The chromosome-level reference genome assembly for Dendrobium officinale and its utility of functional genomics research and molecular breeding study

Genome of Tripterygium wilfordii and identification of cytochrome P450 involved in triptolide biosynthesis

(2020) Lichan Tu et al.   Nature Communications

A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine

(2020) Minghui Kang et al.   Horticulture Research

The honeysuckle genome provides insight into the molecular mechanism of carotenoid metabolism underlying dynamic flower coloration

(2020) Xiangdong Pu et al.   NEW PHYTOLOGIST

The Chimonanthus salicifolius genome provides insight into magnoliid evolution and flavonoid biosynthesis

(2020) Qundan Lv et al.   PLANT JOURNAL

Population sequencing enhances understanding of tea plant evolution

(2020) Xinchao Wang et al.   Nature Communications

Biogenic Synthesis and Spatial Distribution of Endogenous Phytohormones and Ginsenosides Provide Insights on Their Intrinsic Relevance in Panax ginseng

(2019) Kang Chen et al.   Frontiers in Plant Science

Transposable elements drive rapid phenotypic variation in Capsella rubella

(2019) Xiao-Min Niu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Reference Genome Sequence of Scutellaria baicalensis Provides Insights into the Evolution of Wogonin Biosynthesis

(2019) Qing Zhao et al.   Molecular Plant

Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement

(2019) Ning Yang et al.   NATURE GENETICS

The Genome of Artemisia annua Provides Insight into the Evolution of Asteraceae Family and Artemisinin Biosynthesis

(2018) Qian Shen et al.   Molecular Plant

Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits

(2018) Xiongming Du et al.   NATURE GENETICS

The Gastrodia elata genome provides insights into plant adaptation to heterotrophy

(2018) Yuan Yuan et al.   Nature Communications

Accurate authentication of Dendrobium officinale and its closely related species by comparative analysis of complete plastomes

(2018) Shuying Zhu et al.   Acta Pharmaceutica Sinica B

Leveraging multiple transcriptome assembly methods for improved gene structure annotation

(2018) Luca Venturini et al.   GigaScience

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

(2018) Michael J. Roach et al.   BMC BIOINFORMATICS

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Apostasia genome and the evolution of orchids

(2017) Guo-Qiang Zhang et al.   NATURE

MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads

(2017) Chuan-Le Xiao et al.   NATURE METHODS

20 years of the SMART protein domain annotation resource

(2017) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism

(2017) Xiaohan Yang et al.   Nature Communications

Iteration expansion and regional evolution: phylogeography of Dendrobium officinale and four related taxa in southern China

(2017) Beiwei Hou et al.   Scientific Reports

Origin and mechanism of crassulacean acid metabolism in orchids as implied by comparative transcriptomics and genomics of the carbon fixation pathway

(2016) Liangsheng Zhang et al.   PLANT JOURNAL

The Arabidopsis Domain of Unknown Function 1218 (DUF1218) Containing Proteins, MODIFYING WALL LIGNIN-1 and 2 (At1g31720/MWL-1 and At4g19370/MWL-2) Function Redundantly to Alter Secondary Cell Wall Lignin Content

(2016) Ritesh Mewalal et al.   PLoS One

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

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

The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution

(2016) Guo-Qiang Zhang et al.   Scientific Reports

Evolutionary impact of transposable elements on genomic diversity and lineage-specific innovation in vertebrates

(2015) Ian A. Warren et al.   CHROMOSOME RESEARCH

Molecular Identification of Dendrobium Species (Orchidaceae) Based on the DNA Barcode ITS2 Region and Its Application for Phylogenetic Study

(2015) Shangguo Feng et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The Genome of Dendrobium officinale Illuminates the Biology of the Important Traditional Chinese Orchid Herb

(2015) Liang Yan et al.   Molecular Plant

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Identification of genes involved in biosynthesis of mannan polysaccharides in Dendrobium officinale by RNA-seq analysis

(2015) Chunmei He et al.   PLANT MOLECULAR BIOLOGY

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

The genome sequence of the orchid Phalaenopsis equestris

(2014) Jing Cai et al.   NATURE GENETICS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Analysis of the Dendrobium officinale transcriptome reveals putative alkaloid biosynthetic genes and genetic markers

(2013) Xu Guo et al.   GENE

Transposable Elements: Powerful Contributors to Angiosperm Evolution and Diversity

(2013) Keith R. Oliver et al.   Genome Biology and Evolution

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

(2013) Mira V. Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular systematics of Dendrobium (Orchidaceae, Dendrobieae) from mainland Asia based on plastid and nuclear sequences

(2013) Xiao-Guo Xiang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

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

Review of research on Dendrobium, a prized folk medicine

(2012) Tzi Bun Ng et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

Detecting adulteration of Dendrobium officinale by real-time PCR coupled with ARMS

(2012) Huijun Xu et al.   INTERNATIONAL JOURNAL OF FOOD SCIENCE AND TECHNOLOGY

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

Genetic diversity assessment and ex situ conservation strategy of the endangered Dendrobium officinale (Orchidaceae) using new trinucleotide microsatellite markers

(2012) Beiwei Hou et al.   PLANT SYSTEMATICS AND EVOLUTION

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Studying physical chromatin interactions in plants using Chromosome Conformation Capture (3C)

(2009) Marieke Louwers et al.   Nature Protocols

The evolutionary significance of ancient genome duplications

(2009) Yves Van de Peer et al.   NATURE REVIEWS GENETICS