Comparative transcriptomic analysis unveils the deep phylogeny and secondary metabolite evolution of 116 Camellia plants

Phylotranscriptomics of Theaceae: generic-level relationships, reticulation and whole-genome duplication

(2022) Qiong Zhang et al.   ANNALS OF BOTANY

Chromosome‐level genome of Camellia lanceoleosa provides a valuable resource for understanding genome evolution and self‐incompatibility

(2022) Wenfang Gong et al.   PLANT JOURNAL

An ancient whole-genome duplication event and its contribution to flavor compounds in the tea plant (Camellia sinensis)

(2021) Ya Wang et al.   Horticulture Research

CsAlaDC and CsTSI work coordinately to determine theanine biosynthesis in tea plants ( Camellia sinensis L.) and confer high levels of theanine accumulation in a non‐tea plant

(2021) Biying Zhu et al.   PLANT BIOTECHNOLOGY JOURNAL

Tea plant genomics: achievements, challenges and perspectives

(2020) En-Hua Xia et al.   Horticulture Research

Exploring plant metabolic genomics: chemical diversity, metabolic complexity in the biosynthesis and transport of specialized metabolites with the tea plant as a model

(2020) Jian Zhao et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

The reference genome of tea plant and resequencing of 81 diverse accessions provide insights into genome evolution and adaptation of tea plants

(2020) Enhua Xia et al.   Molecular Plant

Transcriptional regulation of amino acid metabolism in response to nitrogen deficiency and nitrogen forms in tea plant root (Camellia sinensis L.)

(2020) Tianyuan Yang et al.   Scientific Reports

Phylogenetic patterns suggest frequent multiple origins of secondary metabolites across the seed plant “tree of life”

(2020) Yongzeng Zhang et al.   National Science Review

Asterid phylogenomics/phylotranscriptomics uncover morphological evolutionary histories and support phylogenetic placement for numerous whole genome duplications

(2020) Caifei Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2020) Weiyi Zhang et al.   Nature Communications

Tea Plant Information Archive ( TPIA ): A comprehensive genomics and bioinformatics platform for tea plant

(2019) En‐Hua Xia et al.   PLANT BIOTECHNOLOGY JOURNAL

Chemistry and Biological Activities of Processed Camellia sinensis Teas: A Comprehensive Review

(2019) Liang Zhang et al.   COMPREHENSIVE REVIEWS IN FOOD SCIENCE AND FOOD SAFETY

One thousand plant transcriptomes and the phylogenomics of green plants

(2019)   NATURE

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Effects of roasting treatment on non-volatile compounds and taste of green tea

(2018) Ajing Mao et al.   INTERNATIONAL JOURNAL OF FOOD SCIENCE AND TECHNOLOGY

Gene co-expression network analysis reveals coordinated regulation of three characteristic secondary biosynthetic pathways in tea plant (Camellia sinensis)

(2018) Yuling Tai et al.   BMC GENOMICS

wgd—simple command line tools for the analysis of ancient whole-genome duplications

(2018) Arthur Zwaenepoel et al.   BIOINFORMATICS

Studies on the Biochemical Formation Pathway of the Amino Acid l-Theanine in Tea (Camellia sinensis) and Other Plants

(2017) Sihua Cheng et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

The Tea Tree Genome Provides Insights into Tea Flavor and Independent Evolution of Caffeine Biosynthesis

(2017) En-Hua Xia et al.   Molecular Plant

Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets

(2017) Liping Zeng et al.   NEW PHYTOLOGIST

De novo transcriptome sequencing of Camellia sasanqua and the analysis of major candidate genes related to floral traits

(2017) Hui Huang et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

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

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

De novo transcriptome assembly of the wild relative of tea tree (Camellia taliensis) and comparative analysis with tea transcriptome identified putative genes associated with tea quality and stress response

(2015) Hai-Bin Zhang et al.   BMC GENOMICS

Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution

(2015) Chien-Hsun Huang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing

(2015) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mining from transcriptomes: 315 single-copy orthologous genes concatenated for the phylogenetic analyses of Orchidaceae

(2015) Hua Deng et al.   Ecology and Evolution

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships

(2014) Hui Huang et al.   BMC EVOLUTIONARY BIOLOGY

Deep sequencing of the Camellia chekiangoleosa transcriptome revealed candidate genes for anthocyanin biosynthesis

(2014) Zhong-wei Wang et al.   GENE

Transcriptome Analysis of the Oil-Rich Tea Plant, Camellia oleifera, Reveals Candidate Genes Related to Lipid Metabolism

(2014) En-Hua Xia et al.   PLoS One

Analysis of plastid and nuclear DNA data in plant phylogenetics—evaluation and improvement

(2014) Wei Wang et al.   Science China-Life Sciences

Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times

(2014) Liping Zeng et al.   Nature Communications

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Transcriptome Sequences Resolve Deep Relationships of the Grape Family

(2013) Jun Wen et al.   PLoS One

Comparative Chloroplast Genomes of Camellia Species

(2013) Jun-Bo Yang et al.   PLoS One

Phylogenetics and biogeography of Theaceae based on sequences of plastid genes

(2013) Mi-Mi LI et al.   Journal of Systematics and Evolution

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Phylogeography of Camellia taliensis (Theaceae) inferred from chloroplast and nuclear DNA: insights into evolutionary history and conservation

(2012) Yang Liu et al.   BMC EVOLUTIONARY BIOLOGY

Transcriptional Regulation of Plant Secondary MetabolismF

(2012) Chang-Qing Yang et al.   Journal of Integrative Plant Biology

Classification of Camellia (Theaceae) Species Using Leaf Architecture Variations and Pattern Recognition Techniques

(2012) Hongfei Lu et al.   PLoS One

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds

(2011) Cheng-Ying Shi et al.   BMC GENOMICS

Taxonomic treatments of Camellia (Theaceae) species with secretory structures based on integrated leaf characters

(2010) B. Jiang et al.   PLANT SYSTEMATICS AND EVOLUTION

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Molecular taxonomy of Camellia (Theaceae) inferred from nrITS sequences

(2009) K. Vijayan et al.   AMERICAN JOURNAL OF BOTANY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Leaf morphology and anatomy ofCamelliasectionCamellia(Theaceae)

(2009) PI ERXU et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY