Electronic Theses and Dissertations (PhDs)
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Item Genome sequencing of the Southern Ground Hornbill (Bucorvus leadbeateri)(University of the Witwatersrand, Johannesburg, 2024-10) Patel, Jasmin Bharatkumar; De Maayer, Pieter; Mollett, JeanThe Southern Ground Hornbill (SGH – Bucorvus leadbeateri) is one of the largest hornbill species worldwide, known for its complex social structures and breeding behaviours. These birds, endemic to Africa, have been of great concern due to their declining populations and disappearance from historic ranges. Despite being the focus of numerous conservation efforts, with research forming an integral part of these initiatives, there is a lack of knowledge regarding the molecular biology aspects of this bird species. This study bridges the gap by presenting the first whole genome sequence of the SGH. The SGH genome was further explored using comparative genomics, genetic variant, and selection analysis, providing deeper insights into the evolution and adaptation of this species. Chapter 1 comprehensively reviews pertinent literature on various aspects of avian evolution, including the role genomics has played in elucidating how these species have adapted and evolved. Furthermore, the current body of knowledge on the SGH is explored. In Chapter 2 the entire genome sequence of the SGH was sequenced using Illumina short-read and Pacific BioSciences long-read datasets. Subsequently, the performance of various assembly approaches was evaluated to attain a high-quality assembly of the SGH. This was coupled with parameter optimisation and reference-based refinement to improve the SGH draft genome assembly. The final draft genome assembly was structurally annotated, providing insight into the genetic blueprint underpinning the SGH. Chapter 3 presents the comparative genomic analysis of the SGH with the genomes of available hornbill species from the genera Bucorvus (Bucorvus abyssinicus and SGH) and Buceros (Buceros bicornis and Buceros rhinoceros subsp. silvestris). This included analysis of the pangenome of the hornbill species, functional characterisation of the core and genus-specific elements of the pan-genome and analysis of orthogroups with evidence of paralogy. In Chapter 4, a species-level comparative genomic analysis of the SGH and the Abyssinian Ground Hornbill (AGH) was performed. Here differences in the species-specific proteome of the two species were analysed and the functional implications of these differences on the adaptation and survival of these species were evaluated. Furthermore, genetic variations between the SGH and AGH were identified and selection analysis of key protein-coding genes with high-impact variants was undertaken. This provided insight into the genetic diversity between the SGH and AGH. Finally, the implications of the study on the understanding of the genetic basis underlying the evolution and adaptation of the SGH is discussed and the future perspective of large-scale population genetic studies is provided.Item Parageobacillus thermoglucosidasius and the water-gas shift reaction: Investigating the influences of gas composition and H2- uptake hydrogenases(University of the Witwatersrand, Johannesburg, 2024) Mol, Michael; Maayer, DeH2 gas is an increasingly important commercial reagent in a range of industries, including as a potential fuel and energy carrier. Production of H2 gas is carried out almost exclusively reliant on fossil fuel reformation through a relatively limited set of environmentally harmful processes. Pressing environmental concerns and the shift in climate policies towards greater incorporation of cleaner H2 gas production strategies and the implementation of H2 as a more sustainable and environmentally friendly alternative energy vector have necessitated development of renewable and cleaner H2 production processes. Chapter one discusses available literature on the present applications, predominant production processes and emerging alternative production strategies of H2 gas, with particular focus on the applicability and mechanism of biological H2 gas production by the thermophile, Parageobacillus thermoglucosidasius, via the water-gas shift reaction. The application of P. thermoglucosidasius to produce H2 gas is presently in its formative laboratory-scale stage of development. Although progress has been made at a fundamental level, various aspects of P. thermoglucosidasius H2 gas metabolism, remain uncharacterised or poorly understood. In Chapter two, the potential influences of two putative H2-uptake hydrogenases, encoded on the genome of a P. thermoglucosidasius strain previously identified to conduct the hydrogenogenic biological water-gas shift reaction was explored through knock- out mutagenesis. Furthermore, in Chapter three, to establish the practical implementation of pertinent and inexpensive gas feedstocks for the water-gas shift reaction, we explored the influences of various industrial mimetic gas feedstock compositions on the H2 gas evolution-, metabolic- and growth-profiles of P. thermoglucosidasius. Considering the highly variable compositions of industrial off-gases, which may contain oxygen and the highly sensitive nature of this system to oxygen, we further explored the impacts of varied volumetric and temporal oxygen perturbations on the system. Aside from hydrogen production, P. thermoglucosidasius and closely related thermophilic taxa from the genera Parageobacillus and Saccharococcus represent appealing targets for various other biotechnological developments. In Chapter four, we performed a comprehensive comparative genomic and phylogenomic analysis to further explore the biotechnological potential of Parageobacillus and Saccharococcus spp. for a range of whole cell applications as well as a source of industrially relevant thermostable enzymes