Please note that we have stopped the regular imports of Gene Expression Omnibus (GEO) data into ArrayExpress. This may not be the latest version of this experiment.

E-GEOD-49226 - The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome

Status
Released on 15 August 2014, last updated on 10 December 2014
Organism
Medicago truncatula
Samples (23)
Protocols (4)
Description
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.
Experiment type
RNA-seq of non coding RNA 
Contacts
Andreas Niebel, Caroline Hartmann, Christine Lelandais-Brière, Christophe Roux, Cécile Ben, Damien Formey, Erika Sallet, Florian Frugier, Jean P Combier, Jérôme Gouzy, Laurent Gentzbittel, Martin Crespi, Patrick Wincker, Pilar Bustos-Sanmamed
Citation
The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome. Formey D, Sallet E, Lelandais-Bri�re C, Ben C, Bustos-Sanmamed P, Niebel A, Frugier F, Combier J, Debell� F, Hartmann C, Poulain J, Gavory F, Wincker P, Roux C, Gentzbittel L, Gouzy J, Crespi M. , PMID:25248950
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-49226.idf.txt
Sample and data relationshipE-GEOD-49226.sdrf.txt
Additional data (1)E-GEOD-49226.additional.1.zip
Links