The chromosome-level genome of dragon fruit reveals whole-genome duplication and chromosomal co-localization of betacyanin biosynthetic genes

Proteogenomic analysis of pitaya reveals cold stress-related molecular signature

(2020) Junliang Zhou et al.   PeerJ

Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?

(2020) Mitsutaka Kadota et al.   GigaScience

Transcriptomic Analysis Reveals Cu/Zn SODs Acting as Hub Genes of SODs in Hylocereus undatus Induced by Trypsin during Storage

(2020) Xinyue Pang et al.   Antioxidants

Transcriptomic analysis of flower induction for long-day pitaya by supplementary lighting in short-day winter season

(2020) Rui Xiong et al.   BMC GENOMICS

Genomes of the Venus Flytrap and Close Relatives Unveil the Roots of Plant Carnivory

(2020) Gergo Palfalvi et al.   CURRENT BIOLOGY

Comparative Transcriptome Analysis Combining SMRT- and Illumina-Based RNA-Seq Identifies Potential Candidate Genes Involved in Betalain Biosynthesis in Pitaya Fruit

(2020) Yawei Wu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Zygnema circumcarinatum UTEX 1559 chloroplast and mitochondrial genomes provide insight into land plant evolution

(2020) Lauren M Orton et al.   JOURNAL OF EXPERIMENTAL BOTANY

A high-quality reference genome of wild Cannabis sativa

(2020) Shan Gao et al.   Horticulture Research

The genome of jojoba (Simmondsia chinensis): A taxonomically isolated species that directs wax ester accumulation in its seeds

(2020) Drew Sturtevant et al.   Science Advances

Insights Into Chloroplast Genome Evolution Across Opuntioideae (Cactaceae) Reveals Robust Yet Sometimes Conflicting Phylogenetic Topologies

(2020) Matias Köhler et al.   Frontiers in Plant Science

Transcriptomic de novo analysis of pitaya (Hylocereus polyrhizus) canker disease caused by Neoscytalidium dimidiatum

(2019) Min Xu et al.   BMC GENOMICS

RNA-Seq De Novo Assembly of Red Pitaya (Hylocereus polyrhizus) Roots and Differential Transcriptome Analysis in Response to Salt Stress

(2019) Quandong Nong et al.   Tropical Plant Biology

Transcriptome Analysis Clarified Genes Involved in Betalain Biosynthesis in the Fruit of Red Pitayas (Hylocereus costaricensis)

(2019) Xingyuan Xi et al.   MOLECULES

Identification and functional characterization of three new terpene synthase genes involved in chemical defense and abiotic stresses in Santalum album

(2019) Xinhua Zhang et al.   BMC PLANT BIOLOGY

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

The evolution of betalain biosynthesis in Caryophyllales

(2019) Alfonso Timoneda et al.   NEW PHYTOLOGIST

Time of day and network reprogramming during drought induced CAM photosynthesis in Sedum album

(2019) Ching Man Wai et al.   PLoS Genetics

Evolution of l ‐ DOPA 4,5‐dioxygenase activity allows for recurrent specialisation to betalain pigmentation in Caryophyllales

(2019) Hester Sheehan et al.   NEW PHYTOLOGIST

De novo assembly of a wild pear ( Pyrus betuleafolia ) genome

(2019) Xingguang Dong et al.   PLANT BIOTECHNOLOGY JOURNAL

Cell Wall Enzymes in Zygnema circumcarinatum UTEX 1559 Respond to Osmotic Stress in a Plant-Like Fashion

(2019) Elisabeth Fitzek et al.   Frontiers in Plant Science

Primary Metabolism in Citrus Fruit as Affected by Its Unique Structure

(2019) Avi Sadka et al.   Frontiers in Plant Science

A High-Quality Reference Genome Assembly of the Saltwater Crocodile, Crocodylus porosus, Reveals Patterns of Selection in Crocodylidae

(2019) Arnab Ghosh et al.   Genome Biology and Evolution

Deciphering drought-induced metabolic responses and regulation in developing maize kernels

(2018) Liming Yang et al.   PLANT BIOTECHNOLOGY JOURNAL

Sugar metabolism and accumulation in the fruit of transgenic apple trees with decreased sorbitol synthesis

(2018) Mingjun Li et al.   Horticulture Research

wgd—simple command line tools for the analysis of ancient whole-genome duplications

(2018) Arthur Zwaenepoel et al.   BIOINFORMATICS

Phylogenetic Relationships and Evolutionary Trends in the Cactus Family

(2018) Pablo C Guerrero et al.   JOURNAL OF HEREDITY

Evolution of Portulacineae Marked by Gene Tree Conflict and Gene Family Expansion Associated with Adaptation to Harsh Environments

(2018) Ning Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

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

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

The Tartary Buckwheat Genome Provides Insights into Rutin Biosynthesis and Abiotic Stress Tolerance

(2017) Lijun Zhang et al.   Molecular Plant

The genome of Chenopodium quinoa

(2017) David E. Jarvis et al.   NATURE

Improved maize reference genome with single-molecule technologies

(2017) Yinping Jiao et al.   NATURE

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

(2017) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

Abscisic acid-regulated protein degradation causes osmotic stress-induced accumulation of branched-chain amino acids in Arabidopsis thaliana

(2017) Tengfang Huang et al.   PLANTA

Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti

(2017) Dario Copetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism

(2017) Xiaohan Yang et al.   Nature Communications

Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions

(2017) Chenxi Xu et al.   Nature Communications

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Why do plants produce so many terpenoid compounds?

(2016) Eran Pichersky et al.   NEW PHYTOLOGIST

Pigment identification and antioxidant properties of red dragon fruit (Hylocereus polyrhizus)

(2016) P S Rebecca O et al.   AFRICAN JOURNAL OF BIOTECHNOLOGY

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The pineapple genome and the evolution of CAM photosynthesis

(2015) Ray Ming et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity

(2015) Susana Magallón et al.   NEW PHYTOLOGIST

Lineage-specific gene radiations underlie the evolution of novel betalain pigmentation in Caryophyllales

(2015) Samuel F. Brockington et al.   NEW PHYTOLOGIST

Metabolic Profiling of Developing Pear Fruits Reveals Dynamic Variation in Primary and Secondary Metabolites, Including Plant Hormones

(2015) Akira Oikawa et al.   PLoS One

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Profiling sugar metabolism during fruit development in a peach progeny with different fructose-to-glucose ratios

(2014) Elsa Desnoues et al.   BMC PLANT BIOLOGY

General mechanisms of drought response and their application in drought resistance improvement in plants

(2014) Yujie Fang et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Metabolite Profiling of Red and White Pitayas (Hylocereus polyrhizus and Hylocereus undatus) for Comparing Betalain Biosynthesis and Antioxidant Activity

(2014) Dong Ho Suh et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

The genome sequence of the orchid Phalaenopsis equestris

(2014) Jing Cai et al.   NATURE GENETICS

Beyond aridification: multiple explanations for the elevated diversification of cacti in the New World Succulent Biome

(2014) Tania Hernández-Hernández et al.   NEW PHYTOLOGIST

Infernal 1.1: 100-fold faster RNA homology searches

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

Genomic analysis in three Hylocereus species and their progeny: evidence for introgressive hybridization and gene flow

(2013) Aroldo Cisneros et al.   EUPHYTICA

Identification of differentially-expressed genes potentially implicated in drought response in pitaya (Hylocereus undatus) by suppression subtractive hybridization and cDNA microarray analysis

(2013) Qing-Jie Fan et al.   GENE

The Physiological Importance of Glucosinolates on Plant Response to Abiotic Stress in Brassica

(2013) María del Carmen Martínez-Ballesta et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

(2013) Juliane C. Dohm et al.   NATURE

The sacred lotus genome provides insights into the evolution of flowering plants

(2013) Yun Wang et al.   PLANT JOURNAL

Effects of abiotic stress on plants: a systems biology perspective

(2012) Grant R Cramer et al.   BMC PLANT BIOLOGY

Reference genome sequence of the model plant Setaria

(2012) Jeffrey L Bennetzen et al.   NATURE BIOTECHNOLOGY

The beet R locus encodes a new cytochrome P450 required for red betalain production

(2012) Gregory J Hatlestad et al.   NATURE GENETICS

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

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

Molecular phylogeny of Gymnocalycium (Cactaceae): Assessment of alternative infrageneric systems, a new subgenus, and trends in the evolution of the genus

(2011) Pablo H. Demaio et al.   AMERICAN JOURNAL OF BOTANY

Accumulation of trehalose increases soluble sugar contents in rice plants conferring tolerance to drought and salt stress

(2011) Mark C. F. R. Redillas et al.   Plant Biotechnology Reports

Contemporaneous and recent radiations of the world's major succulent plant lineages

(2011) M. Arakaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phenotypic and genomic characterization of vine cactus collection (Cactaceae)

(2010) N. Tel-Zur et al.   GENETIC RESOURCES AND CROP EVOLUTION

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Oligosaccharides of pitaya (dragon fruit) flesh and their prebiotic properties

(2009) S. Wichienchot et al.   FOOD CHEMISTRY

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE