The rapid accumulation of numerous sequenced genomes has provided a golden opportunity for ancestral state reconstruction studies, especially in the whole genome reconstruction area. However, most ancestral genome reconstruction methods developed so far only focus on gene or replicon sequences instead of whole genomes. They rely largely on either detailed modeling of evolutionary events or edit distance computation, both of which can be computationally prohibitive for large data sets. Hence, most of these methods can only be applied to a small number of features and species. In this dissertation, we describe the design, implementation, and evaluation of an ancestral genome reconstruction system (REGEN) for bacteria. It is the first bacterial genome reconstruction tool that focuses on ancestral state reconstruction at the genome scale instead of the gene scale. It not only reconstructs ancestral gene content and contiguous gene runs using either a maximum parsimony or a maximum likelihood criterion but also replicon structures of each ancestor. Based on the reconstructed genomes, it can infer all major events at both the gene scale, such as insertion, deletion, and translocation, and the replicon scale, such as replicon gain, loss, and merge. REGEN finishes by producing a visual representation of the entire evolutionary history of all genomes in the study. With a model-free reconstruction method at its core, the computational requirement for ancestral genome reconstruction is reduced sufficiently for the tool to be applied to large data sets with dozens of genomes and thousands of features. To achieve as accurate a reconstruction as possible, we also develop a homologous gene family prediction tool for preprocessing. Furthermore, we build our in-house Prokaryote Genome Evolution simulator (PEGsim) for evaluation purposes. The homologous gene family prediction refinement module can refine homologous gene family predictions generated by third party de novo prediction programs by combining phylogeny and local gene synteny. We show that such refinement can be accomplished for up to 80% of homologous gene family predictions with ambiguity (mixed families). The genome evolution simulator, PEGsim, is the first random events based high level bacteria genome evolution simulator with models for all common evolutionary events at the gene, replicon, and genome scales. The concepts of conserved gene runs and horizontal gene transfer (HGT) are also built in. We show the validation of PEGsim itself and the evaluation of the last reconstruction component with simulated data produced by it. REGEN, REconstruction of GENomes, is an ancestral genome reconstruction tool based on the concept of neighboring gene pairs (NGPs). Although it does not cover the reconstruction of actual nucleotide sequences, it is capable of reconstructing gene content, contiguous genes runs, and replicon structure of each ancestor using either a maximum parsimony or a maximum likelihood criterion. Based on the reconstructed genomes, it can infer all major events at both the gene scale, such as insertion, deletion, and translocation, and the replicon scale, such as replicon gain, loss, and merge. REGEN finishes by producing a visual representation of the entire evolutionary history of all genomes in the study. / Ph. D.

Ancient DNA analyses are reliant on reference genomes to authenticate and identify endogenous genomes. While this has lead to many successful studies involving proboscidians, hominids, and ancient pathogens such as Yersinia pestis, our reliance on at most a small number of genomes greatly limits our ability to functionally describe the genome of interest. Further, given the existence of open bacterial genomes and horizontal gene transfers it is likely that reference biases have been incorporated and cited in following studies as representative of past gene diversity. By implementing and standardizing the use of bacterial pan-genomes the effect of these biases are greatly diminished while also revealing the relative capabilities of the target genome compared to the modern diversity. Describing an ancient strain by both its phylogenetic and functional similarities to modern strains allows for a more nuanced analysis of the species evolutionary history. Incongruencies between the phylogeny and genetic function are ripe for deeper analyses and the implications of its findings resonate beyond the characterization of an ancient genome. A pan-genome centric approach to ancient bacterial studies offers significant improvements compared to the current paradigm. / Dissertation / Doctor of Philosophy (PhD)

Murine embryonic stem (ES) cells have provided researchers with a useful tool to investigate genome function and the consequences of genome mutation. One mutational approach is gene-targeting, this involves the introduction of DNA sequences of choice, precisely, to almost any location in the target genome by homologous recombination. At present, most gene-targeting strategies introduce DNA constructs that derive from plasmids. Plasmids can stably propagate up to approximately 30 kb of DNA. Therefore, this size limit may place a restriction on the range of mutations that may be made to a genome using a single plasmid-derived gene-targeting construct alone. To overcome this limitation, multiple rounds of sequential gene-targeting experiments may be performed, however such an approach may be too lengthy to be practicable. In order to address this current limitation with gene-targeting a novel strategy was tested, implementing Cre-lox site-specific recombination (SSR) technology and the bacterial artificial chromosome (BAC) vector system. Two sequential gene-targeting events in murine E14Tg2a ES cells (HPRT) were performed at separate locations to chromosome 11. The aim of gene-targeting was to create an interval on chromosome 11 that included a single copy of the murine alpha-globin locus, between the hetero-specific lox sites, loxP and lox511, an interval of approximately 64 kb. To this end the first targeting event delivered lox511 /hygromycin/I See Illox51 J sequences and the second event frt/I See I/5'hprt//oxP/neomycin sequences. ES cells that were confirmed to have correctly undergone the two desired targeting events (double-targeted) were then assessed to determine whether these events had occurred to the same chromosome 11 (in eis ), as desired, or to the alternate copies of chromosome 11 (in trans). This assessment involved restricting DNA from the double-targeted ES cell lines with the rare-cutting restriction endonuclease I See I and resolving the products of this restriction by pulsed field gel electrophoresis. This analysis identified two in cis lines (CAT-A3 and CAT-B3) and an in trans line (CATCIO). The double-targeted ES cell lines were then further characterised to determine whether the hetero-specific lox sites they harboured would participate in ere-mediated SSR. The positive result of this analysis was the generation of ES cell clones that were hemizygous for the alpha-globin locus, a deletion of 64 kb. Hemizygous ES cell clones were obtained from the CAT-A3 and CAT-B3 ES cell lines, as predicted, but not from the CAT-C 10 line, although all the lines tested showed evidence of SSR occurring. In parallel to achieving the interval between loxP and lox51 l in ES cells, a BAC, harbouring the alpha-globin locus, was similarly modified with lox sites using recombination-mediated cloning. The aim of the BAC modification was to create an interval between lox sites in the BAC identical to that achieved in the ES cells. The BAC was targeted sequentially with two separate constructs, lox511/k.anamycin/lox511/HSVtk and then blasticidin/loxP/3'hprt/I See 11.frt. The correct targeting of the BAC was verified by restricting its DNA with a panel restriction endonucleases. The lox sites were then tested in an in vitro analysis with purified Cre recombinase and found to be competent to participate in SSR reactions. The modified BAC was co-electroporated with a Cre expression plasmid into the CAT-A3 and CAT-B3 ES cell lines, previously characterised as targeted in eis, with the aim of exchanging the interval sequences in the ES cell with those of the BAC. The ultimate aim of such an exchange would be to deliver any combination of mutations that would be previously engineered to the BAC interval, to that of the ES cell, by a single SSR event. This experimental approach should expedite and facilitate the mutational analysis of gene loci. To generate comparative data the result of SSR between the modified BAC and an in trans targeted ES cell line (CAT-CI 0) was also assessed. The selection for the desired exchange involved reconstruction of an Hprt minigene and exclusion of a thymidine kinase gene, cells which haboured these events could therefore be selected for in HAT and ganciclovir supplemented media respectively. ES cell clones generated from both of the in cis lines tested (CAT-A3 and CAT-B3) had the correct selection resistance profiles, thus indicating that the desired exchange had been achieved in these clones. Additionally, Southern blot analysis from the DNA from these clones was consistent with the achievement of the desired exchange. However, the results obtained from clones generated from the in trans line (CAT-CI 0) were not consistent with their predicted genetic arrangement following SSR with the modified BAC. Thus far similar experimental approaches have been implemented to exchange smaller intervals of I to 5 kb and have been termed recombinase mediated cassette exchange (RMCE). However the experiments described within this thesis are the first test whether the same rationale may be applied to larger intervals. The strategy described and tested in this thesis has therefore been termed large interval RMCE (liRMCE).

Aspects of higher order chromatin structure such as replication timing, lamina association and Hi-C inter-locus interactions have been recently studied in several human and mouse cell types and it has been suggested that most of these features of genome organisation are conserved over evolution. However, the extent of evolutionary divergence in higher order structure has not been rigorously measured across the mammalian genome, and little is known about the characteristics of any divergent loci defined. Here we generate an orthologous dataset combining multiple measurements of chromatin structure and organisation over many embryonic cell types for both human and mouse that, for the first time, allows a comprehensive assessment of the extent of structural divergence between different mammalian genomes. Comparison of orthologous regions confirms that all measurable facets of higher order structure are conserved between human and mouse, across the majority of the orthologous genome. This broad similarity is observed in spite of the substantial time since the species diverged, differences in experimental procedures among the datasets examined, and the presence of cell type specific structures at many loci. However, we also identify hundreds of regions showing consistent evidence of divergence between these species, constituting at least 10% of the orthologous mammalian genome and encompassing many hundreds of human and mouse genes. Divergent regions are enriched in genes implicated in vertebrate development, suggesting important roles for structural divergence in mammalian evolution. They are also relatively enriched for genes showing divergent expression patterns between human and mouse ES cells, implying these regions may underlie divergent regulation. Divergent regions show unusual shifts in compositional bias, sequence divergence and are unevenly distributed across both genomes. We investigate the mechanisms of divergence in higher order structure by examining the influence of sequence divergence and also many features of primary level chromatin, such as histone modification and DNA methylation patterns. Using multiple regression, we identify the dominant factors that appear to have shaped the physical structure of the mammalian genome. These data suggest that, though relatively rare, divergence in higher order chromatin structure has played important roles during evolution.

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