Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops

Abstract

The Cucurbitaceae family (cucurbit) includes several economically important crops, such as melon, cucumber, watermelon, pumpkin, squash and gourds. During the past several years, genomic and genetic data have been rapidly accumulated for cucurbits. To store, mine, analyze, integrate and disseminate these large-scale datasets and to provide a central portal for the cucurbit research and breeding community, we have developed the Cucurbit Genomics Database (CuGenDB; http://cucurbitgenomics.org) using the Tripal toolkit. The database currently contains all available genome and expressed sequence tag (EST) sequences, genetic maps, and transcriptome profiles for cucurbit species, as well as sequence annotations, biochemical pathways and comparative genomic analysis results such as synteny blocks and homologous gene pairs between different cucurbit species. A set of analysis and visualization tools and user-friendly query interfaces have been implemented in the database to facilitate the usage of these large-scale data by the community. In particular, two new tools have been developed in the database, a ‘SyntenyViewer’ to view genome synteny between different cucurbit species and an ‘RNA-Seq’ module to analyze and visualize gene expression profiles. Both tools have been packed as Tripal extension modules that can be adopted in other genomics databases developed using the Tripal system.

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

“…Watermelon is among the first cucurbit crops to have its genome sequenced, assembled and annotated (Zheng et al, 2019). Genome sequence of the East Asian watermelon cultivar, '97103', was released in 2013 (Guo et al, 2013).…”

“…Raw genome and transcriptome sequencing reads have been deposited into the NCBI sequence read archive (SRA) under accessions SRP183199 and SRP183523, respectively. The genome sequence of 'Charleston Gray' and the GBS SNPs are also available at the Cucurbit Genomics Database (http://cucurb itgenomics.org; Zheng et al, 2019).…”

New genetic sources for orange color in cucumber (Cucumis sativus L.) fruit flesh

“…During the trimming process, reads were also trimmed to a uniform 50 bp length. The Gy14 v2 transcriptome was obtained from CuGenDB (Zheng et al , 2019). Forward sequencing reads from each pool were separately mapped to the Gy14 transcriptome using Bowtie 2.3 (Langmead and Salzberg, 2012).…”

A fast, simple, high efficient and one-step generation of composite cucumber plants with transgenic roots by Agrobacterium rhizogenes-mediated transformation

“…Over the past decade, genomics sequencing of cucumber has been completed (Huang et al 2009). Furthermore, root-specific transcriptome, proteome, EST (expressed sequence tags), large scale cDNA sequencing studies, GWAS (genome-wide association studies) in cucumber have been completed and conducted (Du et al 2010;Li et al 2012;Ma et al 2018;Qi et al 2012;Wang et al 2018;Xu et al 2017;Yuan et al 2016;Zheng et al 2019). Efficient transformation methods are the prerequisite for the functional annotations of such numbers of candidate genes and assist the development and improvement of elite cucumber cultivars.…”