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

Integrative omics of Lonicera japonica Thunb. Flower development unravels molecular changes regulating secondary metabolites

(2019) Bingxian Yang et al.   Journal of Proteomics

SLR: a scaffolding algorithm based on long reads and contig classification

(2019) Junwei Luo et al.   BMC BIOINFORMATICS

Honeysuckle-encoded microRNA2911 inhibits Enterovirus 71 replication via targeting VP1 gene

(2018) Xihan Li et al.   ANTIVIRAL RESEARCH

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

Extreme haplotype variation in the desiccation-tolerant clubmoss Selaginella lepidophylla

(2018) Robert VanBuren et al.   Nature Communications

Trends in herbgenomics

(2018) Tianyi Xin et al.   Science China-Life Sciences

Transcriptome Sequencing and Biochemical Analysis of Perianths and Coronas Reveal Flower Color Formation in Narcissus pseudonarcissus

(2018) Xi Li et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The Chrysanthemum nankingense Genome Provides Insights into the Evolution and Diversification of Chrysanthemum Flowers and Medicinal Traits

(2018) Chi Song et al.   Molecular Plant

Database Resources of the BIG Data Center in 2019

(2018) et al.   NUCLEIC ACIDS RESEARCH

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

Reconstructing the genome of the most recent common ancestor of flowering plants

(2017) Florent Murat et al.   NATURE GENETICS

The evolutionary significance of polyploidy

(2017) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

(2017) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

De Novo Assembly of a NewSolanum pennelliiAccession Using Nanopore Sequencing

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

Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce

(2017) Sebastian Reyes-Chin-Wo et al.   Nature Communications

GSA: Genome Sequence Archive *

(2017) Yanqing Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

The Quest for Golden Bananas: Investigating Carotenoid Regulation in a Fe’i Group Musa Cultivar

(2016) Stephen Buah et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

De novo transcriptome assembly and characterization of nine tissues of Lonicera japonica to identify potential candidate genes involved in chlorogenic acid, luteolosides, and secoiridoid biosynthesis pathways

(2016) Amit Rai et al.   Journal of Natural Medicines

The potato carotenoid cleavage dioxygenase 4 catalyzes a single cleavage of β-ionone ring-containing carotenes and non-epoxidated xanthophylls

(2015) Mark Bruno et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

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

(2015) Bao Zhang et al.   NEW PHYTOLOGIST

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Honeysuckle-encoded atypical microRNA2911 directly targets influenza A viruses

(2014) Zhen Zhou et al.   CELL RESEARCH

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

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

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

(2014) F. Denoeud et al.   SCIENCE

Functional characterisation of three members of the Vitis vinifera L. carotenoid cleavage dioxygenase gene family

(2013) Justin G Lashbrooke et al.   BMC PLANT BIOLOGY

A novel carotenoid cleavage activity involved in the biosynthesis of Citrus fruit-specific apocarotenoid pigments

(2013) María J. Rodrigo et al.   JOURNAL OF EXPERIMENTAL BOTANY

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura 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

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

Transcriptome Analysis of Buds and Leaves Using 454 Pyrosequencing to Discover Genes Associated with the Biosynthesis of Active Ingredients in Lonicera japonica Thunb.

(2013) Liu He et al.   PLoS One

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

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

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

The Path from  -Carotene to Carlactone, a Strigolactone-Like Plant Hormone

(2012) A. Alder et al.   SCIENCE

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

Lonicera japonica Thunb.: Ethnopharmacology, phytochemistry and pharmacology of an important traditional Chinese medicine

(2011) Xiaofei Shang et al.   JOURNAL OF ETHNOPHARMACOLOGY

Carotenoids and their cleavage products: Biosynthesis and functions

(2011) Michael H. Walter et al.   NATURAL PRODUCT REPORTS

The Metabolic and Developmental Roles of Carotenoid Cleavage Dioxygenase4 from Potato

(2010) R. Campbell et al.   PLANT PHYSIOLOGY

Cloning and functional characterization of carotenoid cleavage dioxygenase 4 genes

(2009) Fong-Chin Huang et al.   JOURNAL OF EXPERIMENTAL BOTANY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Functional Characterization of FaCCD1: A Carotenoid Cleavage Dioxygenase from Strawberry Involved in Lutein Degradation during Fruit Ripening

(2008) Carmen García-Limones et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Biosynthesis of plant pigments: anthocyanins, betalains and carotenoids

(2008) Yoshikazu Tanaka et al.   PLANT JOURNAL

RNA Interference-Mediated Repression of MtCCD1 in Mycorrhizal Roots of Medicago truncatula Causes Accumulation of C27 Apocarotenoids, Shedding Light on the Functional Role of CCD1

(2008) D. S. Floss et al.   PLANT PHYSIOLOGY