The multi‐omics basis of potato heterosis

(2021) Dawei Li et al.   Journal of Integrative Plant Biology

JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles

(2021) Jaime A Castro-Mondragon et al.   NUCLEIC ACIDS RESEARCH

Quality control and evaluation of plant epigenomics data

(2021) Robert J Schmitz et al.   PLANT CELL

Chromatin and regulatory differentiation between bundle sheath and mesophyll cells in maize

(2021) Xiuru Dai et al.   PLANT JOURNAL

Widely Targeted Metabolomic and Transcriptomic Analyses of a Novel Albino Tea Mutant of “Rougui”

(2020) Pengjie Wang et al.   Forests

MYB21 interacts with MYC2 to control the expression of terpene synthase genes in flowers of Freesia hybrida and Arabidopsis thaliana

(2020) Zhongzhou Yang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Induction of priming by cold stress via inducible volatile cues in neighboring tea plants

(2020) Mingyue Zhao et al.   Journal of Integrative Plant Biology

The Role of Transcriptional Regulation in Hybrid Vigor

(2020) Ramon Botet et al.   Frontiers in Plant Science

Tanshinone and salvianolic acid biosynthesis are regulated by SmMYB98 in Salvia miltiorrhiza hairy roots

(2020) Xiaolong Hao et al.   Journal of Advanced Research

Comparison of Metabolome and Transcriptome of Flavonoid Biosynthesis Pathway in a Purple-Leaf Tea Germplasm Jinmingzao and a Green-Leaf Tea Germplasm Huangdan reveals Their Relationship with Genetic Mechanisms of Color Formation

(2020) Xuejin Chen et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Exploration of the Effects of Different Blue LED Light Intensities on Flavonoid and Lipid Metabolism in Tea Plants via Transcriptomics and Metabolomics

(2020) Pengjie Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

(2020) Chengjie Chen et al.   Molecular Plant

Identification and characterization of two sesquiterpene synthase genes involved in volatile-mediated defense in tea plant (Camellia sinensis)

(2020) Guanhua Liu et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Genome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties

(2020) Weiyi Zhang et al.   Nature Communications

Temporal Regulation of the Metabolome and Proteome in Photosynthetic and Photorespiratory Pathways Contributes to Maize Heterosis

(2020) Zhi Li et al.   PLANT CELL

TCP5 controls leaf margin development by regulating KNOX and BEL-like transcription factors in Arabidopsis

(2020) Hongyang Yu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Chinese oolong tea: An aromatic beverage produced under multiple stresses

(2020) Lanting Zeng et al.   TRENDS IN FOOD SCIENCE & TECHNOLOGY

Patterns of genome-wide allele-specific expression in hybrid rice and the implications on the genetic basis of heterosis

(2019) Lin Shao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification and functional evaluation of accessible chromatin associated with wood formation in Eucalyptus grandis

(2019) Katrien Brown et al.   NEW PHYTOLOGIST

A host–pathogen interactome uncovers phytopathogenic strategies to manipulate plant ABA responses

(2019) Feng Y. Cao et al.   PLANT JOURNAL

Transcriptome and Metabolite Profiling Reveal Novel Insights into Volatile Heterosis in the Tea Plant (Camellia Sinensis)

(2019) Yucheng Zheng et al.   MOLECULES

Identification, expression, and putative target gene analysis of nuclear factor-Y (NF-Y) transcription factors in tea plant (Camellia sinensis)

(2019) Pengjie Wang et al.   PLANTA

Evolutionary flexibility in flooding response circuitry in angiosperms

(2019) Mauricio A. Reynoso et al.   SCIENCE

Identification of CBF Transcription Factors in Tea Plants and a Survey of Potential CBF Target Genes under Low Temperature

(2019) Pengjie Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Nucleotide Metabolism in Plants

(2019) Claus-Peter Witte et al.   PLANT PHYSIOLOGY

Novel functions of the Arabidopsis transcription factor TCP5 in petal development and ethylene biosynthesis

(2018) Sam W. van Es et al.   PLANT JOURNAL

Changes in chromatin accessibility between Arabidopsis stem cells and mesophyll cells illuminate cell type-specific transcription factor networks

(2018) Paja Sijacic et al.   PLANT JOURNAL

Arabidopsis ETHYLENE RESPONSE FACTOR 8 (ERF8) has dual functions in ABA signaling and immunity

(2018) Feng Yi Cao et al.   BMC PLANT BIOLOGY

Heterosis in plants

(2018) Frank Hochholdinger et al.   CURRENT BIOLOGY

Transcriptome Analysis of Poplar Under Salt Stress and Over-Expression of Transcription Factor NAC57 Gene Confers Salt Tolerance in Transgenic Arabidopsis

(2018) Wenjing Yao et al.   Frontiers in Plant Science

TCP7 functions redundantly with several Class I TCPs and regulates endoreplication in Arabidopsis

(2018) Guofang Zhang et al.   Journal of Integrative Plant Biology

Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

(2018) Jisen Zhang et al.   NATURE GENETICS

SnRK1 phosphorylation of FUSCA3 positively regulates embryogenesis, seed yield, and plant growth at high temperature in Arabidopsis

(2017) Aaron Chan et al.   JOURNAL OF EXPERIMENTAL BOTANY

Mapping genome-wide transcription-factor binding sites using DAP-seq

(2017) Anna Bartlett et al.   Nature Protocols

Overexpression of SmMYB9b enhances tanshinone concentration in Salvia miltiorrhiza hairy roots

(2017) Jingxian Zhang et al.   PLANT CELL REPORTS

Natural variation for gene expression responses to abiotic stress in maize

(2017) Amanda J. Waters et al.   PLANT JOURNAL

AaMYB1 and its orthologue AtMYB61 affect terpene metabolism and trichome development in Artemisia annua and Arabidopsis thaliana

(2017) Luis Matías-Hernández et al.   PLANT JOURNAL

Brassinosteroid Biosynthesis Is Modulated via a Transcription Factor Cascade of COG1, PIF4, and PIF5

(2017) Zhuoyun Wei et al.   PLANT PHYSIOLOGY

The Multifaceted Roles of HY5 in Plant Growth and Development

(2016) Sreeramaiah N. Gangappa et al.   Molecular Plant

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

MdMyb93 is a regulator of suberin deposition in russeted apple fruit skins

(2016) Sylvain Legay et al.   NEW PHYTOLOGIST

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments

(2016) Olivia Wilkins et al.   PLANT CELL

ArabidopsisCOGWHEEL1links light perception and gibberellins with seed tolerance to deterioration

(2016) Eduardo Bueso et al.   PLANT JOURNAL

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Complementary activities of TELOMERE REPEAT BINDING proteins and Polycomb Group complexes in transcriptional regulation of target genes

(2015) Yue Zhou et al.   PLANT CELL

TCP transcription factors are critical for the coordinated regulation ofISOCHORISMATE SYNTHASE 1expression inArabidopsis thaliana

(2015) Xiaoyan Wang et al.   PLANT JOURNAL

Natural Variation in Monoterpene Synthesis in Kiwifruit: Transcriptional Regulation of Terpene Synthases by NAC and ETHYLENE-INSENSITIVE3-Like Transcription Factors

(2015) Niels J. Nieuwenhuizen et al.   PLANT PHYSIOLOGY

Decreased seed oil production in FUSCA3 Brassica napus mutant plants

(2015) Nosheen Elahi et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

The expression of a rice secondary wall-specific cellulose synthase gene, OsCesA7, is directly regulated by a rice transcription factor, OsMYB58/63

(2015) Soichiro Noda et al.   PLANTA

The Roles of Arabidopsis CDF2 in Transcriptional and Posttranscriptional Regulation of Primary MicroRNAs

(2015) Zhenfei Sun et al.   PLoS Genetics

High-resolution digital profiling of the epigenome

(2014) Gabriel E. Zentner et al.   NATURE REVIEWS GENETICS

AtMYB93 is a novel negative regulator of lateral root development in Arabidopsis

(2014) Daniel J. Gibbs et al.   NEW PHYTOLOGIST

Nonsyntenic Genes Drive Highly Dynamic Complementation of Gene Expression in Maize Hybrids

(2014) A. Paschold et al.   PLANT CELL

TRANSPARENT TESTA2regulates embryonic fatty acid biosynthesis by targetingFUSCA3during the early developmental stage of Arabidopsis seeds

(2014) Zhong Wang et al.   PLANT JOURNAL

Research progress in allele-specific expression and its regulatory mechanisms

(2013) Uma Gaur et al.   JOURNAL OF APPLIED GENETICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Identification of Direct Targets of FUSCA3, a Key Regulator of Arabidopsis Seed Development

(2013) F. Wang et al.   PLANT PHYSIOLOGY

Functional study of TCP23 in Arabidopsis thaliana during plant development

(2013) Emilia Balsemão-Pires et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Analysis of the role of Arabidopsis class I TCP genes AtTCP7, AtTCP8, AtTCP22, and AtTCP23 in leaf development

(2013) José A. Aguilar-Martínez et al.   Frontiers in Plant Science

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents

(2012) A. Paschold et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Arabidopsis Class I and Class II TCP Transcription Factors Regulate Jasmonic Acid Metabolism and Leaf Development Antagonistically

(2012) S. Danisman et al.   PLANT PHYSIOLOGY

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

The family of terpene synthases in plants: a mid-size family of genes for specialized metabolism that is highly diversified throughout the kingdom

(2011) Feng Chen et al.   PLANT JOURNAL

Heterosis

(2010) J. A. Birchler et al.   PLANT CELL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Arabidopsis DOF Transcription Factors Act Redundantly to Reduce CONSTANS Expression and Are Essential for a Photoperiodic Flowering Response

(2009) Fabio Fornara et al.   DEVELOPMENTAL CELL

Global Analysis of Allele-Specific Expression in Arabidopsis thaliana

(2009) Xu Zhang et al.   GENETICS

MYB58 and MYB63 Are Transcriptional Activators of the Lignin Biosynthetic Pathway during Secondary Cell Wall Formation in Arabidopsis

(2009) J. Zhou et al.   PLANT CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY