Release note (April, 2022)

Version 2 of Cucurbit Genomics Database (CuGenDBv2; http://cucurbitgenomics.org/v2) includes the latest versions of 34 cucurbit genome assemblies from more than 20 different cucurbit species/subspecies. The list of these genome assemblies is provided here.

Protein-coding genes of the 34 cucurbit genomes have been functionally annotated.

Pathways have been predicted for each of the 34 cucurbit genomes.

Synteny blocks have been identified between and within all 34 cucurbit genomes.

The "Expression" module has been redesigned and reimplemented. RNA-Seq raw reads have been downloaded from NCBI SRA and processed to derive gene expression values for each gene of the 34 genome assemblies in the database. Here is an example: cucumber Chinese Long gene CsaV3_4G023380

A "Genotype" module has been newly developed. The module provides a suite of functions to extract/download variants from large-scale genome resequencing and genotyping-by-sequencing projects, to visualize variant patterns in different populations, and to provide genome sequences flanking the variant for marker development. Here are examples: 1) SNPs within the watermelon gene Cla97C04G070940; 2) Flanking sequences and allele patterns of SNP Cla97Chr04_15442987; 3) Alleles of SNP Cla97Chr04_15442987 in individual accessions.