A comparative approarch to genome annotation in Tribolium

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This project entails the in silico identification of the genes and the dsRNA templates for the RNAi screen of Tribolium castaneum as well as bioinformatics method development for gene-finding. The genome annotation of T. castaneum will be further improved in order to obtain a high success rate for high throughput template generation and of RNAi knockdowns for the remaining roughly 6850 not-yetscreened genes that are harder to correctly predict, because highly expressed and easier to predict genes have been targeted in the first phase of iBeetle already. Likely to be correct fragments of mRNAs will be identified in this project and delivered to the company Eupheria for filtering for regions with high content of efficient siRNAs and minimal off-target effects, for primer design and physical dsRNA template generation. To increase confidence in - and therefore the success rate of - the reported mRNA fragments, a new method for comparative gene finding to supplement expression evidence will be developed and applied to four Tribolium species' genomes that are currently sequenced and assembled in the Brown lab (Kansas State University). The goals of method development will go beyond Tribolium-specific applications and target other genome-dense eukaryotic clades, like vertebrates, too. The new gene prediction tool that will be designed and implemented in this project will identify all genes in all species simultaneously. The iBeetle Gr-Sta1 page 3 of 5 interdependency between the gene structures of different species will be introduced via a graph structure that is based on a multiple genome alignment and a phylogenetic tree in which the nodes are candidate exons