Abstract
BackgroundMiRNAs 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, the most used miRNA database, and no phasiRNAs have been identified for the model legume 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 for this organism and, particularly, we suggest new protagonists in the symbiotic nodulation events.ResultsWe identified a set of 185 mature miRNAs, including 121 previously unpublished sequences, encoded by 307 precursors and distributed in 98 families.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: those known to play crucial roles in the establishment of nodules, and novel miRNAs present only in common bean, suggesting a specific role for these sequences. In addition, we identified 125 loci that potentially produce phased small RNAs, with 47 of them having all the characteristics of being triggered by a total of 31 miRNAs, including 14 new miRNAs identified in this study.ConclusionsWe provide here a set of new small RNAs that contribute to the broader knowledge 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 present here the probable functional regulation associated with the sRNAome and, particularly, in N2-fixing symbiotic nodules.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1639-5) contains supplementary material, which is available to authorized users.
Highlights
MiRNAs and phasiRNAs are negative regulators of gene expression
Overview of the sequencing data In this study, we used four published high-throughput sequencing libraries of small RNAs [29] obtained from flowers, leaves, seedlings and roots of Phaseolus vulgaris and a novel library acquired from symbiotic nodules of the same organism obtained by infection with Rhizobium tropici
An average of 51 and 37 % of reads were matched to the common bean genome, respectively (Table 1), and 8.3 % of the sequences from the nodule library matched with the corresponding bacterial genome (Rhizobium tropici CIAT899, [32])
Summary
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, the most used miRNA database, and no phasiRNAs have been identified for the model legume Phaseolus vulgaris. The miRNAs are small non-coding RNA sequences of ~ 22 nt that negatively regulate gene expression, usually, post-transcriptionally by base-pairing to complementary. Formey et al BMC Genomics (2015) 16:423 transcripts In plants, these small RNAs are processed from longer hairpin-shaped precursors encoded in the genome and almost all of them are transcribed by RNA polymerase II. The miRNA action leads to the loss of function of the gene by inhibiting protein production (see Voinnet [16] for review)
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