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| Status |
Public on Aug 15, 2014 |
| Title |
The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome |
| Organism |
Medicago truncatula |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
23 libraries of small RNA (smRNA) of roots submitted to symbiotic and pathogenic interactions.
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| Contributor(s) |
Formey D, Sallet E, Lelandais-Brière C, Ben C, Gentzbittel L, Bustos-Sanmamed P, Roux C, Niebel A, Frugier F, Combier JP, Hartmann C, Wincker P, Gouzy J, Crespi M |
| Citation(s) |
25248950 |
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| Submission date |
Jul 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Erika Sallet |
| E-mail(s) |
Erika.Sallet@toulouse.inra.fr
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| Organization name |
INRA/CNRS
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| Department |
Plant Health and the Environment
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| Lab |
LIPM
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| Street address |
24 Chemin de Borde Rouge, CS 52627
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| City |
Castanet Tolosan |
| ZIP/Postal code |
31326 |
| Country |
France |
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| Platforms (1) |
| GPL17491 |
Illumina HiSeq 2000 (Medicago truncatula) |
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| Samples (23)
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| Relations |
| BioProject |
PRJNA213313 |
| SRA |
SRP028249 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE49226_sMIRMED.nr.annotated.18-25.fa.gz |
1.0 Gb |
(ftp)(http) |
FA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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