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E-GEOD-67432 - Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing [degradome-seq]

Status
Released on 1 September 2015, last updated on 5 September 2015
Organism
Phaseolus vulgaris
Samples (2)
Protocols (2)
Description
Background: MiRNAs and phasiRNAs are negative regulators of gene expression. These small RNAs have been extensively studied in plant model species but only 10 mature microRNAs are present in miRBase version 21 and no phasiRNAs have been identified for the legume model Phaseolus vulgaris. Thanks to the recent availability of the first version of the common bean genome, degradome data and small RNA libraries, we are able to present here a catalog of the microRNAs and phasiRNAs of this organism and, particularly, new protagonists of the symbiotic nodulation events. Results: We identified a set of 185 mature miRNAs, including 121 previously unpublished sequences, encoded by 307 precursors and distributed in 98 families. Degradome data allowed us to identify a total of 181 targets for these miRNAs. We reveal two regulatory networks involving conserved miRNAs, known to play crucial roles in the well-establishment of nodules, and novel miRNAs specific of the common bean suggesting a specific action of these sequences. In parallel, we identified 125 loci that potentially produce phased small RNAs and 47 of them present all the characteristics to be triggered by a total of 31 miRNAs, including 14 new miRNAs identified in this study. Conclusions: We provide here a set of new small RNAs, which contribute to the broader scene of the sRNAome of Phaseolus vulgaris. Thanks to the identification of the miRNA targets from degradome analysis and the construction of regulatory networks between the mature microRNAs, we draw up here the probable functional regulation associated with the sRNAome and particularly in N2-fixing symbiotic nodules. Degradome sequencing from Phaseolus vulgaris seedling
Experiment type
other 
Contacts
Damien Formey <damien.formey@gmail.com>, Ramanjulu Sunkar, Yong-Fang Li
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-67432.idf.txt
Sample and data relationshipE-GEOD-67432.sdrf.txt
Processed data (1)E-GEOD-67432.processed.1.zip
Links