The genome and transcriptome analysis of snake gourd provide insights into its evolution and fruit development and ripening

An Improved Melon Reference Genome With Single-Molecule Sequencing Uncovers a Recent Burst of Transposable Elements With Potential Impact on Genes

(2020) Raúl Castanera et al.   Frontiers in Plant Science

Phylotranscriptomics in Cucurbitaceae Reveal Multiple Whole Genome Duplications and Key Morphological and Molecular Innovations

(2020) Jing Guo et al.   Molecular Plant

The genome of Cucurbita argyrosperma (silver-seed gourd) reveals faster rates of protein-coding gene and long noncoding RNA turnover and neofunctionalization within Cucurbita

(2019) Josué Barrera-Redondo et al.   Molecular Plant

A Comparison of sun, ovate, fs8.1 and Auxin Application on Tomato Fruit Shape and Gene Expression

(2019) Yanping Wang et al.   PLANT AND CELL PHYSIOLOGY

Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection

(2019) Shan Wu et al.   PLANT BIOTECHNOLOGY JOURNAL

A chromosome-scale genome assembly of cucumber (Cucumis sativus L.)

(2019) Qing Li et al.   GigaScience

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits

(2019) Shaogui Guo et al.   NATURE GENETICS

The wax gourd genomes offer insights into the genetic diversity and ancestral cucurbit karyotype

(2019) Dasen Xie et al.   Nature Communications

Long‐read sequencing and de novo assembly of the Luffa cylindrica (L.) Roem. genome

(2019) Tao Zhang et al.   Molecular Ecology Resources

Transcriptome analysis of genes related to fruit texture in watermelon

(2019) Ye Gao et al.   SCIENTIA HORTICULTURAE

Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi

(2018) Jens Keilwagen et al.   BMC BIOINFORMATICS

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

(2018) Arthur Zwaenepoel et al.   BIOINFORMATICS

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

(2018) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

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

(2017) Sergey Koren et al.   GENOME RESEARCH

An Overlooked Paleotetraploidization in Cucurbitaceae

(2017) Jinpeng Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Karyotype Stability and Unbiased Fractionation in the Paleo-Allotetraploid Cucurbita Genomes

(2017) Honghe Sun et al.   Molecular Plant

De novo assembly of the zucchini genome reveals a whole-genome duplication associated with the origin of the Cucurbita genus

(2017) Javier Montero-Pau et al.   PLANT BIOTECHNOLOGY JOURNAL

The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ring-spot virus resistance locus

(2017) Shan Wu et al.   PLANT JOURNAL

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Identification of protein coding regions in RNA transcripts

(2015) Shiyuyun Tang et al.   NUCLEIC ACIDS RESEARCH

Comparative Transcriptome Analysis of Cultivated and Wild Watermelon during Fruit Development

(2015) Shaogui Guo et al.   PLoS One

Identification of differentially expressed genes related to aphid resistance in cucumber (Cucumis sativus L.)

(2015) Danna Liang et al.   Scientific Reports

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Exploring new dating approaches for parasites: The worldwide Apodanthaceae (Cucurbitales) as an example

(2014) Sidonie Bellot et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

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

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

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

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

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity

(2013) Jianjian Qi et al.   NATURE GENETICS

Transcriptome analyses of early cucumber fruit growth identifies distinct gene modules associated with phases of development

(2012) Kaori Ando et al.   BMC GENOMICS

Carotenoid Accumulation and Carotenogenic Gene Expression during Fruit Development in Novel Interspecific Inbred Squash Lines and Their Parents

(2012) Korakot Nakkanong et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

(2012) Shaogui Guo 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

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Chromosome rearrangements during domestication of cucumber as revealed by high-density genetic mapping and draft genome assembly

(2012) Luming Yang et al.   PLANT JOURNAL

The genome of melon (Cucumis melo L.)

(2012) J. Garcia-Mas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phyto-Constituents And Anti-Oxidant Activity Of The Pulp Of Snake Tomato (Trichosanthes cucumerina L.)

(2011) OC Adebooye   African Journal of Traditional Complementary and Alternative Medicines

RNA-Seq improves annotation of protein-coding genes in the cucumber genome

(2011) Zhen Li et al.   BMC GENOMICS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The UniProt-GO Annotation database in 2011

(2011) E. C. Dimmer et al.   NUCLEIC ACIDS RESEARCH

ATG2, an autophagy-related protein, negatively affects powdery mildew resistance and mildew-induced cell death in Arabidopsis

(2011) Yiping Wang et al.   PLANT JOURNAL

The Genome Sequence of the North-European Cucumber (Cucumis sativus L.) Unravels Evolutionary Adaptation Mechanisms in Plants

(2011) Rafał Wóycicki et al.   PLoS One

Cloning, functional characterization, and co-expression studies of a novel aquaporin (FaPIP2;1) of strawberry fruit

(2010) Karina Alleva et al.   JOURNAL OF EXPERIMENTAL BOTANY

CDD: a Conserved Domain Database for the functional annotation of proteins

(2010) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

The plant ADH gene family

(2010) Judith Strommer   PLANT JOURNAL

The Autophagic Degradation of Chloroplasts via Rubisco-Containing Bodies Is Specifically Linked to Leaf Carbon Status But Not Nitrogen Status in Arabidopsis

(2010) M. Izumi et al.   PLANT PHYSIOLOGY

Autophagy is required for tolerance of drought and salt stress in plants

(2009) Yimo Liu et al.   Autophagy

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.)

(2009) Albert Mascarell-Creus et al.   BMC GENOMICS

Hepatoprotective effect of Trichosanthes cucumerina Var cucumerina L. on carbon tetrachloride induced liver damage in rats

(2009) S. Sathesh Kumar et al.   JOURNAL OF ETHNOPHARMACOLOGY

The genome of the cucumber, Cucumis sativus L.

(2009) Sanwen Huang et al.   NATURE GENETICS

The evolutionary significance of ancient genome duplications

(2009) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

Gene expression in developing watermelon fruit

(2008) W Patrick Wechter et al.   BMC GENOMICS

Autophagy regulated by day length determines the number of fertile florets in wheat

(2008) Hernán O. Ghiglione et al.   PLANT JOURNAL

Gourds afloat: a dated phylogeny reveals an Asian origin of the gourd family (Cucurbitaceae) and numerous oversea dispersal events

(2008) H. Schaefer et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2008) Brian J Haas et al.   GENOME BIOLOGY