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Open Access Research article

CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes

Gert Sclep1102, Joke Allemeersch113, Robin Liechti4, Björn De Meyer12, Jim Beynon5, Rishikesh Bhalerao6, Yves Moreau3, Wilfried Nietfeld7, Jean-Pierre Renou8, Philippe Reymond9, Martin TR Kuiper12* and Pierre Hilson12

Author Affiliations

1 Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium

2 Department of Molecular Genetics, Ghent University, 9052 Ghent, Belgium

3 ESAT/SISTA, K.U.Leuven, Kasteelpark Arenberg 10, 3001 Heverlee, Belgium

4 Swiss Institute of Bioinformatics, Genopode building, 1015 Lausanne, Switzerland

5 Department of Plant Genetics & Biology, HRI, University of Warwick, Warwick, CV35 9EF, UK

6 Department of Forest Genetics and Plant Physiology, SLU, SE-901 83 Umeå, Sweden

7 Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany

8 Unité de Recherche en Génomique Végétale, INRA, 91057 Evry cedex, France

9 Department of Plant Molecular Biology, Biophore Building, University of Lausanne, 1015 Lausanne, Switzerland

10 Genomics Platform, Parco Tecnologico Padano, Via Einstein, 26900 Lodi, Italy

11 Microarray facility, VIB, Gasthuisberg Onderwijs en Navorsing 1, Herestraat 49, 3000 Leuven, Belgium

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BMC Bioinformatics 2007, 8:400  doi:10.1186/1471-2105-8-400

Published: 18 October 2007

Abstract

Background

The Complete Arabidopsis Transcript MicroArray (CATMA) initiative combines the efforts of laboratories in eight European countries [1] to deliver gene-specific sequence tags (GSTs) for the Arabidopsis research community. The CATMA initiative offers the power and flexibility to regularly update the GST collection according to evolving knowledge about the gene repertoire. These GST amplicons can easily be reamplified and shared, subsets can be picked at will to print dedicated arrays, and the GSTs can be cloned and used for other functional studies. This ongoing initiative has already produced approximately 24,000 GSTs that have been made publicly available for spotted microarray printing and RNA interference.

Results

GSTs from the CATMA version 2 repertoire (CATMAv2, created in 2002) were mapped onto the gene models from two independent Arabidopsis nuclear genome annotation efforts, TIGR5 and PSB-EuGène, to consolidate a list of genes that were targeted by previously designed CATMA tags. A total of 9,027 gene models were not tagged by any amplified CATMAv2 GST, and 2,533 amplified GSTs were no longer predicted to tag an updated gene model. To validate the efficacy of GST mapping criteria and design rules, the predicted and experimentally observed hybridization characteristics associated to GST features were correlated in transcript profiling datasets obtained with the CATMAv2 microarray, confirming the reliability of this platform. To complete the CATMA repertoire, all 9,027 gene models for which no GST had yet been designed were processed with an adjusted version of the Specific Primer and Amplicon Design Software (SPADS). A total of 5,756 novel GSTs were designed and amplified by PCR from genomic DNA. Together with the pre-existing GST collection, this new addition constitutes the CATMAv3 repertoire. It comprises 30,343 unique amplified sequences that tag 24,202 and 23,009 protein-encoding nuclear gene models in the TAIR6 and EuGène genome annotations, respectively. To cover the remaining untagged genes, we identified 543 additional GSTs using less stringent design criteria and designed 990 sequence tags matching multiple members of gene families (Gene Family Tags or GFTs) to cover any remaining untagged genes. These latter 1,533 features constitute the CATMAv4 addition.

Conclusion

To update the CATMA GST repertoire, we designed 7,289 additional sequence tags, bringing the total number of tagged TAIR6-annotated Arabidopsis nuclear protein-coding genes to 26,173. This resource is used both for the production of spotted microarrays and the large-scale cloning of hairpin RNA silencing vectors. All information about the resulting updated CATMA repertoire is available through the CATMA database http://www.catma.org.