The miRNAome of globe artichoke: conserved and novel micro RNAs and target analysis

Domenico De Paola,Federica Cattonaro,Domenico Pignone,Gabriella Sonnante

doi:10.1186/1471-2164-13-41

Abstract

BackgroundPlant microRNAs (miRNAs) are involved in post-transcriptional regulatory mechanisms of several processes, including the response to biotic and abiotic stress, often contributing to the adaptive response of the plant to adverse conditions. In addition to conserved miRNAs, found in a wide range of plant species a number of novel species-specific miRNAs, displaying lower levels of expression can be found. Due to low abundance, non conserved miRNAs are difficult to identify and isolate using conventional approaches. Conversely, deep-sequencing of small RNA (sRNA) libraries can detect even poorly expressed miRNAs.No miRNAs from globe artichoke have been described to date. We analyzed the miRNAome from artichoke by deep sequencing four sRNA libraries obtained from NaCl stressed and control leaves and roots.ResultsConserved and novel miRNAs were discovered using accepted criteria. The expression level of selected miRNAs was monitored by quantitative real-time PCR. Targets were predicted and validated for their cleavage site. A total of 122 artichoke miRNAs were identified, 98 (25 families) of which were conserved with other plant species, and 24 were novel. Some miRNAs were differentially expressed according to tissue or condition, magnitude of variation after salt stress being more pronounced in roots. Target function was predicted by comparison to Arabidopsis proteins; the 43 targets (23 for novel miRNAs) identified included transcription factors and other genes, most of which involved in the response to various stresses. An unusual cleaved transcript was detected for miR393 target, transport inhibitor response 1.ConclusionsThe miRNAome from artichoke, including novel miRNAs, was unveiled, providing useful information on the expression in different organs and conditions. New target genes were identified. We suggest that the generation of secondary short-interfering RNAs from miR393 target can be a general rule in the plant kingdom.

Highlights

Plant microRNAs are involved in post-transcriptional regulatory mechanisms of several processes, including the response to biotic and abiotic stress, often contributing to the adaptive response of the plant to adverse conditions
Artichoke small RNA (sRNA) population To discover the artichoke miRNAome and the possible involvement of miRNAs in the response to saline stress, four sRNA libraries were generated from leaves and roots of young artichoke plants subjected or not to NaCl treatment
Results of quantitative real-time PCR (qPCR) evidenced that a total of 11 and 17 miRNAs were significantly up or down regulated in artichoke leaves or roots, respectively

Summary

Introduction

Plant microRNAs (miRNAs) are involved in post-transcriptional regulatory mechanisms of several processes, including the response to biotic and abiotic stress, often contributing to the adaptive response of the plant to adverse conditions. Deep-sequencing of small RNA (sRNA) libraries can detect even poorly expressed miRNAs. No miRNAs from globe artichoke have been described to date. We analyzed the miRNAome from artichoke by deep sequencing four sRNA libraries obtained from NaCl stressed and control leaves and roots. MicroRNAs (miRNAs) are a class of small RNAs (sRNAs), generally 21-24 nucleotide in length, involved in post-transcriptional regulatory mechanisms of several processes, including the response to biotic and abiotic stress [1,2]. After incorporation into AGO1 protein complex, plant mature miRNAs target mRNAs, which are cleaved by AGO1 at a specific position, opposite to the 10th and 11th nucleotides of the miRNA [3]

Methods

Results

Discussion

Conclusion