CuGenDB (Cucurbit Genomic Database) specializes in genomic and genetic data of cucurbit crops. It’s a platform for researchers to access and analyze crop info – genomes, markers, gene annotations. CuGenDB accelerates cucurbit genomics research and breeding via a central repository of data and tools for the scientific community.
As of January 2023, CuGenDB launched CuGenDBv2, its latest version. CuGenDBv2 houses 34 reference genomes of 27 cucurbit species/subspecies across 10 genera. Noteworthy is the improved annotation of protein-coding genes by comparing them with public protein and domain databases.
Different tools have been added and updated. The ‘Genotype‘ module allows researchers to efficiently explore annotated variome data from multiple genome sequencing projects, including SNPs and indels. Moreover, the genotype function provides a search functionality to search genetic variants in the VCFs, a topic previously covered in this blog. An updated ‘Expression‘ module provides an all-encompassing gene expression atlas tailored for cucurbits, deepening our grasp of their intricate molecular dynamics. Furthermore, CuGenDBv2’s standout feature is its ability to illustrate synteny blocks, within and across the 34 genomes. This leads to a staggering 595 pair-wise genome comparisons accessible in the database. The launch of CuGenDBv2 signifies a substantial leap in cucurbit genomics, amplifying its potential for discovery and insights.
You can find more detailed information in its original paper: Jingyin Yu et al., 2023.
Yu, J., Wu, S., Sun, H., Wang, X., Tang, X., Guo, S., … & Fei, Z. (2023). CuGenDBv2: an updated database for cucurbit genomics. Nucleic acids research, 51(D1), D1457-D1464.
