BRAD, the genetics and genomics database for Brassica plants

Abstract

Background: Brassica species include both vegetable and oilseed crops, which are very important to the daily life of common human beings. Meanwhile, the Brassica species represent an excellent system for studying numerous aspects of plant biology, specifically for the analysis of genome evolution following polyploidy, so it is also very important for scientific research. Now, the genome of Brassica rapa has already been assembled, it is the time to do deep mining of the genome data.

Description: BRAD, the Brassica database, is a web-based resource focusing on genome scale genetic and genomic data for important Brassica crops. BRAD was built based on the first whole genome sequence and on further data analysis of the Brassica A genome species, Brassica rapa (Chiifu-401-42). It provides datasets, such as the complete genome sequence of B. rapa, which was de novo assembled from Illumina GA II short reads and from BAC clone sequences, predicted genes and associated annotations, non coding RNAs, transposable elements (TE), B. rapa genes' orthologous to those in A. thaliana, as well as genetic markers and linkage maps. BRAD offers useful searching and data mining tools, including search across annotation datasets, search for syntenic or non-syntenic orthologs, and to search the flanking regions of a certain target, as well as the tools of BLAST and Gbrowse. BRAD allows users to enter almost any kind of information, such as a B. rapa or A. thaliana gene ID, physical position or genetic marker.

Conclusion: BRAD, a new database which focuses on the genetics and genomics of the Brassica plants has been developed, it aims at helping scientists and breeders to fully and efficiently use the information of genome data of Brassica plants. BRAD will be continuously updated and can be accessed through http://brassicadb.org.

Figure 1

Navigating BRAD. There are four major sections: Browse, Search, Tools, and Resources (Download and Links). Moving the cursor over tabs will activate the pull-down menus, which will lead users directly to the specific pages in BRAD.

Figure 2

Syntenic gene searching between A. thaliana and B. rapa's three subgenomes. Taking the A. thaliana gene AT4G23980 as an example, search results are presented in a table. The first column lists the A. thaliana gene IDs, followed by genomic blocks in the ancestral karyotype. Tandem genes are packed, and only the first gene of the tandem array is listed (AT4G23990) while the others can be obtained by clicking 'tandem'. The next three columns show genes from the subgenomes, LF, MF1 and MF2 of B. rapa. For each row, listed genes are in syntenic relationships. Moving the cursor over an A. thaliana gene gives a floating box containing the gene's annotation, while moving the cursor over a B. rapa gene produces the supporting information of its syntenic relationship to the gene in A. thaliana.

Figure 3

Genome sequence view in Gbrowse of a region in chromosome A02 of B. rapa. The tracks shown in the detailed section are gene models from the 1.01 genome version of B. rapa (B. rapa Genome Sequencing Project) and indicate mRNA, CDS, genetic marker, TEprotein, Transposon, miRNA, tRNA, snRNA, rRNA and SSR. For the gene model track, a click on a gene provides a contextual menu with relevant links to the gene's annotations and to its best hit gene (BLASTX) in A. thaliana accompanied by its annotation text. For other tracks, a click on a feature leads users to its detailed annotation and sequence information.