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

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.Conserved 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.The 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.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]. In plants, miRNAs derive from non-coding transcripts produced from MIR genes, mainly located in intergenic regions. The primary transcripts (pri-miRNA) possess internal stem-loop secondary structures, which form parts of double-stranded RNA (dsRNA) not perfectly complementary to miRNA, contained in one of the two arms of the stem-loop structure. The pri-miRNA is processed into a stem-loop precursor (pre-miRNA), which is cut by the enzyme DCL1