The plastid genomes of land plants are generally highly conserved in gene content and order, genome organization, and rates of sequence evolution; however, a few groups have experienced genomic change. The previously published sequence of Pelargonium X hortorum (Geraniaceae) reveals the largest, most rearranged plastid genome among land plants, and rate heterogeneity and genomic change have been documented in the monocot family Poaceae. Three initiatives were taken to characterize plastid genome evolution better in these groups. First, I estimate and compare genome-wide rates of sequence evolution in Geraniaceae genes relative to other angiosperms. An analysis of nucleotide substitutions for 72 plastid genes from 47 angiosperms, including nine Geraniaceae, shows that values of dN are accelerated in ribosomal protein and RNA polymerase genes. dN/dS, an indicator of selection, is significantly elevated in the same two classes of genes and ATPase genes. Second, I sequenced three additional Geraniaceae plastid genomes (Erodium texanum, Geranium palmatum, and Monsonia speciosa) and compare these sequences to each other, P. X hortorum, and other rosids. Geraniaceae plastid genomes are highly variable in size, gene content and order, and base composition. The genome of M. speciosa is among the smallest land plant plastid genomes, and one copy of the IR region in E. texanum has been lost. Gene/intron loss and gene duplication are rampant in Geraniaceae plastid genomes, and a number of losses are phylogenetically inconsistent. To explain the unusual rates and patterns of genome evolution in Geraniaceae, I propose a model of aberrant DNA repair coupled with altered gene expression. Lastly, I characterize genome evolution in the family Poaceae and order Poales. There has been a recent surge in the availability of Poaceae sequences, but a comprehensive analysis of genome evolution had not been performed that included any non-grass Poales taxa. I present the sequence of Typha latifolia (Typhaceae), the first non-grass Poales sequenced to date, and I show that Poaceae plastid genomes exhibit increased genomic rearrangements and nucleotide substitutions. These analyses show the extent of lineage-specific rate acceleration on the branch leading to Poaceae and deceleration during the diversification of the family. / text

The availability of complete plastid genomes has been playing an important role in resolving phylogenetic relationships among the major clades of land plants and in improving our understanding of the evolution of genomic organization. The increased availability of complete genome sequences has enabled researchers to build large multi-gene datasets for phylogenetic and molecular evolutionary studies. In chapter 2 of this thesis a web-based multiple sequence web viewer and alignment tool (MSWAT) is developed to handle large amount of data generated from complete genome sequences for phylogenetic and evolutionary analyses. We expect that MSWAT will be of general interest to biologists who are building large data matrices for evolutionary analyses. The third chapter presents the sequenced plastid genomes of three magnoliids, Drimys (Canellales), Liriodendron (Magnoliales), and Piper (Piperales). Data from these genomes, in combination with 32 other angiosperm plastid genomes, were used to assess phylogenetic relationships of magnoliids to other angiosperms and to examine patterns of variation of GC content. Evolutionary comparisons of three new magnoliid plastid genome sequences, combined with other published angiosperm genomes, confirm that GC content is unevenly distributed across the genome by location, codon position, and functional group. Furthermore, phylogenetic analyses provide the strongest support so far for the hypothesis that the magnoliids are sister to a large clade that includes both monocots and eudicots. The fourth chapter presents the Trifolium subterraneum plastid genome sequence, which is unusual in genome size and organization relative to other angiosperm plastid genomes. The Trifolium plastid genome is an excellent model system to examine mechanisms of rearrangements and the evolution of repeats and unique DNA. / text

published_or_final_version / abstract / toc / Computer Science and Information Systems / Master / Master of Philosophy

Transposons, also known as transposable elements (TEs), are genetic elements capable of changing their location in the genome and amplifying in number. Because of their ability to cause mutations in the host genome, often with detrimental consequences to the host, yet avoid being eliminated by natural selection, transposons have been labeled selfish elements or genomic parasites. However, the advent of genomics has allowed the identification of numerous instances where transposons have played a crucial role in host genome evolution. In this thesis, I evaluate the extent to which transposons have influenced the genomes of their hosts, with an emphasis on plant genomes. I review the present knowledge of different mechanisms by which this is achieved and provide examples to illustrate them. Next, I tackle the problem of annotating transposons in the completed genomic sequence of domestic rice by comparing RepeatMasker, the standard approach used in transposon annotation, with an alternative approach employing hidden Markov models. In addition, I perform a genome-wide analysis of gene fragment capture by rice Mutator-like transposons. I conclude that, while this is a widespread phenomenon in rice, it is unlikely to represent a major force in generating novel protein-coding genes. Nevertheless, the duplicated gene fragments that are transcribed may playa role in the regulation of host genes they arose from via an RNAi-like mechanism. Finally, I conduct an in silico analysis of a gene family derived from a domesticated Mutator-like transposase, called MUSTANG (MUG), in conjunction with an experimental characterization of the MUG family in Arabidopsis. The results of the study indicate that the MUG family arose in a common ancestor of flowering plants and that the Arabidopsis genes AtMUG1 and/or AtMUG2 may act as global regulators of mitochondrial function. I conclude that our appreciation of the role of transposons in host function and evolution will undoubtedly continue to grow as our understanding of these processes deepens.

No description available.

Reciprocal crosses between plants containing different genome numbers have been demonstrated to show alternate phenotypes in many species and are often lethal. The effects of interploidy crosses on kernel development in maize (Zea mays) have been reassessed using markers for two cell domains: the aleurone and the basal endosperm transfer layer (BETL); and by monitoring gene expression. The study confirms previous observations and offers novel insights into genomic interactions. Endosperms from maternal excess crosses (tetraploid mother, diploid father) displayed reduced mitotic activity, and an accelerated rate of differentiation generally, including early starch accumulation, and earlier, atypical aleurone formation. The BETL failed to form normally, being replaced with aleuronelike cells, except for a few interspersed cells. Gene expression was altered, including those encoding cell domain markers and storage molecules. Paternal excess endosperms (diploid mother, tetraploid father), showed an increase in cellular proliferation. Generally, differentiation was delayed: starch accumulation began late, and formation of the aleurone layer was delayed, and was morphologically highly irregular. BETL specification was also disturbed, with only a few cells showing characteristic wall modifications very late in development. Later development of the whole endosperm was characterized by ectopic gene expression, and zones of high cell proliferation. A greater proportion of the genome was mis-expressed in these crosses, reflecting the more extreme phenotype. Although expression levels of marker genes did not reflect the failure to develop a normal BETL, it may be that the cells in the BETL region had undergone an modified developmental program. This work is considered in the context of evolutionary models which state that different parental roles lead to differential expression of genes from their respective genomes, and is compared with evidence from arabidopsis. The current study is considered generally supportive of such models.

<p>While the many completely sequenced genomes of bacterial pathogens contain all the determinants of the host-pathogen interaction, and also every possible drug target and recombinant vaccine candidate, computational tools for selecting suitable candidates for further experimental analyses are limited to date. The overall objective of my PhD project was to attempt to design reusable systems that employ the two most important features of bacterial evolution, horizontal gene transfer and adaptive mutation, for the identification of potentially novel virulence-associated factors and possible drug targets. In this dissertation, I report the development of two novel technologies that uncover novel virulence-associated factors and mechanisms employed by bacterial pathogens to effectively inhabit the host niche. More importantly, I illustrate that these technologies may present a reliable starting point for the development of screens for novel drug targets and vaccine candidates, significantly reducing the time for the development of novel therapeutic strategies. Our initial analyses of proteins predicted from the preliminary genomic sequences released by the Sanger Center indicated that a significant number appeared to be more similar to eukaryotic proteins than to their bacterial orthologs. In order determine whether acquisition of genetic material from eukaryotes has played a role in the evolution of pathogenic bacteria, we developed a system that detects genes in a bacterial genome that have been acquired by interkingdom horizontal gene transfer.. Initially, 19 eukaryotic genes were identified in the genome of Mycobacterium tuberculosis of which 2 were later found in the genome of Pseudomonas aeruginosa, along with two novel eukaryotic genes.</p> <p>Surprisingly, six of the M. tuberculosis genes and all four eukaryotic genes in P. aeruginosa may be involved in modulating the host immune response through altering the steroid balance and the production of pro-inflammatory lipids. We also compared the genome of the H37Rv M. tuberculosis strain to that of the CDC- 1551 strain that was sequenced by TIGR and found that the organisms were virtually identical with respect to their gene content, and hypothesized that the differences in virulence may be due to evolved differences in shared genes, rather than the absence/presence of unique genes. Using this observation as rationale, we developed a system that compares the orthologous gene complements of two strains of a bacterial species and mines for genes that have undergone adaptive evolution as a means to identify possibly novel virulence &ndash / associated genes. By applying this system to the genome sequences of two strains of Helicobacter pylori and Neisseria meningitidis, we identified 41 and 44 genes that are under positive selection in these organisms, respectively. As approximately 50% of the genes encode known or potential virulence factors, the remaining genes may also be implicated in virulence or pathoadaptation. Furthermore, 21 H. pylori genes, none of which are classic virulence factors or associated with a pathogenicity island, were tested for a role in colonization by gene knockout experiments. Of these, 61% were found to be either essential, or involved in effective stomach colonization in a mouse infection model. A significant amount of strong circumstantial and empirical evidence is thus presented that finding genes under positive selection is a reliable method of identifying novel virulence-associated genes and promising leads for drug targets.</p>

<p>Despite the fact that the sequence of the human genome is now complete it has become clear that the elucidation of the transcriptome is more complicated than previously expected. There is mounting evidence for unexpected and previously underestimated phenomena such as alternative splicing in the transcriptome. As a result, the identification of novel transcripts arising from the genome continues. Furthermore, as the volume of transcript data grows it is becoming increasingly difficult to integrate expression information which is from different sources, is stored in disparate locations, and is described using differing terminologies. Determining the function of translated transcripts also remains a complex task. Information about the expression profile &ndash / the location and timing of transcript expression &ndash / provides evidence that can be used in understanding the role of the expressed transcript in the organ or tissue under study, or in developmental pathways or disease phenotype observed.<br /> <br /> In this dissertation I present novel computational approaches with direct biological applications to two distinct but increasingly important areas of research in gene expression research. The first addresses detection and characterisation of alternatively spliced transcripts. The second is the construction of an hierarchical controlled vocabulary for gene expression data and the annotation of expression libraries with controlled terms from the hierarchies. In the final chapter the biological questions that can be approached, and the discoveries that can be made using these systems are illustrated with a view to demonstrating how the application of informatics can both enable and accelerate biological insight into the human transcriptome.</p>

Mitochondrial DNA encodes thirteen protein subunits in the oxidative phosphorylation system (OXPHOS) that is responsible for cellular energy production. Mitochondrial disorders have been identified to be associated with mtDNA mutations. However, the molecular mechanisms of specific mtDNA mutations are still being explored in order to establish causative links. This study tries to elucidate the mutational effects of mtDNA on OXPHOS complex activities and cell growths. Using mouse 3T3 fibroblasts as a cell model, single-cell clones with different growth rates were isolated. The entire mtDNA genome was sequenced for mutations. The enzymatic activities of OXPHOS complex I to V were analysed. Three growth patterns represented by five clones were identified. Three clones (clone #2, #3, and #6) had the shortest doubling times (11.5 - 14.9 hours). Clone #1 had a medium growth rate (19.2 hous); and clone #5 had a significantly slow growth rate (22 hours). MtDNA sequencing results revealed that clone #5 had several heteroplasmic mutations (one in 16S rRNA, two in tRNAser (UCN), three in tRNAasp, one in tRNAlys, one in COI, five in COII, and one in ATPase8) while the other four clones showed sequence homology. Enzymatic analyses showed that on average clone #5 had significantly low complex III, IV, and V activities (p < 0.05). Changes in biochemical properties and protein structure were analyzed to deduct possible mechanisms for reduced respiration. In conclusion, the slow growth rate is associated with reduced OXPHOS enzyme functions. It is most likely that the combination of COI and COII mutations resulted in the reduction of complex IV function. It is still unclear whether the ATPase8 mutation (T7869A) in the non-conserved region alone can have such a pronounced phenotypic effect. A reduction in complex III also cannot be explained since there were no mutations in the only mtDNA-encoded complex III gene, but it is possible that there are mutations in the nDNA-encoded complex III genes. Mutations in tRNA and rRNA genes may also be responsible for reduced protein syntheses and consequently reduced OXPHOS activities. It is unclear why complex I activity was not affected. Although the mutational effect of individual mtDNA mutation observed cannot be clearly identified, this study establishes a correlation between mtDNA mutation and cell energy production and growth.

Thesis (Ph. D.)--University of Oregon, 2008. / Typescript. Includes vita and abstract. Includes bibliographical references (leaves 45-52). Also available online in ProQuest, free to University of Oregon users.