DATABASES and other information resources

Overview

A range of databases exist which manage information relating to Brassica genetics, genomics and related activities. There remains achallenge to extend the scope of nomenclature standards, management of 'registries' of widely used resources and information, and development of tools for integrating and navigating between disparate datasets.

Genome browsers

• WebApollo (B. rapa at Australian BioCommons
• Brassica Pan-Genomes from the Edwards Lab (GBrowse and downloads)
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• B. rapa Chiifu-401 (v1.0)
• B. napus Darmor (v1)
• B. oleracea TO1000 (v1)
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• B.napus Darmor
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• B. rapa Chiifu-401 v3.0 (Jbrowse)
• BrGDB - Brassica rapa Genome DB (part of PlantGDB, data from BRAD)
• BolBase B. oleracea (GBrowse)

Genetics and trait databases

• Brassica Information Portal at Earlham Institute, UK: a web repository for population and trait scoring information related to the Brassica breeding community. It provides information about quantitative trait loci and links curated Brassica phenotype experimental data with genotype information stored in external data sources. Advanced data submission capabilities and APIs enable users to store and publish their own study results.

Other links and portals

• CropSNPdb - variants from genotyping arrays, with Brassica genomes
• York Oilseed Rape Knowledgebase
• Brassica Genome site (brassicagenome.net from the Edwards' lab)
• Brassica TED) (Transposable Element Database
• Brassibase: a developing online-accessible knowledge and database system of cross-referenced information and resources on Brassicaceae (Cruciferae) taxonomy, systematics and evolution, including chromosome numbers, traits and characters, germplasm resources, and accurate enumeration of all species, genera and tribes.
• Brassica Genome Gateway
• COGE: Comparative Genomics resource
• UK Oilseed RapE Genetic Improvement Network (OREGIN)
• UK Brassica Research Community (UK-BRC)
• BrassicaDB was funded until 2003 by BBSRC under the UK-CropNet programme. It aimed to curate a comprehensive set of sequence accessions, bibliography, and a range of genetic maps, markers etc. In addition, this database is currently the original source of information for the 'BBSRC set' of Brassica SSR markers. Martin Trick at JIC ensures that the database is still automatically refreshed with newly deposited Brassica sequences every night and is occasionally rebuilt from scratch. There is also a useful Brassica BLAST server associated with this database.
• BrGDB - Brassica rapa Genome DB (part of PlantGDB)
• GnpIS: Genetic & Genomic Information System (URGI)
• IMSORB genetic marker and QTL database
• NASC Arabidopsis Ensembl with Brassica tracks
• UK BBSRC Physical Mapping DB
• TransPLANT: trans-National Infrastructure for Plant Genomic Science (EU-FP7)

Physical maps

Several projects have generated fingerprint and hybridisation data relating to long cloned sequences of Brassica, mostly in BAC libraries. Databases that manage these data include:

• Brassica IGF project (UK) fingerprint and hybridisation of B. rapa and B. oleracea libraries
• Korean Sequencing project B. rapa BAC fingerprinting database
  
• MBrGSP BAC registry: This database holds information about the status of BACs that were being sequenced within the original Brassica rapa Genome Sequencing Project, with the data published via this website.