title: Expression dynamics of the Medicago truncatula transcriptome during the symbiotic interaction with Sinorhizobium meliloti: which role for nitric oxide?
abstract: Medicago truncatula is one of the most studied model plants. Nevertheless, the genome of this legume remains incompletely determined. We used RNA-Seq to characterize the transcriptome during the early organogenesis of the nodule and during its functioning. We detected 37,333 expressed transcription units; to our knowledge, 1,670 had never been described before and were functionally annotated. We identified 7,595 new transcribed regions, mostly corresponding to 5' and 3' untranslated region extensions and new exons associated with 5,264 previously annotated genes. We also inferred 23,165 putative transcript isoforms from 6,587 genes and measured the abundance of transcripts for each isoform, which suggests an important role for alternative splicing in the generation of proteome diversity in M. truncatula. Finally, we carried out a differential expression analysis, which provided a comprehensive view of transcriptional reprogramming during nodulation. In particular, depletion of nitric oxide in roots inoculated with Sinorhizobium meliloti greatly increased our understanding of the role of this reactive species in the optimal establishment of the symbiotic interaction, revealing differential patterns of expression for 2,030 genes and pointing to the inhibition of the expression of defense genes.
authors.affiliation: Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1355, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7254, and Université de Nice-Sophia Antipolis, Unité Mixte de Recherche Institut Sophia Agrobiotech, 06903 Sophia Antipolis, France.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Boscari
authors.forename: Jennifer
authors.initials: J
authors.lastname: Del Giudice
authors.forename: Alberto
authors.initials: A
authors.lastname: Ferrarini
authors.forename: Luca
authors.initials: L
authors.lastname: Venturini
authors.forename: Anne-Lise
authors.initials: AL
authors.lastname: Zaffini
authors.forename: Massimo
authors.initials: M
authors.lastname: Delledonne
authors.forename: Alain
authors.initials: A
authors.lastname: Puppo
mesh_terms: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D017398:Alternative Splicing; D005091:Exons; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D059014:High-Throughput Nucleotide Sequencing; D007438:Introns; D046913:Medicago truncatula / Q000235:genetics / Q000378:metabolism / Q000382:microbiology*; D058977:Molecular Sequence Annotation; D009569:Nitric Oxide / Q000378:metabolism*; D055170:Plant Root Nodulation; D018517:Plant Roots / Q000378:metabolism / Q000382:microbiology; D018749:RNA, Plant / Q000235:genetics; D016962:Sinorhizobium meliloti / Q000254:growth & development*; D013559:Symbiosis; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D018749:RNA, Plant; D014157:Transcription Factors; D009569:Nitric Oxide