Atzinger, Aletheia Tamewitz
(2021)
Dinucleotide Periodicity: A genomic Architecture That Shapes Evolution.
Doctoral Dissertation, University of Pittsburgh.
(Unpublished)
Abstract
Despite rampant gene transfer among distantly related organisms, bacteria still cluster into groups with strong genotypic and phenotypic cohesion. One proposed model is that successful donors are preferentially those that are more closely related to the recipient; however, the mechanisms for limiting gene transfer remain unknown. It has been demonstrated that maintenance of information embedded within and between genes, termed genomic architecture, affects gene exchange. Because this information is important, the acquisition of genes that disrupt it incurs a fitness detriment for the organism. Unless the benefit of an acquired gene is strong enough to offset the detriment of architecture disruption, it will likely be eliminated from the population. Here we identify the overabundance of particular dinucleotide motifs at intervals of ~10.5 bp, termed genomic periodicity, as another such genomic architecture. We demonstrate that, on average, genomic periodicity differs more between organisms with increased phylogenetic distance. We show that this architecture is under selection and that periodicity of a core set of motifs is maintained in all domains of life. We demonstrate that recently acquired genomic islands are more similar in periodicity to host genomes than would be seen at random. Thus, similarity in genomic periodicity affects gene flow in a manner that contributes to genotypic and phenotypic cohesion within taxa. We explore the interaction between periodicity and a previously published architecture and show that, on average, they act as additive barriers to gene exchange. However, we also demonstrate that distantly related taxa occasionally converge upon the same architecture. We then propose a model for the ramifications of the maintenance of multiple genomic architectures: if distantly related taxa coincide in multiple architectures, this may remove some detriments to gene exchange and thus create “wormholes” for acquiring novel abilities. This work will provide a foundation for exploring the mechanisms underlying the biased gene exchange that shapes microbial evolution.
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Details
| Item Type: |
University of Pittsburgh ETD
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| Status: |
Unpublished |
| Creators/Authors: |
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| ETD Committee: |
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| Date: |
18 December 2021 |
| Date Type: |
Publication |
| Defense Date: |
2 August 2021 |
| Approval Date: |
13 September 2024 |
| Submission Date: |
21 September 2021 |
| Access Restriction: |
No restriction; Release the ETD for access worldwide immediately. |
| Number of Pages: |
187 |
| Institution: |
University of Pittsburgh |
| Schools and Programs: |
Dietrich School of Arts and Sciences > Biological Sciences |
| Degree: |
PhD - Doctor of Philosophy |
| Thesis Type: |
Doctoral Dissertation |
| Refereed: |
Yes |
| Uncontrolled Keywords: |
genomic architecture
genomic periodicity
lateral gene transfer |
| Date Deposited: |
13 Sep 2024 18:56 |
| Last Modified: |
13 Sep 2024 19:04 |
| URI: |
http://d-scholarship.pitt.edu/id/eprint/41956 |
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