Comparative Genomics and the Evolution of Transposable Elements in Unicellular Eukaryotes

Abstract

Background
Transposable elements are mobile DNA sequences, which are ubiquitous in the majority of eukaryotic genomes. Unicellular eukaryotes have limited research on transposable elements and therefore the picture of evolution is far from conclusive. Similarly, codon usage bias, the frequency of synonymous codons present in a host species coding DNA, has been focused on multicellular organisms, with no clear explanation of the evolutionary pressures that drive bias in unicellular eukaryotic species.

Methods
Eight Kazachstania budding yeast species, and choanoflagellate species, Salpingoeca rosetta, were screened for the presence of mobile elements, with use of homology based methods. Protein and nucleotide phylogenies were constructed to review ancestral patterns and similarity across superfamilies. Codon usage statistics were employed to review patterns of bias in the host genes and mobile elements of the Kazachstania species, and S.rosetta, as well as two additional holozoan species, Monosiga brevicollis and Capsaspora owczarzaki.

Results
A diverse repetoire of transposable element families were uncovered in the species reviewed. A complete absence of DNA transposons was found in the Kazachstania species, however both classes of elements were uncovered in S. rosetta. Element phylogenies indicated vertical transfer for the majority of families, with the exception of one family in S. rosetta, which suggested acquisition by horizontal transfer. Patterns of codon usage were revealed in the genus Kazachstania and conservation was seen in the three holozoan species, with similar trends observed in the majority of host species mobile elements.

Conclusions
The known diversity of TE families for the yeast superfamily, and Choanoflagellatea has increased as a result of the study presented here. Codon usage bias for host genes and mobile elements provided evidence of selection, as well as mutational bias, suggesting that models of evolutionary pressures are more complex in unicellular eukaryotes.

Date of Award	2023
Original language	English
Supervisor	Martin Carr (Main Supervisor) & Jarek Bryk (Co-Supervisor)