BRAD V3.0: an upgraded Brassicaceae database. Issue Volume 50:Issue D1(2022) (10th November 2021)

• Record Type: Journal Article
• Authors: Chen, Haixu; Wang, Tianpeng; He, Xiaoning; Cai, Xu; Lin, Runmao; Liang, Jianli; Wu, Jian; King, Graham; Wang, Xiaowu
• Is Part Of: Nucleic acids research. Volume 50:Issue D1(2022)
• Page Start: D1432
• Page End: D1441
• Publication Date: 2021-11-10
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkab1057
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: 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. Since the last update in 2015, the complex genomes of numerous Brassicaceae species have been decoded, accompanied by many omics datasets. To provide an up-to-date service, we report here a major upgrade of the portal. The Model-View-ViewModel (MVVM) framework of BRAD has been re-engineered to enable easy and sustainable maintenance of the database. The collection of genomes has been increased to 26 species, along with optimization of the user interface. Features of the previous version have been retained, with additional new tools for exploring syntenic genes, gene expression and variation data. In the 'Syntenic Gene @ Subgenome' module, we added features to view the sequence alignment and phylogenetic relationships of syntenic genes. New modules include 'MicroSynteny' for viewing synteny of selected fragment pairs, and 'Polymorph' for retrieval of variation data. The updated BRAD provides a substantial expansion of genomic data and a comprehensive improvement of the service available to the Brassicaceae research community.