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Brassicaceae Database. The Brassicaceae Database (BRAD) was previously a searchable Database of Brassiceae genomic data hosted on the website " http://brassicadb.org". For the policy and safety reasons, we moved it to the new website " http://brassicadb.cn ".
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BRAD CuGenDB Sol Genomics Network Radish Genome Database...
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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).
- Brassica database
- 2011
- 2021
Nov 10, 2021 · The Brassicaceae Database (BRAD version 3.0, BRAD V3.0; http://brassicadb.cn) has evolved from the former Brassica Database (BRAD V2.0), and represents an important community portal hosting genome information for multiple Brassica and related Brassicaceae plant species.
Nov 20, 2015 · The Brassica database (BRAD) was built initially to assist users apply Brassica rapa and Arabidopsis thaliana genomic data efficiently to their research. However, many Brassicaceae genomes have been sequenced and released after its construction.
- Xiaobo Wang, Jian Wu, Jianli Liang, Feng Cheng, Xiaowu Wang
- 2015
- Introduction
- D V2.0: Feature Updates
- Genome Synteny Resource Guidelines
- Discussion and Conclusions
- Funding
Brassicaceae is a large eudicot family that includes the model plant Arabidopsis thaliana . The Brassicaceae family has a remarkable diversity of species, genetics and morphotypes, as well as scientific and economic importance. Brassicaceae species have become model systems for studies of polyploidy and evolution ( 1 ). The important genus Brassica...
Overview of BRAD V2.0
In BRAD V1.0, datasets of genome and gene sequences, gene annotations, non-coding RNAs, transposable elements, genetic markers and linkage maps of B. rapa were provided ( 15 , 16 ). A navigation dialog-window for every gene of B. rapa and A. thaliana was provided to help users obtain all related information. Furthermore, BLAST and GBrowse tools ( 16) were embedded in BRAD for sequence alignment and for visualizing genomic elements, respectively. BRAD V1.0 has now been updated to V2.0 to inclu...
Technical details
All genomic data were processed using the tool SynOrths tool ( 15 ) to generate genome and gene level synteny datasets. Then, syntenic figures were generated based on these synteny datasets and stored in a MySQL ( 18) database. Genome sequences, gene models and the processed datasets, including all syntenic genes, gene annotation information and specific gene families were all imported into MySQL, which enables multifaceted browsing and searching in BRAD. Furthermore, a standalone BLAST ( 19)...
BRAD stocks: Brassicaceae genomes
Statistics of the Brassicaceae genomic data, including genome sequences, predicted gene models, protein-coding gene sequences and protein sequences are shown in Table 1 . In total, about 4 Gb of data have been collected in BRAD V2.0. In addition to the original genome sequences and gene models, seven types of annotation for the predicted genes have been generated. The annotations have been sourced from the Swiss-Prot, TrEMBL ( 20 ), KEGG (Kyoto Encyclopedia of Genes and Genomes) ( 21 ), Inter...
Mining syntenic genes
BRAD V2.0 has five main sections: Browse, Search, Tools, Download and Links. Placing the cursor over the Search section activates a drop-down menu. Clicking on the ‘Syntenic gene’ option ( Figure 1 A) opens the search syntenic genes page where checkboxes for 11 Brassicaceae species ( B. napus contains the Brassica A and C subgenomes) allow users to choose their required searches; a syntenic gene search between A. thaliana and B. rapa is set as the default ( Figure 1 B). Next, users are requir...
Visualization of synteny analysis
A new ‘Syntenic figure’ function is available under the Search section in BRAD V2.0, which can be used to better illustrate the genomic synteny relationship between two Brassicaceae species. This function can be used to plot genomic synteny relationships as two-dimensional figures. One of the four ancestral species ( A. thaliana , A. lyrata , C. rubella and S. parvula ) can be selected for display on the y axis and one of eight other Brassicaceae species can be selected for display on the x a...
Syntenic blocks analysis for multiple genome resources
The GBrowse_syn ( 16 ) tool for visualizing synteny or collinear genomic regions among multiple genomes can be accessed from the Tools section of BRAD 2.0. GBrowse_syn uses species name and genomic position consisting of the chromosome label, and start and stop positions as input. For example, if ‘c01:601,285..801,285’ is input in the Landmark search box and A. lyrata is selected as the target species from the Genome to Search drop-down list, then the genomic region from 601 285 bp to 801 285...
Many Brassica databases have been built to better understand and use the genomic datasets from Brassica species. These databases include the Brassica Database BRAD ( http://brassicadb.org ), Brassica.info ( http://www.brassica.info/ ), BrassEnsembl ( http://www.brassica.info/BrassEnsembl/index.html ), BrassicaDB ( http://brassica.nbi.ac.uk/Brassica...
973 program (2012CB113900 and no. 2013CB127000), the 863 program (2012AA100101), the National Natural Science Foundation of China (grant no. 31301771) and the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences. Research was carried out in the Key Laboratory of Biology and Genetic Improvement of Horticultural C...
- Xiaobo Wang, Jian Wu, Jianli Liang, Feng Cheng, Xiaowu Wang
- 2015
Jan 7, 2022 · The Brassicaceae Database (BRAD version 3.0, BRAD V3.0; http://brassicadb.cn) has evolved from the former Brassica Database (BRAD V2.0), and represents an important community portal hosting genome information for multiple Brassica and related Brassicaceae plant species.
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What is Brad database?
Oct 13, 2011 · 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).
