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 59 and 39 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.

Multiple mutualist effects on genomewide expression in the tripartite association between Medicago truncatula, nitrogen‐fixing bacteria and mycorrhizal fungi

“…; Boscari et al . ). For example, mycorrhizal fungi induce genes that function in building cell walls, metabolism and transport (Hohnjec et al .…”

An integrated analysis of plant and bacterial gene expression in symbiotic root nodules using laser‐capture microdissection coupled to RNA sequencing

“…Analyses of nodules harvested at various times after inoculation, or blocked at an early stage of bacteroid differentiation, made it possible to distinguish the Sinorhizobium meliloti bacteroid transcriptome at early and late differentiation stages (Capela et al, 2006). The coordinated regulation of numerous M. truncatula genes has also been shown, with successive waves depending notably on bacterial infection and bacteroid differentiation (El Yahyaoui et al, 2004;Mitra et al, 2004;Lohar et al, 2006;Van de Velde et al, 2006;Godiard et al, 2007;Benedito et al, 2008;Maunoury et al, 2010;Moreau et al, 2011;Boscari et al, 2013). As an example of genes revealed thanks to transcriptomic analyses, members of the large family of plant genes encoding small cysteine-rich proteins (NCRs) (Fedorova et al, 2002;Mergaert et al, 2003;Graham et al, 2004) were shown to play essential roles during bacteroid differentiation in indeterminate nodules but not in Lotus japonicus or soybean determinate-type nodules (Colebatch et al, 2002(Colebatch et al, , 2004Kouchi et al, 2004;Hogslund et al, 2009;Libault et al, 2010;Severin et al, 2010).…”

An RNA Sequencing Transcriptome Analysis Reveals Novel Insights into Molecular Aspects of the Nitrate Impact on the Nodule Activity of Medicago truncatula

“…In addition to a precise and extensive covering of the expression of known genes, this method can potentially provide information on possibly regulated RNA which produced unmapped reads or the importance of alternative splicing events. RNA-seq has already been successfully applied to M. truncatula tissue including nodules (Boscari et al, 2013).…”