MicroRNAs (miRNAs) are a class of non-coding small RNAs (sRNAs) approximately 20-24 nuceotides long. miRNAs play an essential role in regulating plant growth and development by post-transcriptional regulatory mechanisms of several target genes, and act in response to biotic and abiotic stress tuning the adaptive response of the plant to adverse conditions. In recent years an enormous number of sRNAs has been identified using next-generation sequencing technologies, and to date 3362 plant miRNAs belonging to 46 different species have been cataloged and annotated in the miRNA Registry Database (Release 17, April 2011, http://www.mirbase.org/). We analyzed the artichoke miRNAome (the full complement of miRNAs in a genome) using Illumina sequencing technology to detect miRNAs expressed in plants subjected to diverse growth conditions including salt stress, fungi and virus infections. More than 100 known miRNAs were found to be expressed in artichoke, some of which (e.g., cca-miR156a and cca-miR167a) had relatively high expression abundance and exhibited evolutionary conservation across multiple plant species. Evaluation of miRNA expression abundance in plants grown under different stress conditions, compared to control plants showed that a number of miRNAs are significantly differentially expressed as highlighted by a higher or lower abundance in sRNA libraries. In addition to conserved ones, 24 novel miRNAs were identified in artichoke, supported by expression evidences and the analysis of in silico predicted stem-loop structure of precursor sequences. Putative target genes were identified for artichoke miRNAs detected in this study, and function was assessed by comparison with other plants proteins. The small RNA transcriptomes obtained by different artichoke libraries were screened providing evidences that a large number of miRNAs are expressed in this plant. Evaluation of miRNAs differentially expressed among different stress conditions and the identification of the putative target genes are the basis for further investigation of the physiological roles of miRNAs in artichoke.
