Dawson, Holly (2020) The Early Evolution of tRNA Modification in Eukaryotes. Masters thesis, University of Huddersfield.

Deamination of tRNA molecules has already been shown in holozoan species with the
evolution deemed to have occurred within the ancestor to the choanoflagellates, metazoans
and filastereans. The aim of this project is to determine an estimate of the origin of evolution
for this process, by providing evidence for this outside of the holozoans to the opisthokonts
and further still, across the eukaryotic supergroup if possible. The determination of a time
frame for this allows theories to be drawn regarding the possible expansion of this.

This research project used bioinformatic techniques modified from Southworth et al., (2018)
in order to analyse the genomes of species: Thecamonas trahens (Apusozoa), Fonticula alba
(Opisthokonta), Leishmania tarentolae (Excavata), Chondrus crispus (Archaeplastida),
Chlamydomonas reinhardtii (Archaeplastida) and Bigelowiella natans (Rhizaria). The optimal
codons for each species were determined using programs CodonW and SMALT in order to see
whether these perfectly matched the most abundant tRNA species, or whether deamination is
a possible explanation for why there is a lack of perfect matches. Other techniques such as
tRNAscan-SE-2.0 analyses on whole genome sequences for some species under investigation,
were utilised in order to see what tRNA genes are present, by analysing transcripts of the

BLAST analysis of modified and unmodified tRNA genes identified using the tRNAscan output
of their genome files showed that both copies were present within the species F. alba and T.
trahens. SMALT analyses of these transcriptome files identified multiple copies of both
variations within additional eukaryotic species which fall on the opposite side of the eukaryotic
root to the original species.

Initial results of T. trahens and F. alba provided direct evidence for the evolution of
deamination of tRNA being ancestral to the Opisthokonta group, and allowed this research to
undertake analysis of multiple additional species outside of the opisthokonts, where direct
evidence for deamination of tRNAs was identified within rhizarians (SAR), archaeplastids and

The aims this research project set out with have been achieved as the dataset generated by
this work provides evidence for deamination being an ancestral eukaryotic trait. One
explanation could be that this has undergone an expansion; from the deamination of the
previously identified arginine, isoleucine, serine and threonine amino acid tRNAs in bacterial
species, through their symbiosis with Archaea, forming the eukaryotes.

FINAL THESIS - Dawson.pdf - Accepted Version
Available under License Creative Commons Attribution Non-commercial No Derivatives.

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