Skip to main content
Article thumbnail
Location of Repository

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

By Gert Sclep, Joke Allemeersch, Robin Liechti, Björn De Meyer, Jim Beynon, Rishikesh P. Bhalerao, Yves Moreau, Wilfried Nietfeld, Jean-Pierre Renou, Philippe Reymond, Martin T.R. Kuiper and Pierre Hilson


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\ud flexibility to regularly update the GST collection according to evolving knowledge about the gene\ud 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.\ud 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,\ud 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\ud 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 proteinencoding\ud 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\ud Tags or GFTs) to cover any remaining untagged genes. These latter 1,533 features constitute the CATMAv4 addition.\ud 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\ud cloning of hairpin RNA silencing vectors. All information about the resulting updated CATMA\ud repertoire is available through the CATMA database

Topics: QR
Publisher: BioMed Central Ltd.
Year: 2007
OAI identifier:

Suggested articles


  1. (1999). A: CAP3: A DNA Sequence Assembly Program. Genome Res doi
  2. (2006). Apweiler R: EMBL Nucleotide Sequence Database: developments in 2005. Nucleic Acids Res doi
  3. (2003). ArrayExpress Public Repository for Microarray Data [http:/ /] 19. Yamada doi
  4. (2003). Aubourg S: Automatic design of gene-specific sequence tags for genome-wide functional studies. Bioinformatics doi
  5. (2003). CATMA – A complete Arabidopsis GST database. Nucleic Acids Res
  6. (2001). EuGène: A eucaryotic gene finder that combines several sources of evidence. doi
  7. (2004). I: Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications. Genome Res
  8. (2003). Kuiper MTR: European consortia building integrated resources for Arabidopsis functional genomics. Curr Opin Plant Biol doi
  9. (1997). Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res doi
  10. (1981). MS: Identification of common molecular subsequences. doi
  11. (2004). Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression. Nucleic Acids Res doi
  12. (2006). Rokhsar D: The genome of black cottonwood, Populus trichocarpa doi
  13. (2000). Skaletsky H: Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol doi
  14. Sussman MR: Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. doi
  15. (2005). The Compendium of Arabidopsis Gene Expression (CAGE) [] 17. Parkinson
  16. (2005). TIGR5 Arabidopsis Nuclear Genome Annotation [ f t p : / /] 9. Haas
  17. (1998). W: A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.