Comparative Genomics and the Evolution of Transposable Elements in Unicellular Eukaryotes

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.