Whole-genome, transcriptome, and methylome analyses provide insights into the evolution of platycoside biosynthesis in Platycodon grandiflorus, a medicinal plant

GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes

(2020) T. Rhyker Ranallo-Benavidez et al.   Nature Communications

Genome and evolution of the shade-requiring medicinal herb Panax ginseng

(2018) Nam-Hoon Kim et al.   PLANT BIOTECHNOLOGY JOURNAL

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

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

Whole-Genome Sequencing and Analysis of the Chinese Herbal Plant Panax notoginseng

(2017) Wei Chen et al.   Molecular Plant

The Medicinal Herb Panax notoginseng Genome Provides Insights into Ginsenoside Biosynthesis and Genome Evolution

(2017) Dan Zhang et al.   Molecular Plant

The genome of Chenopodium quinoa

(2017) David E. Jarvis et al.   NATURE

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

(2017) Hélène Badouin et al.   NATURE

Cytochrome P450 Monooxygenase CYP716A141 is a Unique β-Amyrin C-16β Oxidase Involved in Triterpenoid Saponin Biosynthesis in Platycodon grandiflorus

(2017) Keita Tamura et al.   PLANT AND CELL PHYSIOLOGY

The ancient CYP716 family is a major contributor to the diversification of eudicot triterpenoid biosynthesis

(2017) Karel Miettinen et al.   Nature Communications

Triterpene Structural Diversification by Plant Cytochrome P450 Enzymes

(2017) Sumit Ghosh   Frontiers in Plant Science

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

(2016) Massimo Iorizzo et al.   NATURE GENETICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Platycodon grandiflorus – An Ethnopharmacological, phytochemical and pharmacological review

(2015) Le Zhang et al.   JOURNAL OF ETHNOPHARMACOLOGY

MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing

(2015) Mark A Urich et al.   Nature Protocols

P450s and UGTs: Key Players in the Structural Diversity of Triterpenoid Saponins

(2015) Hikaru Seki et al.   PLANT AND CELL PHYSIOLOGY

The bHLH Transcription Factors TSAR1 and TSAR2 Regulate Triterpene Saponin Biosynthesis in Medicago truncatula

(2015) Jan Mertens et al.   PLANT PHYSIOLOGY

Triterpene Biosynthesis in Plants

(2014) Ramesha Thimmappa et al.   Annual Review of Plant Biology

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Metabolic and functional diversity of saponins, biosynthetic intermediates and semi-synthetic derivatives

(2014) Tessa Moses et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm

(2014) Alexandre Lomsadze et al.   NUCLEIC ACIDS RESEARCH

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

(2014) F. Denoeud et al.   SCIENCE

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

GapFiller: a de novo assembly approach to fill the gap within paired reads

(2012) Francesca Nadalin et al.   BMC BIOINFORMATICS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Effect of methyl jasmonate on the ginsenoside content of Panax ginseng adventitious root cultures and on the genes involved in triterpene biosynthesis

(2012) Juan Wang et al.   RESEARCH ON CHEMICAL INTERMEDIATES

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin

(2011) Hikaru Seki et al.   PLANT CELL

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Consensus generation and variant detection by Celera Assembler

(2008) G. Denisov et al.   BIOINFORMATICS