Zimmerly, StevenWu, Li2018-12-032018-12-032018-11-29Wu, L. (2018). Bioinformatic and phylogenetic analyses of retroelements in bacteria (Doctoral thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca. doi:10.11575/PRISM/34667http://hdl.handle.net/1880/109215Retroelements are mobile elements that are capable of transposing into new loci within genomes via an RNA intermediate. Various types of retroelements have been identified from both eukaryotic and prokaryotic organisms. This dissertation includes four individual projects that focus on using bioinformatic tools to analyse retroelements in bacteria, especially group II introns and diversity-generating retroelements (DGRs). The introductory Chapter I gives an overview of several newly-identified retroelements in eukaryotes and prokaryotes. In Chapter II, a general search for bacterial RTs from the GenBank DNA sequenced database was performed using automated methods. It not only enlarged the collection of bacterial reverse transcriptases (RTs), but also revealed several new classes of RTs. In Chapter III, another automated search was performed to identify group II introns. All predicted introns were automatically folded and then manually refined. Other information, such as multiple copies and non-standard intron organisations, were also identified. Next, all introns were subjected in several analyses in order to depict common properties for each class, such as preferences in target sites and DNA strands. Using this enlarged dataset, Chapter IV aimed to resolve the phylogeny of group II introns and investigate whether the intron-encoded protein (IEP) and RNA portions coevolved. Among trees constructed from various datasets, such as using different sequence masks, smaller sampled subsets or morphological features, the hypothesis that the IEP and RNA coevolved was supported by comparisons among most trees, even though it seemed to be rejected by formal topology tests. Finally, Chapter V compiled and systematically classified the most recent set of DGRs, which can be used as a reliable reference to direct future DGR-related studies and experimental designs.engUniversity of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission.DGRgroup II intronsphylogeneticsretroelementBioinformaticsdoctoral thesis10.11575/PRISM/34667