Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis

• Published in: Nucleic acids research 2002, Vol.30 (24), p.5579-5592
• Main Authors: Journet, Etienne-Pascal, van Tuinen, Diederik, Gouzy, Jerome, Crespeau, Hervé, Carreau, V., Farmer, M.J., Niebel, A., Schiex, Thomas, Jaillon, Olivier, Chatagnier, Odile, Godiard, Laurence, Micheli, Fabienne, Kahn, Daniel, Gianinazzi-Pearson, Vivienne, Gamas, Pascal
• Format: Article
• Language: English
• Subjects: Biochemistry; Biochemistry, Molecular Biology; Life Sciences
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkf685

We report on a large-scale expressed sequence tag(EST) sequencing and analysis program aimed atcharacterizing the sets of genes expressed in rootsof the model legumeMedicago truncatuladuringinteractions with either of two microsymbionts,the nitrogen-Æxing bacteriumSinorhizobium melilotior the arbuscular mycorrhizal fungusGlomusintraradices.We have designed speciÆc tools forinsilicoanalysis of EST data, in relation to chimericcDNA detection, EST clustering, encoded proteinprediction, and detection of differential expression.Our 21 473 5¢- and 3¢-ESTs could be grouped into6359 EST clusters, corresponding to distinct virtualgenes, along with 52 498 otherM.truncatulaESTsavailable in the dbEST (NCBI) database that wererecruited in the process. These clusters were manu-ally annotated, using a speciÆcally developed anno-tation interface. Analysis of EST cluster distributionin variousM.truncatulacDNA libraries, supportedby a reÆnedRtest to evaluate statistical signiÆ-cance and by `electronic northern' representation,enabled us to identify a large number of novelgenes predicted to be up- or down-regulated duringeither symbiotic root interaction. Thesein silicoanalyses provide a Ærst global view of the geneticprograms for root symbioses inM.truncatula.Asearchable database has been built and can beaccessed through a public interfaceWe report on a large-scale expressed sequence tag(EST) sequencing and analysis program aimed atcharacterizing the sets of genes expressed in rootsof the model legumeMedicago truncatuladuringinteractions with either of two microsymbionts,the nitrogen-Æxing bacteriumSinorhizobium melilotior the arbuscular mycorrhizal fungusGlomusintraradices.We have designed speciÆc tools forinsilicoanalysis of EST data, in relation to chimericcDNA detection, EST clustering, encoded proteinprediction, and detection of differential expression.Our 21 473 5¢- and 3¢-ESTs could be grouped into6359 EST clusters, corresponding to distinct virtualgenes, along with 52 498 otherM.truncatulaESTsavailable in the dbEST (NCBI) database that wererecruited in the process. These clusters were manu-ally annotated, using a speciÆcally developed anno-tation interface. Analysis of EST cluster distributionin variousM.truncatulacDNA libraries, supportedby a reÆnedRtest to evaluate statistical signiÆ-cance and by `electronic northern' representation,enabled us to identify a large number of novelgenes predicted to be up- or down-regulated duringeither symbiotic root interaction. Th