Dissertation/ Thesis
Προβολή σε EDS

Identification of a possible sequence of structural events associated with genome evolution

Λεπτομέρειες βιβλιογραφικής εγγραφής
Τίτλος: Identification of a possible sequence of structural events associated with genome evolution
Συγγραφείς: Dakurah, Ottovon Bismark
Συνεισφορές: Patterton, Hugh-George, Stellenbosch University. Faculty of Science. Centre for Bioinformatics and Computational Biology.
Στοιχεία εκδότη: Stellenbosch University
Έτος έκδοσης: 2025
Συλλογή: Stellenbosch University: SUNScholar Research Repository
Θεματικοί όροι: Genomics, Comparative genomics, Saccharomyces cerevisiae -- Genetics -- Computer simulation, Genomes -- Evolution -- Mathematical models, Bioinformatics -- Computer simulation, Computational biology -- Mathematical models, UCTD
Περιγραφή: 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 Unpublished doctoral dissertation.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, ...
Τύπος εγγράφου: thesis
Περιγραφή αρχείου: xv, 181 pages : illustrations; application/pdf
Γλώσσα: English
Relation: https://scholar.sun.ac.za/handle/10019.1/134581
Διαθεσιμότητα: https://scholar.sun.ac.za/handle/10019.1/134581
Rights: Stellenbosch University
Αριθμός Καταχώρησης: edsbas.5A8FAD8F
Βάση Δεδομένων: BASE
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  – Url: https://scholar.sun.ac.za/handle/10019.1/134581#
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  Data: Patterton, Hugh-George<br />Stellenbosch University. Faculty of Science. Centre for Bioinformatics and Computational Biology.
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  Data: 2025
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  Data: 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, ...
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      – SubjectFull: Comparative genomics
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      – SubjectFull: Saccharomyces cerevisiae -- Genetics -- Computer simulation
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      – SubjectFull: Genomes -- Evolution -- Mathematical models
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      – TitleFull: Identification of a possible sequence of structural events associated with genome evolution
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            NameFull: Dakurah, Ottovon Bismark
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              Y: 2025
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