Abstract
Introduction: Carcharodon carcharias (great white shark) is a species of large mackerel shark in the Chondrichthyes (cartilaginous fish) classification, with an annotated genome that is readily available, despite this not much research has been done into the mechanismsbehind the codon bias it exhibits. Codon bias is the unequal usage of synonymous codons over others when encoding specific amino acids. For example, Phenylalanine can use either UUU or UUC, it is expected that the usage of these codons would be split 50/50 however this is not the case. In highly expressed genes, optimal codons are significantly enriched, whilst in genes that have a low expression codon usage is random, optimal codons are those that are abundant in higher frequency for the higher expressed genes when compared to genes have a low expression. The TAPSILVR amino acids are a group of high degeneracy amino acids that possess the ability to undergo deamination when adenosine is present at the 34th position in the tRNA. Adenosine gets deaminated into inosine which can bind to A,T and C codons.
Method: optimal codons were identified for C. carcharias via expression analysis using CodonW. The expression of the genes was calculated for by mapping a transcriptome file from NCBI onto the sharks CDS and the length of each gene was divided by the amount of reads to give a proxy for expression. These were then separated into the top 5% and bottom 5% expressed genes. CodonW was then used to calculate the frequency of codons in these genes with optimal codons being identified as those that have a significantly higher frequency in the top5% expressed genes than those in the bottom 5%. tRNA was also analysed for 20 Chondrichthyes, including C. carcharias using tRNAScan-SE to test for translational efficiency. The most abundant tRNA gene for each amino acid was then calculated and put onto a phylogenetic tree. Finally, FOP for domain and non-domain coding proteins were then calculated in the top 100 most expressed genes along with flanking GC content to test for mutation pressure and translational accuracy. Finally, the Frequency of Optimal Codons (FOP) for domain and non-domain proteins were then calculated to test for potential selection for translational accuracy.
Results: C. carcharias had GC ending optimal codons, despite its AT rich genome. This showed consistency with selection for translational efficiency, especially when paired with the results of the tRNA analysis which showed that 53% of optimal codons corresponded to their respective major tRNA gene. As well as this FOP analysis and flanking GC content both showed results that would suggest that mutation pressure and selection for translational accuracy are also present. Whilst C. carcharodon also had a large amount of TAPSILVR tRNAs with adenosine at t34 meaning that it can be deaminated into inosine by ADAT.
Conclusions: Codon bias in C. carcharias is due to different forces that act on the genome. Highly expressed genes tend to be selected for with selection for efficiency and accuracy both influencing their codon usage, whilst genes that are not highly expressed tend to have their codon usage driven by mutation, this can be seen with the small difference between C. carcharias ’ GC content of 0.454 and GC3s of 0.453.
| Date of Award | 25 Jun 2025 |
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| Original language | English |
| Supervisor | Martin Carr (Main Supervisor) & Jarek Bryk (Co-Supervisor) |