DISCOVERY AND DIFFERENTIAL EXPRESSION OF ARTICHOKE microRNAs IN RESPONSE TO SALT STRESS

MicroRNAs (miRNAs) are small noncoding endogenous RNAs playing a regulatory role bynegatively affecting gene expression at the post-transcriptional level. miRNAs vary in lengthbetween 16 and 35 nucleotides with a mode of 22-nt, and are produced from longer hairpin-likeprecursor transcripts. Functional studies have demonstrated that miRNAs are involved in variousdevelopmental and physiological processes, and recent reports indicate their association with bioticand abiotic stress responses in plants.High-throughput sequencing technology has allowed the identification and profiling ofseveral conserved and non-conserved miRNAs. Additionally, deep sequencing provides quantitativeexpression information, since frequency of an individual miRNA generally reflects its relativeabundance in the sample. This strategy has been successfully applied to both model and non-modelplants.In the present study, small RNA (sRNA) libraries were generated separately from roots andleaves of globe artichoke, obtained from plants subjected or not to saline treatment. Libraries weresequenced using Illumina technology, and results were analysed by bioinformatics tools.The majority of sRNAs were 18-28 nt long with 21 nt and 24 nt sRNA as major peaks in thelength distribution graph. To identify conserved miRNAs in globe artichoke, all sRNA sequenceswere Blastn searched against the currently known miRNAs contained in miRbase(http://www.mirbase.org/). Only perfectly matched sequences were considered as putativeconserved miRNAs: this analysis highlighted the presence of at least 29 different miRNA familiesin artichoke.Comparison to artichoke EST database was performed to find potential miRNA targets andprecursors, and to predict hairpin structure. Subsequently, miRNAs were validated using a PCRapproach.Differential expression of miRNA between tissues (leaves and roots) and untreated and salt-treated samples was analysed after sample normalization (count per million).In conclusion we have characterized the sRNA transcriptome in artichoke, in different tissues,in the presence or absence of salt stress, using deep sequencing strategy by Illumina platform.