4.8 Article

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

Related references

Note: Only part of the references are listed.
Article Multidisciplinary Sciences

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

Martha Rendon-Anaya et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Biochemistry & Molecular Biology

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

Sudhir Kumar et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Plant Sciences

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

Olivia Costantina Demurtas et al.

PLANT PHYSIOLOGY (2018)

Article Multidisciplinary Sciences

Extreme haplotype variation in the desiccation-tolerant clubmoss Selaginella lepidophylla

Robert VanBuren et al.

NATURE COMMUNICATIONS (2018)

Article Multidisciplinary Sciences

The opium poppy genome and morphinan production

Li Guo et al.

SCIENCE (2018)

Article Biochemical Research Methods

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

Michael J. Roach et al.

BMC BIOINFORMATICS (2018)

Article Plant Sciences

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

Keiichi Mochida et al.

PLANT JOURNAL (2017)

Article Biochemistry & Molecular Biology

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

Sergey Koren et al.

GENOME RESEARCH (2017)

Review Food Science & Technology

Chemistry and bioactivity of Gardenia jasminoides

Wenping Xiao et al.

JOURNAL OF FOOD AND DRUG ANALYSIS (2017)

Letter Biochemistry & Molecular Biology

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

Wei Chen et al.

MOLECULAR PLANT (2017)

Article Biochemistry & Molecular Biology

De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing

Maximilian H. -W. Schmidt et al.

PLANT CELL (2017)

Article Ecology

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

Kenji Fukushima et al.

NATURE ECOLOGY & EVOLUTION (2017)

Article Biochemical Research Methods

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

Heng Li

BIOINFORMATICS (2016)

Letter Biochemistry & Molecular Biology

Analysis of the Genome Sequence of the Medicinal Plant Salvia miltiorrhiza

Haibin Xu et al.

MOLECULAR PLANT (2016)

Review Plant Sciences

Plant metabolic clusters - from genetics to genomics

Hans-Wilhelm Nutzmann et al.

NEW PHYTOLOGIST (2016)

Article Multidisciplinary Sciences

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

Ruiqi Huang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Review Plant Sciences

Synthesis and Function of Apocarotenoid Signals in Plants

Xin Hou et al.

TRENDS IN PLANT SCIENCE (2016)

Article Biochemical Research Methods

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

Felipe A. Simao et al.

BIOINFORMATICS (2015)

Article Biochemical Research Methods

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

Siavash Mirarab et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2015)

Article Biochemical Research Methods

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

Alexandros Stamatakis

BIOINFORMATICS (2014)

Article Multidisciplinary Sciences

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

Sarah Frusciante et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Multidisciplinary Sciences

Genomic Signatures of Specialized Metabolism in Plants

Lee Chae et al.

SCIENCE (2014)

Article Multidisciplinary Sciences

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

France Denoeud et al.

SCIENCE (2014)

Article Biochemical Research Methods

Infernal 1.1: 100-fold faster RNA homology searches

Eric P. Nawrocki et al.

BIOINFORMATICS (2013)

Article Multidisciplinary Sciences

Architecture and evolution of a minute plant genome

Enrique Ibarra-Laclette et al.

NATURE (2013)

Article Biotechnology & Applied Microbiology

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

Joshua N. Burton et al.

NATURE BIOTECHNOLOGY (2013)

Article Biochemistry & Molecular Biology

UGT75L6 and UGT94E5 mediate sequential glucosylation of crocetin to crocin in Gardenia jasminoides

Mai Nagatoshi et al.

FEBS LETTERS (2012)

Article Biochemical Research Methods

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

Cole Trapnell et al.

NATURE PROTOCOLS (2012)

Article Biochemical Research Methods

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

Jon-Matthew Belton et al.

METHODS (2012)

Article Biochemical Research Methods

Scaffolding pre-assembled contigs using SSPACE

Marten Boetzer et al.

BIOINFORMATICS (2011)

Article Biotechnology & Applied Microbiology

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

Manfred G. Grabherr et al.

NATURE BIOTECHNOLOGY (2011)

Article Multidisciplinary Sciences

FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments

Morgan N. Price et al.

PLOS ONE (2010)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Review Biochemistry & Molecular Biology

Structure, mechanism and engineering of plant natural product glycosyltransferases

Xiaoqiang Wang

FEBS LETTERS (2009)

Article Biochemistry & Molecular Biology

MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes

Brandi L. Cantarel et al.

GENOME RESEARCH (2008)

Article Biochemical Research Methods

Clustal W and clustal X version 2.0

M. A. Larkin et al.

BIOINFORMATICS (2007)

Article Biochemical Research Methods

CAFE: a computational tool for the study of gene family evolution

T De Bie et al.

BIOINFORMATICS (2006)

Article Biochemistry & Molecular Biology

OrthoMCL: Identification of ortholog groups for eukaryotic genomes

L Li et al.

GENOME RESEARCH (2003)

Article Biochemistry & Molecular Biology

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

K Katoh et al.

NUCLEIC ACIDS RESEARCH (2002)

Article Biochemistry & Molecular Biology

An efficient algorithm for large-scale detection of protein families

AJ Enright et al.

NUCLEIC ACIDS RESEARCH (2002)