Tandem gene duplications drive divergent evolution of caffeine and crocin biosynthetic pathways in plants

The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation

(2019) Martha Rendón-Anaya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome Analysis of the Ancient Tracheophyte Selaginella tamariscina Reveals Evolutionary Features Relevant to the Acquisition of Desiccation Tolerance

(2018) Zhichao Xu et al.   Molecular Plant

Crocus sativus a natural food coloring and flavoring has potent anti-tumor properties

(2018) Zahra Khorasanchi et al.   PHYTOMEDICINE

Candidate Enzymes for Saffron Crocin Biosynthesis Are Localized in Multiple Cellular Compartments

(2018) Olivia Costantina Demurtas et al.   PLANT PHYSIOLOGY

Extreme haplotype variation in the desiccation-tolerant clubmoss Selaginella lepidophylla

(2018) Robert VanBuren et al.   Nature Communications

The opium poppy genome and morphinan production

(2018) Li Guo et al.   SCIENCE

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

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

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Evolutionarily distinct carotenoid cleavage dioxygenases are responsible for crocetin production in Buddleja davidii

(2017) Oussama Ahrazem et al.   JOURNAL OF EXPERIMENTAL BOTANY

Chemistry and bioactivity of Gardenia jasminoides

(2017) Wenping Xiao et al.   JOURNAL OF FOOD AND DRUG ANALYSIS

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

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

(2017) Jarkko Salojärvi et al.   NATURE GENETICS

De Novo Assembly of a NewSolanum pennelliiAccession Using Nanopore Sequencing

(2017) Maximilian H.-W. Schmidt et al.   PLANT CELL

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

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

(2017) Benjamin Istace et al.   GigaScience

Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory

(2017) Kenji Fukushima et al.   Nature Ecology & Evolution

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

(2016) Heng Li   BIOINFORMATICS

Analysis of the Genome Sequence of the Medicinal Plant Salvia miltiorrhiza

(2016) Haibin Xu et al.   Molecular Plant

Plant metabolic clusters - from genetics to genomics

(2016) Hans-Wilhelm Nützmann et al.   NEW PHYTOLOGIST

Draft genome assembly and annotation of Glycyrrhiza uralensis , a medicinal legume

(2016) Keiichi Mochida et al.   PLANT JOURNAL

Convergent evolution of caffeine in plants by co-option of exapted ancestral enzymes

(2016) Ruiqi Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synthesis and Function of Apocarotenoid Signals in Plants

(2016) Xin Hou et al.   TRENDS IN PLANT SCIENCE

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences

(2015) Siavash Mirarab et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The carotenoid cleavage dioxygenase CCD2 catalysing the synthesis of crocetin in spring crocuses and saffron is a plastidial enzyme

(2015) Oussama Ahrazem et al.   NEW PHYTOLOGIST

Disruption of aCAROTENOID CLEAVAGE DIOXYGENASE 4gene converts flower colour from white to yellow inBrassicaspecies

(2015) Bao Zhang et al.   NEW PHYTOLOGIST

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

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

Novel carotenoid cleavage dioxygenase catalyzes the first dedicated step in saffron crocin biosynthesis

(2014) S. Frusciante et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Signatures of Specialized Metabolism in Plants

(2014) L. Chae et al.   SCIENCE

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

(2014) F. Denoeud et al.   SCIENCE

Infernal 1.1: 100-fold faster RNA homology searches

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

Architecture and evolution of a minute plant genome

(2013) Enrique Ibarra-Laclette et al.   NATURE

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

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Enzymatic Formation of  -Citraurin from  -Cryptoxanthin and Zeaxanthin by Carotenoid Cleavage Dioxygenase4 in the Flavedo of Citrus Fruit

(2013) G. Ma et al.   PLANT PHYSIOLOGY

Phylogenomics of the benzoxazinoid biosynthetic pathway of Poaceae: gene duplications and origin of the Bx cluster

(2012) Leslie Dutartre et al.   BMC EVOLUTIONARY BIOLOGY

UGT75L6 and UGT94E5 mediate sequential glucosylation of crocetin to crocin inGardenia jasminoides

(2012) Mai Nagatoshi et al.   FEBS LETTERS

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

(2012) Jon-Matthew Belton et al.   METHODS

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

(2012) Cole Trapnell et al.   Nature Protocols

Aldehyde dehydrogenase (ALDH) superfamily in plants: gene nomenclature and comparative genomics

(2012) Chad Brocker et al.   PLANTA

Study of 'Redhaven' peach and its white-fleshed mutant suggests a key role of CCD4 carotenoid dioxygenase in carotenoid and norisoprenoid volatile metabolism

(2011) Federica Brandi et al.   BMC PLANT BIOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Structure, mechanism and engineering of plant natural product glycosyltransferases

(2009) Xiaoqiang Wang   FEBS LETTERS

Crocin and geniposide profiles and radical scavenging activity of gardenia fruits (Gardenia jasminoides Ellis) from different cultivars and at the various stages of maturation

(2009) Yang Chen et al.   FITOTERAPIA

Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids

(2008) E. Lyons et al.   PLANT PHYSIOLOGY

The Value of Nonmodel Genomes and an Example Using SynMap Within CoGe to Dissect the Hexaploidy that Predates the Rosids

(2008) Eric Lyons et al.   Tropical Plant Biology