Clostridium scatologenes is an anaerobic bacterium that demonstrates some unusual metabolic traits such as the production of 3-methyl indole. The availability of genome level sequencing has lent itself to the exploration and elucidation of unique metabolic pathways in other organisms such as Clostridium botulinum. The Clostridium scatologenes genome, with an estimated length 4.2 million bp, was sequenced by the Applied Biosystems Solid method and the Roche 454 pyrosequencing method. The resulting DNA sequences were combined and assembled into 8267 contigs with an average length of 1250 bp with the Newbler Assembler program. Comparision of published subunits of csd gene and assembled contigs identified that one contig contained all three subunits. In addition a gene with similarity to clostridium carboxidivorans butyrate kinase was found lined next to csd gene. An alignment of the contig and csdgene sequences identified three deletions in the contig within the 4066 bases of the alignment. This implies that there is about 0.07% error rate in the sequencing itself requiring more finishing. Even without finishing the genome assembly into single contig, contigs were annotated in RAST pipeline predicting 2521 protein encoding genes (PEGs). The PEGs were classified by their metabolic function and compared to classified PEGs found in the closely related clostridium species, Clostridium carboxidivorans and Clostridium. ljungdahlii, which have similarly sized genomes. According to the RAST analysis, Clostridium scatologenes had 35% subsystem coverage of all known metabolic processes with its 2521 PEGs. This compares to 41% for Clostridium carboxidivorans with 4174 PEGs (29) and 42% for Clostridium ljungdahlii with 4184 PEGs (30), indicating that Clostridium scatologenesmay still have more genes to be identified. Comparison of the percent genes found in the metabolic subsystems was similar except in motility and chemotaxis. The contigs, on which the csd gene and tryptophan metabolizing genes lay, were examined to see if additional genes might support these metabolic pathways. Butyrate kinase was associated with the csd genes but no other associations were found for the two tryptophan metabolizing genes. The tryptophan biosynthesis operon genes were all found on one contig (contig 6771) and were syntenic with other bacterial species.

Thesis (Ph.D.)--Syracuse University, 2008. / "Publication number: AAT 3323087."

Thesis (M.S.)--University of North Carolina at Wilmington, 2004. / Includes bibliographical references (leaves : [31]-32).

Thesis (M.S.)--University of North Carolina at Wilmington, 2004. / Includes bibliographical references (leaves : [31]-32).

Thesis (Ph.D.) - University of Queensland, 2004. / Includes bibliography.

Fungi are one of the major organisms that cause allergic disease in human. A number of proteins from fungi have been found to be allergenic or possess immunostimulatory properties. Identifying and characterizing allergens from fungal genomes will help facilitate our understanding of the mechanism underlying host-pathogen interactions in allergic diseases. Currently, there is a lack of tools that allow us to rapidly and accurately predict allergens from whole genomes. In the context of whole genome annotation, allergens are rare compared to non-allergens and thus the data is considered highly skewed. In order to achieve a confident set of predicted allergens from a genome, false positive rates must be lowered. Current allergen prediction tools often produce many false positives when applied to large-scale data set such as whole genomes, and thus lower the precision. Moreover, the most accurate tools are relatively slow because they use sequence alignment to construct feature vectors for allergen classifiers. This dissertation presents computational approaches in characterizing the allergen repertoire in fungal genomes as part of the whole genome studies of Alternaria, an important allergenic/opportunistic human pathogenic fungus and necrotrophic plant parasite. In these studies, the genomes of multiple Alternaria species were characterized for the first time. Functional elements (e.g. genes, proteins) were first identified and annotated from these genomes using computational tools. Protein annotation and comparative genomics approaches revealed the link between Alternaria genotypes and its prolific saprophytic lifestyle that provides at least a partial explanation for the development of pathological relationships between Alternaria and humans. A machine learning based tool (Allerdictor) was developed to address the neglected problem of allergen prediction in highly skewed large-scale data sets. Allerdictor exhibited high precision over high recall at fast speed and thus it is a more practical tool for large-scale allergen annotation compared with existing tools. Allerdictor was then used together with a comparative genomics approach to survey the allergen repertoire of known allergenic fungi. We predicted a number of mold allergens that have not been experimentally characterized. These predicted allergens are potential candidates for further experimental and clinical validation. Our approaches will not only facilitate the study of allergens in the increasing number of sequenced fungal genomes but also will be useful for allergen annotation in other species and rapid prescreening of synthesized sequences for potential allergens. / Ph. D.

Speciation and adaptation have always been of great interest to biologists. The Hawaiian archipelago provides a natural arena for understanding adaptive radiation and speciation, and genomics and bioinformatics offer new approaches for studying these fundamental processes. The mode of speciation should have profound impacts on the genomic architecture and patterns of reproductive isolation of new species. The Hawaiian Drosophila are a spectacular example of sequential colonization, adaptive radiation, and speciation in the islands with nearly 1,000 estimated species, of which more than 500 have been described to date. This dissertation gives an overview of the Hawaiian Drosophila system (Chapter 1), new insights into genomes of three recently diverged species of Hawaiian picture-winged Drosophila (Chapter 2), as well as estimated gene flow patterns (Chapter 3). Additionally, I present a new approach of mapping genomic scaffolds onto chromosomes, based on NextGen sequencing from chromosomal microdissections (Chapter 4), and gene expression profiles of backcross hybrids and their parental forms (Chapter 5). Overall, obtained results were used to address such fundamental questions as the role of adaptive changes, founder effects (small effective population size in isolation), and genetic admixture during speciation. / Ph. D. / Speciation, or the origin of new species, and adaptation have always been of great interest not only to biologists, but also to the general public. Understanding how the fascinating diversity of nature is formed, and the processes behind it, may benefit the development and improvement of human society as a whole. The Hawaiian archipelago provides a natural arena for apprehending topics related to colonization, adaptation, and speciation. This microcosm, with the new approaches in genomics and bioinformatics, offers us the study of these very fundamental processes. The Hawaiian <i>Drosophila</i>’s 1,000 estimated species are a spectacular example of adaptive radiation and speciation, and an excellent model of research, as exemplified by this study. Using Hawaiian <i>Drosophila</i>, it addresses such fundamental questions in speciation as the roles of adaptive changes, founder effects (small effective population size in isolation), and genetic admixture during speciation.

Thesis (MSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Zygophyllum orbiculatum Welwitsch ex Oliv. from Angola and Zygophyllum stapffii Schinz from Namibia were described in the late 1800’s. Recent comparisons of these two species revealed that they were morphologically very similar except that Zygophyllum orbiculatum has unifoliolate leaves and Zygophyllum stapffii has bifoliolate leaves. The similarity of these two species was investigated using nuclear ITS (Internal Transcribed Spacer, i.e. ITS1, 5.8SrDNA, ITS2) region sequence data as phylogenetic markers. Due to almost identical sequences and phylogenetic grouping, it was concluded that they were conspecific. However, the phylogenetic relationships of the major groups within the subfamily Zygophylloideae based on ITS sequences, were unresolved and unsupported, as was found in previous studies using chloroplast gene marker sequences. To resolve the phylogenetic relationships of the major groups within the subfamily Zygophylloideae, a next generation sequencing (NGS) approach was taken. Chloroplasts of taxa representing the major groups within the subfamily were isolated and chloroplast genome sequence data were generated using the Ion Torrent™ sequencer. Additional nuclear ITS cassette data (18SrDNA, ITS1, 5.8SrDNA, ITS2, 26SrDNA) were generated as a by-product and used to produce a large combined aligned sequence matrix for phylogenetic analysis. Model-based phylogenetic programs were able to retrieve strongly supported and resolved phylogenetic relationships of the major groups within Zygophylloideae. Two basal groupings were retrieved in the subfamily. The first grouping consisted of the genera Tetraena, Fagonia and Melocarpum. The second grouping consisted of the monotypic genus Augea and Zygophyllum orbiculatum/stapffii which were embedded within the genus Roepera. Using a gene duplication approach, the chloroplast marker data of genus Zygophyllum sensu stricto placed this genus basal to the Augea, Zygophyllum orbiculatum/stapffii, Roepera clade whilst the nuclear marker data of Zygophyllum sensu stricto, was found in a basal position to the entire subfamily. From this it is concluded that Zygophyllum sensu stricto shows evidence of incomplete lineage sorting. A revised taxonomy for the entire subfamily Zygophylloideae is proposed. / AFRIKAANSE OPSOMMING: Zygophyllum orbiculatum Welwitsch ex Oliv. uit Angola en Zygophyllum stapffii Schinz van Namibië is in die laat 1800's beskryf. Onlangse vergelykings van hierdie twee spesies het getoon dat hulle morfologies baie eners is, behalwe dat Zygophyllum orbiculatum unifoliolate blare besit en dat Zygophyllum stapffii bifoliolate blare besit. Hierdie ooreenkoms is ondersoek, met behulp van die nukleêre “ITS” (Internal Transcribed Spacer d.w.s. ITS1, 5.8SrDNA, ITS2) DNS-strook volgordedata as filogenetiese merkers. As gevolg van feitlik identiese geenopeenvolgings is bevind dat die twee spesies konspesifiek is. Die filogenetiese verwantskappe van die groot binnegroepe van die subfamilie Zygophylloideae, gebaseer op ITS geenopeenvolgings, was egter onopgelos en nie ondersteun nie, net soos in vorige studies waarin chloroplast geenmerkervolgordes gebruik was. Om die filogenetiese verwantskappe van die groot binnegroepe van die subfamilie Zygophylloideae op te los, was ‘n betreklik nuwe DNS volgordebepalingstegniek, naamlik “Next Generation Sequencing” (NGS), gebruik. Chloroplaste van taksa, wat die groot groepe binne-in die subfamilie verteenwoordig, is geïsoleer en chloroplast genoomdata is gegenereer met behulp van die Ion Torrent ™ (NGS) DNS-volgordebepaler. Bykomend was die nukleêre “ITS”-kasset volgordedata (18SrDNS, ITS1, 5.8SrDNS, ITS2, 26SrDNS) ook as 'n by-produk gegenereer en ook gebruik om 'n groot gesamentlike DNS oplyningmatriks vir filogenetiese doeleindes. Model-gebaseerde filogenetiese programme was in staat was om sterk ondersteuning en opgeloste filogenetiese verwantskappe van die groot groepe binne-in Zygophylloideae te ontravel. Die subfamilier toon twee basale groeperinge. Die eerste groepering bestaan uit die genera Tetraena, Fagonia en Melocarpum. Die tweede groepering bestaan uit die monotipiese genus Augea en Zygophyllum orbiculatum/stapffii, wat ingebed is binne-in die genus Roepera. Deur ‘n geendupliseringsbenadering te gebruik op die DNS geenopeenvolgings van die verteenwoordigende takson van Zygophyllum sensu stricto, is bevind dat die chloroplast DNS volgordes hierdie groep basaal aan ‘n Roepera/Augea/Zygophyllum orbiculatum/stapffii klade plaas, terwyl die nukleêre DNS volgordes hierdie groep basaal aan die hele subfamilie Zygophylloideae plaas. Hieruit is die gevolgtrekking gemaak dat Zygophyllum sensu scricto bewyse van onvolledige afstammelingsortering toon. ‘n Gewysigde taksonomie vir die hele subfamilie Zygophylloideae word voorgestel.

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