Transcriptomics

Dataset Information

302

The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome


ABSTRACT: Plants show a remarkable plasticity to adapt their root architecture to biotic and abiotic constraints of the soil environment. Although some of these modifications are fine-tuned by miRNAs, there are still shadow zones in these regulations. In the model legume Medicago truncatula, we analyzed the small RNA (smRNA) transcriptome of roots submitted to symbiotic and pathogenic interactions. Mapping on the genome and prediction of pre-miRNA hairpins allowed the identification of 416 candidates. Out of them, we found known and novel variants of 77 miRNA families, already reported in miRBase. In addition, thanks stringent criteria of miRNA prediction, 53 mtr-miRNAs were discovered, including 27 putative miRtrons. Exploring polymorphism in 26 M. truncatula ecotypes, higher polymorphism was observed in conserved rather than legume-specific miRNA genes. An average of 19 targets, mainly involved in environmental responses and signaling, was predicted per novel miRNA. In addition, taking advantage of our large number of smRNA libraries, we identified sets of miRNAs responsive to root pathogens or to symbiotic interactions and the related Nod and myc-LCO signals. 23 libraries of small RNA (smRNA) of roots submitted to symbiotic and pathogenic interactions.

ORGANISM(S): Medicago truncatula  

SUBMITTER: Florian Frugier   Patrick Wincker  Andreas Niebel  Martin Crespi  Christine Lelandais-Brière  Laurent Gentzbittel  Erika Sallet  Caroline Hartmann  Damien Formey  Cécile Ben  Jérôme Gouzy  Christophe Roux  Pilar Bustos-Sanmamed  Jean P Combier 

PROVIDER: E-GEOD-49226 | ArrayExpress | 2014-08-15

SECONDARY ACCESSION(S): SRP028249GSE49226PRJNA213313

REPOSITORIES: GEO, ArrayExpress, ENA

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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 computati  ...[more]

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