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Genome-Wide Medicago truncatula Small RNA Analysis Revealed Novel MicroRNAs and Isoforms Differentially Regulated in Roots and Nodules^[W]

^a Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, F-91198 Gif-sur-Yvette Cedex, France
^b Université Paris Diderot-Paris 7, 75205 Paris Cedex 13, France
^c Laboratoire des Interactions Plantes Micro-organismes, Unité Mixte de Recherche, Centre National de la Recherche Scientifique–Institut National de la Recherche Agronomique 2594/441, F- 31320 Castanet Tolosan, France
^d Plateforme Bioinformatique du Génopole Toulouse Midi-Pyrénées, Groupement d'Intérêt Scientifique Toulouse Genopole, F-31320 Castanet Tolosan, France

³ Address correspondence to crespi{at}isv.cnrs-gif.fr.

Posttranscriptional regulation of a variety of mRNAs by small 21- to 24-nucleotide RNAs, notably the microRNAs (miRNAs), is emerging as a novel developmental mechanism. In legumes like the model Medicago truncatula, roots are able to develop a de novo meristem through the symbiotic interaction with nitrogen-fixing rhizobia. We used deep sequencing of small RNAs from root apexes and nodules of M. truncatula to identify 100 novel candidate miRNAs encoded by 265 hairpin precursors. New atypical precursor classes producing only specific 21- and 24-nucleotide small RNAs were found. Statistical analysis on sequencing reads abundance revealed specific miRNA isoforms in a same family showing contrasting expression patterns between nodules and root apexes. The differentially expressed conserved and nonconserved miRNAs may target a large variety of mRNAs. In root nodules, which show diverse cell types ranging from a persistent meristem to a fully differentiated central region, we discovered miRNAs spatially enriched in nodule meristematic tissues, vascular bundles, and bacterial infection zones using in situ hybridization. Spatial regulation of miRNAs may determine specialization of regulatory RNA networks in plant differentiation processes, such as root nodule formation.

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