title: The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome.
abstract: BACKGROUND
  Legume roots show a remarkable plasticity to adapt their architecture to biotic and abiotic constraints, including symbiotic interactions. However, global analysis of miRNA regulation in roots is limited, and a global view of the evolution of miRNA-mediated diversification in different ecotypes is lacking.
  
  
  RESULTS
  In the model legume Medicago truncatula, we analyze the small RNA transcriptome of roots submitted to symbiotic and pathogenic interactions. Genome mapping and a computational pipeline identify 416 miRNA candidates, including known and novel variants of 78 miRNA families present in miRBase. Stringent criteria of pre-miRNA prediction yield 52 new mtr-miRNAs, including 27 miRtrons. Analyzing miRNA precursor polymorphisms in 26 M. truncatula ecotypes identifies higher sequence polymorphism in conserved rather than Medicago-specific miRNA precursors. An average of 19 targets, mainly involved in environmental responses and signalling, is predicted per novel miRNA. We identify miRNAs responsive to bacterial and fungal pathogens or symbionts as well as their related Nod and Myc-LCO symbiotic signals. Network analyses reveal modules of new and conserved co-expressed miRNAs that regulate distinct sets of targets, highlighting potential miRNA-regulated biological pathways relevant to pathogenic and symbiotic interactions.
  
  
  CONCLUSIONS
  We identify 52 novel genuine miRNAs and large plasticity of the root miRNAome in response to the environment, and also in response to purified Myc/Nod signaling molecules. The new miRNAs identified and their sequence variation across M. truncatula ecotypes may be crucial to understand the adaptation of root growth to the soil environment, notably in the agriculturally important legume crops.
authors.forename: Damien
authors.initials: D
authors.lastname: Formey
authors.forename: Erika
authors.initials: E
authors.lastname: Sallet
authors.forename: Christine
authors.initials: C
authors.lastname: Lelandais-Brière
authors.forename: Cécile
authors.initials: C
authors.lastname: Ben
authors.forename: Pilar
authors.initials: P
authors.lastname: Bustos-Sanmamed
authors.forename: Andreas
authors.initials: A
authors.lastname: Niebel
authors.forename: Florian
authors.initials: F
authors.lastname: Frugier
authors.forename: Jean Philippe
authors.initials: JP
authors.lastname: Combier
authors.forename: Frédéric
authors.initials: F
authors.lastname: Debellé
authors.forename: Caroline
authors.initials: C
authors.lastname: Hartmann
authors.forename: Julie
authors.initials: J
authors.lastname: Poulain
authors.forename: Frédérick
authors.initials: F
authors.lastname: Gavory
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
authors.forename: Christophe
authors.initials: C
authors.lastname: Roux
authors.forename: Laurent
authors.initials: L
authors.lastname: Gentzbittel
authors.forename: Jérôme
authors.initials: J
authors.lastname: Gouzy
authors.forename: Martin
authors.initials: M
authors.lastname: Crespi
mesh_terms: D017124:Conserved Sequence; D018506:Gene Expression Regulation, Plant; D059647:Gene-Environment Interaction; D017343:Genes, Plant; D046913:Medicago truncatula / Q000235:genetics* / Q000378:metabolism; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D018517:Plant Roots / Q000235:genetics* / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D018749:RNA, Plant / Q000235:genetics* / Q000378:metabolism; D015398:Signal Transduction; D013312:Stress, Physiological; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant