Abstract
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. These genomes are rich resources for comparative genomics, gene annotation and functional evolutionary studies of Brassica crops. Therefore, we have updated BRAD to version 2.0 (V2.0). In BRAD V2.0, 11 more Brassicaceae genomes have been integrated into the database, namely those of Arabidopsis lyrata, Aethionema arabicum, Brassica oleracea, Brassica napus, Camelina sativa, Capsella rubella, Leavenworthia alabamica, Sisymbrium irio and three extremophiles Schrenkiella parvula, Thellungiella halophila and Thellungiella salsuginea. BRAD V2.0 provides plots of syntenic genomic fragments between pairs of Brassicaceae species, from the level of chromosomes to genomic blocks. The Generic Synteny Browser (GBrowse_syn), a module of the Genome Browser (GBrowse), is used to show syntenic relationships between multiple genomes. Search functions for retrieving syntenic and non-syntenic orthologs, as well as their annotation and sequences are also provided. Furthermore, genome and annotation information have been imported into GBrowse so that all functional elements can be visualized in one frame. We plan to continually update BRAD by integrating more Brassicaceae genomes into the database.Database URL: http://brassicadb.org/brad/
Highlights
Brassicaceae is a large eudicot family that includes the model plant Arabidopsis thaliana
Brassica database (BRAD) V2.0 provides a comprehensive framework for comparative genomic analysis and studies of the evolution of gene function across Brassicaceae species, especially for the Brassica crops
Genome and gene sequences, gene annotations and syntenic and non-syntenic orthologs between A. thaliana and other Brassicaceae species have been integrated into different sections of BRAD V2.0
Summary
Brassicaceae is a large eudicot family that includes the model plant Arabidopsis thaliana. BRAD V2.0 contains updated datasets and functions that include all syntenic gene pairs between A. thaliana and the other Brassicaceae species, more genome and gene sequences and gene annotations, as well as syntenic figures and genome visualization of all the incorporated Brassicaceae species in the Genome Browser (GBrowse) [14].
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