Dissertation/ Thesis
Identification of a possible sequence of structural events associated with genome evolution
| Title: | Identification of a possible sequence of structural events associated with genome evolution |
|---|---|
| Authors: | Dakurah, Ottovon Bismark |
| Contributors: | Patterton, Hugh-George, Stellenbosch University. Faculty of Science. Centre for Bioinformatics and Computational Biology. |
| Publisher Information: | Stellenbosch University |
| Publication Year: | 2025 |
| Collection: | Stellenbosch University: SUNScholar Research Repository |
| Subject Terms: | Genomics, Comparative genomics, Saccharomyces cerevisiae -- Genetics -- Computer simulation, Genomes -- Evolution -- Mathematical models, Bioinformatics -- Computer simulation, Computational biology -- Mathematical models, UCTD |
| Description: | Thesis (PhD)--Stellenbosch University, 2025. ; Dakurah, O. 2025.Identification of a possible sequence of structural events associated with genome evolution. Unpublished doctoral dissertation. Stellenbosch: Stellenbosch University [online]. Available: https://scholar.sun.ac.za/items/847245e1-4946-4f38-8c28-cd4903023a02 ; ENGLISH ABSTRACT: The precise order, quantity, and nature of genomic rearrangements required to convert one genome into another serve as fundamental parameters in comparative evolutionary genomics. Current computational models for studying these transformations frequently omit biological constraints, resulting in systematic errors such as miscalculations of rearrangement frequencies. To address this gap, we present Genolve+, an open-source command-line tool that incorporates two critical biological parameters: intergenic region length conservation and three-dimensional chromatin spatial proximity. This framework enables more precise reconstruction of evolutionary trajectories between closely related genomes. Application of Genolve+ to Saccharomyces cerevisiae lineages (a forest strain and its domesticated counterpart) revealed 13 evolutionary events required for genomic transformation: 9 conservative (7 translocations, 1 fission, 1 fusion) and 4 non-conservative (2 insertions, 2 deletions), yielding a minimal edit distance of 13. Conservative events dominated evolutionary dynamics, contributing disproportionately to reduced genomic divergence, while non-conservative events incurred greater evolutionary "cost." Notably, these rearrangements localized to distinct genomic loci: recombination hotspots (associated with sequence-driven instability) and three-dimensional chromatin contact regions (linked to spatial genome organization). This spatial specificity underscores the dual influence of sequence context and higher-order nuclear architecture in shaping evolutionary pathways. The analysis revealed a strong correlation between recombination hotspots, regions of three-dimensional chromatin contact, ... |
| Document Type: | thesis |
| File Description: | xv, 181 pages : illustrations; application/pdf |
| Language: | English |
| Relation: | https://scholar.sun.ac.za/handle/10019.1/134581 |
| Availability: | https://scholar.sun.ac.za/handle/10019.1/134581 |
| Rights: | Stellenbosch University |
| Accession Number: | edsbas.5A8FAD8F |
| Database: | BASE |
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