Poster abstracts

Poster number 1 submitted by Wei Zhang

Prediction of nad6 in Didymium iridis using the PIE algorithm for finding edited mRNA

Wei Zhang (The Ohio State University), Ralf Bundschuh (The Ohio State University)

Abstract:
Gene prediction in Dydimium iridis is complicated because of frequent shifts in the reading frame due to mRNA editing. Here, we apply our algorithm Predictor of Insertional Editing (PIE) that has previously been tested on the related organism Physarum polycephalum. We choose the nad6 gene as our test case. We build a position specific scoring matrix (PSSM) which summarizes the multiple alignment of all known nad6 protein sequences in other organisms. Then we align this PSSM to the mitochondrial genome of Dydimium mitochondria. We identified the general location of the nad6 gene. The positions of the start and stop codon were determined by a statistical analysis of predictions from 111 PSSMs. The predicted mRNA sequence for nad6 has a length of 466 bases and 11 editing sites. While an experimental verification of our prediction is still outstanding, the high statistical significance of the prediction indicates that PIE is applicable to Didymium sequences and that PIE is likely able to predict other genes in Dydimium. This work will thus help discover edited genes in the mitochondrial genome of Didymium iridis and provide some clues about the mechanism of mRNA editing.

Keywords: RNA editing, computational prediction