Nucleic Acids Research, 2002, Vol. 30, No. 24 5579-5592
© 2002 Oxford University Press
Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis
Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, CNRS-INRA, 1 Laboratoire de Biométrie et Intelligence Artificielle, INRA, 31326 Castanet-Tolosan Cedex, France, 2 UMR 1088 Biochimie, Biologie Cellulaire et Ecologie des Interactions Plantes-Microorganismes, INRA-Université de Bourgogne, 21065 Dijon, France and 3 Genoscope and CNRS UMR 8030, 91057 Evry Cedex, France
*To whom correspondence should be addressed. Tel: +33 561 285 324; Fax: +33 561 285 061; Email: journet{at}toulouse.inra.fr
We report on a large-scale expressed sequence tag (EST) sequencing and analysis program aimed at characterizing the sets of genes expressed in roots of the model legume Medicago truncatula during interactions with either of two microsymbionts, the nitrogen-fixing bacterium Sinorhizobium meliloti or the arbuscular mycorrhizal fungus Glomus intraradices. We have designed specific tools for in silico analysis of EST data, in relation to chimeric cDNA detection, EST clustering, encoded protein prediction, and detection of differential expression. Our 21 473 5'- and 3'-ESTs could be grouped into 6359 EST clusters, corresponding to distinct virtual genes, along with 52 498 other M.truncatula ESTs available in the dbEST (NCBI) database that were recruited in the process. These clusters were manually annotated, using a specifically developed annotation interface. Analysis of EST cluster distribution in various M.truncatula cDNA libraries, supported by a refined R test to evaluate statistical significance and by ‘electronic northern’ representation, enabled us to identify a large number of novel genes predicted to be up- or down-regulated during either symbiotic root interaction. These in silico analyses provide a first global view of the genetic programs for root symbioses in M.truncatula. A searchable database has been built and can be accessed through a public interface.
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