A chromosome-level Camptotheca acuminata genome assembly provides insights into the evolutionary origin of camptothecin biosynthesis

Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis

(2021) Amit Rai et al.   Nature Communications

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

Bifunctional Cytochrome P450 Enzymes Involved in Camptothecin Biosynthesis

(2019) Yun Yang et al.   ACS Chemical Biology

Cytochrome P450 enzymes: A driving force of plant diterpene diversity

(2019) Ulschan Bathe et al.   PHYTOCHEMISTRY

Loganic Acid Methyltransferase: Insights into the Specificity of Methylation on an Iridoid Glycoside

(2018) Nektaria Petronikolou et al.   CHEMBIOCHEM

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads

(2017) Jonas Korlach et al.   GigaScience

Effects of light on production of camptothecin and expression of key enzyme genes in seedlings of Camptotheca acuminate Decne

(2016) Yuanyuan Hu et al.   ACTA PHYSIOLOGIAE PLANTARUM

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV

(2016)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Metabolite Diversity in Alkaloid Biosynthesis: A Multilane (Diastereomer) Highway for Camptothecin Synthesis in Camptotheca acuminata

(2016) Radin Sadre et al.   PLANT CELL

Evolution of gene duplication in plants

(2016) Nicholas Panchy et al.   PLANT PHYSIOLOGY

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Perspectives on Biologically Active Camptothecin Derivatives

(2015) Ying-Qian Liu et al.   MEDICINAL RESEARCH REVIEWS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Genome-guided investigation of plant natural product biosynthesis

(2015) Franziska Kellner et al.   PLANT JOURNAL

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information

(2014) Marco Biasini et al.   NUCLEIC ACIDS RESEARCH

7-Deoxyloganetic acid synthase catalyzes a key 3 step oxidation to form 7-deoxyloganetic acid in Catharanthus roseus iridoid biosynthesis

(2014) Vonny Salim et al.   PHYTOCHEMISTRY

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

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

The seco-iridoid pathway from Catharanthus roseus

(2014) Karel Miettinen et al.   Nature Communications

Camptothecin-producing endophytic fungus Trichoderma atroviride LY357: isolation, identification, and fermentation conditions optimization for camptothecin production

(2013) Xiang Pu et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Geraniol hydroxylase and hydroxygeraniol oxidase activities of the CYP76 family of cytochrome P450 enzymes and potential for engineering the early steps of the (seco)iridoid pathway

(2013) René Höfer et al.   METABOLIC ENGINEERING

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

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

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

A 7-Deoxyloganetic Acid Glucosyltransferase Contributes a Key Step in Secologanin Biosynthesis in Madagascar Periwinkle

(2013) K. Asada et al.   PLANT CELL

Virus-induced gene silencing identifiesCatharanthus roseus7-deoxyloganic acid-7-hydroxylase, a step in iridoid and monoterpene indole alkaloid biosynthesis

(2013) Vonny Salim et al.   PLANT JOURNAL

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

An alternative route to cyclic terpenes by reductive cyclization in iridoid biosynthesis

(2012) Fernando Geu-Flores et al.   NATURE

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

(2012) Cole Trapnell et al.   Nature Protocols

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

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

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Development of Transcriptomic Resources for Interrogating the Biosynthesis of Monoterpene Indole Alkaloids in Medicinal Plant Species

(2012) Elsa Góngora-Castillo et al.   PLoS One

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

The Leaf Epidermome of Catharanthus roseus Reveals Its Biochemical Specialization

(2008) J. Murata et al.   PLANT CELL

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY