The European Plant Genome Database Network (PLANET)

The PLANET Consortium aims to develop a high level plant genome database for the systematic exploration of Arabidopsis and other plants. The work is funded by and EC grant QLR1-Ct-2001-00006, and ends on 31.06.05. The project is coordinated by Hans-Werner Mewes from GSF in Munich and includes partners from VIB Gent, Genoplant- EVRY, NASC, PRI Wageningen, CSIC Madrid and JIC.

At the JIC Sean Walsh in the Computation Biology Group has established the AtIDB database as part of JIC's contribution to this project (www.atidb.org).

The AtIDB database combines the results obtained from DNA tagging programmes in Arabidopsis at the John Innes Centre, UK, the Sainsbury Laboratory, UK, the Cold Spring Harbor Laboratory, USA, the Salk Institute Genomic Analysis Laboratory, USA, the GABI-Kat, Germany, the FST/FLAGDB, France, the Institute of Molecular and Cell Biology, Singapore, and the Huck Institute for Life Sciences, USA and integrates these directly with TIGR V5 Arabidopsis genome annotations.

Gene expression patterns resulting from systematic screening of Ds-GT insertion lines from the EC EXOTIC project are also included in AtIDB. These are described by tissue ontologies and representative images.

The position and sequence of Affymetrix array elements and CATMA primer sequences are shown and related to current gene models in order to help users plan and report gene expression experiments. To help initiate comparative genomics work we mapped end-sequenced Brassica BACs and EST sequences to v5 sequence using BLAST mapping, in collaboration with Dr Martin Trick at the JIC. The JAtY complementing BAC resource from Garnet (the UK Arabidopsis functional genomics project) are also displayed using BLAST mapping.

Affymetrix array data from Arabidopsis is probably the most rapidly expanding set of data, and several sophisticated meta- analysis databases have been set up. Genevestigator is an excellent example (https://www.genevestigator.ethz.ch/ ) . A remaining set of objectives is to link AtIDB gene models with summaries of gene expression data from Genevestigator and to incorporate whole genome tiling array gene expression data into AtiDB. This will give users an integrated source of gene expression data linked to gene models and insertional mutant data.

BioMOBY services for a variety of data sets in AtIDB have been developed to make gene reports. These include gene information and protein structural predictions.

Publications

M. Bevan and S. Walsh. (2004). Positioning Arabidopsis in plant biology: A key step towards unification of plant research. Plant Physiology 135, 602- 606.

Pan X., Liu H., Clarke J., Jones J., Bevan M., Stein L. (2003) ATIDB: Arabidopsis thaliana insertion database. Nucleic Acids Research 31, 1245-1251.