Identification of conserved microRNAs and their targets in Cichorium intybus and Cichorium endivia

MicroRNAs (miRNAs) are a class of short and endogenously initiated non-coding RNAs that post-transcriptionally control gene expression via either translational repression or mRNA degradation. Mature miRNAs are reported to be highly conserved throughout the plant kingdom; therefore, comparative genomics approaches are used to predict the novel miRNA genes and their target genes. In this study, bioinformatics and laboratory approaches followed by the EST and miRNA sequences in the databases for chicory species were employed for the identification of potential miRNAs and their potential targets either in Cichorium intybus or Cichorium endivia. To identify the potential miRNAs in the C. intybus and C. endivia, all the publicly available EST sequences of the plant were blasted against the previously known Plant miRNAs. Ultimately, four novel miRNAs belonging to four different families of miR166, miR156, miR162 and miR393 were identified. Also, a large number of genes, such as TIR1, Squamusa promoter binding proteins genes were identified as target genes of these miRNAs. Furthermore, the results of Real Time PCR showed that the transcriptional activities of miR156 in the leaf tissue of C. endivia are extremely high, not only than those observed for flower tissue of the same species, but also as compared with the leaf and flower tissues of the another species of C. intybus.