The chromosome-scale genome reveals the evolution and diversification after the recent tetraploidization event in tea plant

NBS-Encoding Genes in Brassica napus Evolved Rapidly After Allopolyploidization and Co-localize With Known Disease Resistance Loci

(2019) Ying Fu et al.   Frontiers in Plant Science

The tea plant reference genome and improved gene annotation using long-read and paired-end sequencing data

(2019) Enhua Xia et al.   Scientific Data

Functional analysis of flavonoid 3′-hydroxylase and flavonoid 3′,5′-hydroxylases from tea plant (Camellia sinensis), involved in the B-ring hydroxylation of flavonoids

(2019) Lina Guo et al.   GENE

A high-quality Actinidia chinensis (kiwifruit) genome

(2019) Haolin Wu et al.   Horticulture Research

Beneficial Effects of Green Tea Catechins on Neurodegenerative Diseases

(2018) Monira Pervin et al.   MOLECULES

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

(2018) Joshua C. Stein et al.   NATURE GENETICS

Draft genome sequence ofCamellia sinensisvar.sinensisprovides insights into the evolution of the tea genome and tea quality

(2018) Chaoling Wei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data

(2018) Rubina Jibran et al.   Horticulture Research

High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing

(2018) Li-Yi Xu et al.   BMC GENOMICS

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

(2018) Jisen Zhang et al.   NATURE GENETICS

An Overlooked Paleotetraploidization in Cucurbitaceae

(2017) Jinpeng Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

(2017) Derek M Bickhart et al.   NATURE GENETICS

Green tea effects on cognition, mood and human brain function: A systematic review

(2017) Edele Mancini et al.   PHYTOMEDICINE

Transcriptional profiling of catechins biosynthesis genes during tea plant leaf development

(2017) Fei Guo et al.   PLANTA

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Functional natural allelic variants of flavonoid 3′,5′-hydroxylase gene governing catechin traits in tea plant and its relatives

(2016) Ji-Qiang Jin et al.   PLANTA

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

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

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

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

De Novo Plant Genome Assembly Based on Chromatin Interactions: A Case Study of Arabidopsis thaliana

(2015) Ting Xie et al.   Molecular Plant

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Sequence-based ultra-dense genetic and physical maps reveal structural variations of allopolyploid cotton genomes

(2015) Sen Wang et al.   GENOME BIOLOGY

Large-Scale SNP Discovery and Genotyping for Constructing a High-Density Genetic Map of Tea Plant Using Specific-Locus Amplified Fragment Sequencing (SLAF-seq)

(2015) Jian-Qiang Ma et al.   PLoS One

Ethylamine Content and Theanine Biosynthesis in Different Organs of Camellia sinensis Seedlings

(2015) Wei-Wei Deng et al.   ZEITSCHRIFT FUR NATURFORSCHUNG SECTION C-A JOURNAL OF BIOSCIENCES

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

The genome of Eucalyptus grandis

(2014) Alexander A. Myburg et al.   NATURE

Association Mapping across Numerous Traits Reveals Patterns of Functional Variation in Maize

(2014) Jason G. Wallace et al.   PLoS Genetics

Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation

(2013) Jizeng Jia et al.   NATURE

High-throughput genome scaffolding from in vivo DNA interaction frequency

(2013) Noam Kaplan et al.   NATURE BIOTECHNOLOGY

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Functional Characterization of Proanthocyanidin Pathway Enzymes from Tea and Their Application for Metabolic Engineering

(2013) Y. Pang et al.   PLANT PHYSIOLOGY

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

(2012) Andrew H. Paterson et al.   NATURE

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

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

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

The Cassava Genome: Current Progress, Future Directions

(2012) Simon Prochnik et al.   Tropical Plant Biology

Molecular regulation of catechins biosynthesis in tea [Camellia sinensis (L.) O. Kuntze]

(2011) Arti Rani et al.   GENE

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Diversity distribution and population structure of tea germplasms in China revealed by EST-SSR markers

(2011) Ming-Zhe Yao et al.   Tree Genetics & Genomes

An early gene of the flavonoid pathway, flavanone 3-hydroxylase, exhibits a positive relationship with the concentration of catechins in tea (Camellia sinensis)

(2011) K. Singh et al.   TREE PHYSIOLOGY

CDD: a Conserved Domain Database for the functional annotation of proteins

(2010) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Polyploidy and angiosperm diversification

(2009) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

Bias in Plant Gene Content Following Different Sorts of Duplication: Tandem, Whole-Genome, Segmental, or by Transposition

(2009) Michael Freeling   Annual Review of Plant Biology

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

p-Coumarate:CoA ligase as a key gene in the yield of catechins in tea [Camellia sinensis (L.) O. Kuntze]

(2008) Arti Rani et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Recurrent Tandem Gene Duplication Gave Rise to Functionally Divergent Genes in Drosophila

(2008) C. Fan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Importance of Lineage-Specific Expansion of Plant Tandem Duplicates in the Adaptive Response to Environmental Stimuli

(2008) K. Hanada et al.   PLANT PHYSIOLOGY