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BIOINFORMATICS

The Arabidopsis Root Transcriptome by Serial Analysis of Gene Expression. Gene Identification Using the Genome Sequence¹

Biochimie et Physiologie Moléculaire des Plantes, Unité Mixte de Recherche 5004, Agro-M/Centre National de la Recherche Scientifique/Institut National de la Recherche Agronomique/UM2, Place Viala, 34060 Montpellier cedex 1, France (C.F., S.M., C.C., P.N., J.B., F.G., P.D., H.S., A.G.); Institut de Génétique Humaine, Centre National de la Recherche Scientifique Unité Propre de Recherche 1142, University of Montpellier II, Place Eugène Bataillon, 34095 Montpellier cedex 5, France (D.P., T.C., J.M.); and Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Centre National de la Recherche Scientifique/Institut de Recherche en Développement/University of Perpignan, 52 Av de Villeneuve, 66860 Perpignan cedex, France (V.D., R.C.)

Large-scale identification of genes expressed in roots of the model plant Arabidopsis was performed by serial analysis of gene expression (SAGE), on a total of 144,083 sequenced tags, representing at least 15,964 different mRNAs. For tag to gene assignment, we developed a computational approach based on 26,620 genes annotated from the complete sequence of the genome. The procedure selected warrants the identification of the genes corresponding to the majority of the tags found experimentally, with a high level of reliability, and provides a reference database for SAGE studies in Arabidopsis. This new resource allowed us to characterize the expression of more than 3,000 genes, for which there is no expressed sequence tag (EST) or cDNA in the databases. Moreover, 85% of the tags were specific for one gene. To illustrate this advantage of SAGE for functional genomics, we show that our data allow an unambiguous analysis of most of the individual genes belonging to 12 different ion transporter multigene families. These results indicate that, compared with EST-based tag to gene assignment, the use of the annotated genome sequence greatly improves gene identification in SAGE studies. However, more than 6,000 different tags remained with no gene match, suggesting that a significant proportion of transcripts present in the roots originate from yet unknown or wrongly annotated genes. The root transcriptome characterized in this study markedly differs from those obtained in other organs, and provides a unique resource for investigating the functional specificities of the root system. As an example of the use of SAGE for transcript profiling in Arabidopsis, we report here the identification of 270 genes differentially expressed between roots of plants grown either with NO₃^- or NH₄NO₃ as N source.

¹ The work was supported by Génoplante (project nos. Af 1999 064 and Bi 1999 065) and by the Montpellier LR Génopole.

² These authors contributed equally to this work.

³ Present address: Unité de Génétique et d'Amélioration des Fruits et Légumes, UR 1052 Institut National de la Recherche Agronomique, Domaine St Maurice, BP 94, 84 143 Montfavet cedex, France.

^* Corresponding author; e-mail gojon{at}ensam.inra.fr; fax 33–4–67–52–57–37.

Received July 18, 2003; returned for revision September 7, 2003; accepted October 22, 2003.

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