Artichoke microRNAs involved in the response to biotic stresses

Plant response to environmental stresses and pathogen attacks involves several biological processes that require fine and precise regulation at transcriptional and post-transcriptional levels. MicroRNAs (miRNAs) are small RNAs (sRNAs) widely diffused in animals and plants and implicated in post-transcriptional regulation of gene transcripts. Identification of differentially expressed miRNAs, following infection, may provide an insight into the processes involved in signalling and defence of plants against pathogens. In order to characterize artichoke miRNAs differentially expressed during fungus or virus infection, we sequenced five sRNA libraries obtained from artichoke using Illumina technology. Libraries were obtained from leaves and roots of control plants, and from plants infected with Tomato spotted wilt virus (TSWV), or Verticillium dahliae. After removing low quality reads and adapter sequences, all artichoke libraries were annotated according to small noncoding RNAs contained in Rfam, and all previously known plant miRNAs extracted from the miRNA Registry Database (miRBase Release 18). Change in miRNA read counts between infected and non infected artichoke tissues was recorded and used to select putative infection-responsive miRNAs. Differential expression of miRNAs was validated by quantitative real-time PCR (qPCR). Artichoke miRNA precursors were identified and their fold-back structure was predicted using Mfold program. Artichoke miRNA target genes were also identified and characterized according to the homologous Arabidopsis proteins. In conclusion, miRNAs involved in the response to virus or fungus infection were detected and validated in artichoke plant tissues.