Comparative analysis of plant regulatory genomes
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- Master's theses (KBM) 
With the availability of a large number of plant genomes comes the task of gaining insights from them through comparative studies. One important feature in the evolution of all organisms is changes to the genomic cis-regulatory elements (CREs), usually found in non-coding genomic regions. With several genomes available, comparative studies of CREs can provide insights about the evolution of CREs. In this project a method is developed that seeks to identify key CREs across different taxa and thus providing a platform for investigating cis-regulatory divergence. Genomic data from 25 different plant species is used. Annotations providing extensive coverage of CREs are rare, so a computational approach based on sequence motifs is used to predict CREs in regions upstream of the coding genes. Important CREs are identified as being conserved in significantly many gene families within a specified clade. The findings are compared with results from gene expression data and functional annotations from select model organisms. The method identified some conserved high prevalence CREs that were already known to have deep evolutionary roots. When divergence in important CREs were investigated between two important plant groups, no consistent pattern emerged. Although the gene expression and functional enrichment analyses provided interesting insights in themselves, they could not support the hypothesis that conserved high prevalence CREs is a good measure for motif importance.