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Genome characterisation, with special reference to gene silencing mechanisms, of armillaria fuscipes
Dissertation (MSc (BioInformatics))--University of Pretoria, 2014.
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| Format: | Thesis |
| Language: | English |
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2026
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| _version_ | 1867613567547604992 |
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| access_status_str | Open Access |
| author2 | Coetzee, Martin Petrus Albertus |
| author_browse | Coetzee, Martin Petrus Albertus |
| author_facet | Coetzee, Martin Petrus Albertus |
| collection | Thesis |
| description | Dissertation (MSc (BioInformatics))--University of Pretoria, 2014. |
| format | Thesis |
| id | oai:repository.up.ac.za:2263/110021 |
| institution | University of Pretoria (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:38:12.302Z |
| license_str | Not specified — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UPSpace — University of Pretoria Institutional Repository |
| publishDate | 2026 |
| publishDateRange | 2026 |
| publishDateSort | 2026 |
| record_format | dspace |
| source_str | UPSpace — University of Pretoria Institutional Repository |
| spelling | oai:repository.up.ac.za:2263/110021 Genome characterisation, with special reference to gene silencing mechanisms, of armillaria fuscipes Coetzee, Martin Petrus Albertus jon@ambler.co.za Steenkamp, Emma Theodora Joubert, Fourie Ambler, Jon Mitchell Gene silencing Genome sequencing comparative genomics Armillaria Repeat induced polymorphisms Dissertation (MSc (BioInformatics))--University of Pretoria, 2014. The mushroom forming fungus Armillaria fuscipes is indigenous to South Africa, where it is known to cause disease in woody plants, including members of the economically important Pinus species. In order to aid in further research of this pathogen, an annotated genome assembly for this species was produced using the latest whole genome sequencing technologies. This represents the first genome sequence of this species, and was used to investigate the relationship between silencing mechanisms within the genome and the genetic elements they seek to control. The first chapter contains a literature review, which deals with four topics. The first section is a review of the current sequencing and assembly technologies. The second section discusses transposable elements, and the effect they have on the genome that they occupy. The third section is concerned with the various mechanisms of gene silencing in fungi and their origins, specifically repeat-induced point mutation, quelling and meiotic silencing of unpaired DNA. The final section reviews the current literature on the organism that is the focus of this project, namely A. fuscipes. The second chapter details the development of an online tool for the detection of repeat-induced point mutation in the sequences of transposable elements. This tool was named Transposable Element Analysis for Repeatinduced point mutation (TEAR), and used an original profile based approach to detect deviant sequence composition in the transposable elements that may be a signature of RIP. Testing showed the tool to have a high level of sensitivity and specificity in the detection of RIP in the sequences of transposable elements. The final chapter details the sequencing and annotation of the Armillaria fuscipes genome using a combination of Illumina and the newly developed Pacific Biosciences single molecule real time sequencing technology. The transposable element sequences within the genome were screened using the TEAR tool developed in the second chapter of this dissertation. It revealed a mutation pattern consistent with RIP. Additionally, the genome was compared to other available fungal genomes in terms of various genome statistics, with particular focus placed on the transposable element composition and presence of silencing mechanisms. BioInformatics MSc (BioInformatics) 2026-05-15T17:26:05Z 2026-05-15T17:26:05Z 14/08/07 2014 Dissertation http://hdl.handle.net/2263/110021 en application/pdf |
| spellingShingle | Gene silencing Genome sequencing comparative genomics Armillaria Repeat induced polymorphisms Genome characterisation, with special reference to gene silencing mechanisms, of armillaria fuscipes |
| title | Genome characterisation, with special reference to gene silencing mechanisms, of armillaria fuscipes |
| title_full | Genome characterisation, with special reference to gene silencing mechanisms, of armillaria fuscipes |
| title_fullStr | Genome characterisation, with special reference to gene silencing mechanisms, of armillaria fuscipes |
| title_full_unstemmed | Genome characterisation, with special reference to gene silencing mechanisms, of armillaria fuscipes |
| title_short | Genome characterisation, with special reference to gene silencing mechanisms, of armillaria fuscipes |
| title_sort | genome characterisation with special reference to gene silencing mechanisms of armillaria fuscipes |
| topic | Gene silencing Genome sequencing comparative genomics Armillaria Repeat induced polymorphisms |
| url | http://hdl.handle.net/2263/110021 |