In silico determination of abiotic and biotic stress related miRNAs in ornamental plants

Micro RNAs are small non-coding RNAs, regulating gene expression at post-transcriptional or post-translational levels. Ornamental plants hold an important status within the horticultural industry of the world. In addition to their aesthetic value in landscape architecture, they are also medicinally and economically important plants. The aim of this thesis was computational characterisation of abiotic and biotic stress-related novel miRNA sequences in ornamental plants including Petunia hybrida, Castanea sativa, Yucca filamentosa, Opuntia streptacantha, Cichorium intybus, Cynara cardunculus, Asparagus officinalis and Ginkgo biloba. In silico identification of new miRNAs based on BLAST searches of the EST database of these plants was performed by using stringent criteria. The secondary structures of pre-miRNAs were determined by using RNAfold Web Server. Evolutionary relationships between novel miRNAs and reference miRNAs were investigated via Clustal Omega and MEGAX. GO and KEGG analyses were also performed to identify the roles of potential target genes by BLAST2GO. Nine novel miRNAs belonging to five miRNA families in eight ornamental plants consisting of Petunia hybrida (phy-miR168 and phy-miR399), Castanea sativa (csa-miR169), Yucca filamentosa (yfi-miR169), Opuntia streptacantha (osa-miR169), Cichorium intybus (cin-miR169), Cynara cardunculus (cca-miR169), Asparagus officinalis (aof-miR2930) and Ginkgo biloba (gbi-miR10982) were identified for the first time. Phylogenetic analyses showed that there are very similar sequences between novel miRNAs and reference miRNAs. Enrichment analysis of GO with biological processes, cellular component and molecular functions revealed that potential target genes were involved in response to stress, oxidation-reduction process, cellular metabolic process, protein binding, etc. Moreover, KEGG results also indicated that these genes play important roles in twenty-six different metabolic pathways such as steroid biosynthesis, purine metabolism, carotenoid biosynthesis, etc. This thesis is the first detailed investigation about the determination of different miRNA families and their targets in genomes of ornamental plants. Obtaining results are expected to contribute for production of stress resistance ornamental plants with different colour and scent.