Master of Science (MSc)
Faculty of Science
Jonathan Mark Wilson
The stomach, which is physiologically defined in vertebrates by its function in acid-peptic digestion, has been lost independently multiple times during the evolution of the teleost fishes. The function of the stomach is facilitated by the proton pump H+/K+-ATPase, which acidifies the stomach, and pepsinogens, which are converted to proteolytic pepsins in this acidic environment. It is well documented that in agastric (stomachless) fish, the genes what code for the expression of this proton pump (atp4a and atp4b) and the pepsinogens (pga, pgb, pgf, pgc and cym,) are absent from the genome (with the exception of a single pepsinogen in agastric Takifugu). However, certain aspects of this genetic connection are still in question and involve a limited set of species. Therefore, the purpose of this thesis is to resolve this knowledge gap, focusing on the gastric genes atp4a and atp4b. This includes identifying loss events, reinforcing the correlation between gene loss and stomach loss, and provide insight into how gene loss is occurring, why it occurs, and why this trait remains fixed. This thesis was completed through a two-pronged approach involving both bioinformatics and molecular genetics. Genes were identified in silico though sequence alignment or directly through genomic DNA extraction and gene isolation using PCR (polymerase chain reaction). It was clear from the in silico analysis of 66 genomes that there was a direct correlation between the presence of atp4a and atp4b and the presence of the stomach. In incidence of loss, pseudogenization was not confirmed in any teleosts. The PCR screening of 33 vertebrates (29 teleosts) also demonstrated this relationship with the exception of the agastric Plotosidae, producing an amplicon for both atp4a and atp4b primer pairs. These findings were contextualized with the species evolutionary relationships, which allowed for the tracking of nine loss events. This included Cypriniformes, Perciformes, Tetraodontiformes, Syngnathiformes, Pleuronectiformes, Cyprinodontiformes, Beloniformes, and two loss events in the Gobiiformes. These results expanded on the relationship between stomach loss and the gastric genes, demonstrating the advantage of adopting a comparative genomic method for stomach phenotype prediction. Especially in cases where stomach presence is unclear with current identification methods.
Pfeifer, Louis, "A Genomic Investigation of the Stomach Phenotype in Teleosts" (2020). Theses and Dissertations (Comprehensive). 2237.