Codon Usage

Codon usage in labyrinthulomycete coding sequences

We analyzed the recently available whole genome sequences from two thraustochytrids (Aurantiochytrium limacinum ATCC MYA-1381, Schizochytrium aggregatum ATCC 28209) and one aplanochytrid (Aplanochytrium PBS07) (Table 1).

Table 1. Labyrinthulomycete genome sequencing and annotation results (Joint Genome Institute).

Species Size (Mb)/ coverage # scaffolds N50/ L50 # gaps # proteins predicted Introns per gene/ Median length %EST mapped
Aplanochytrium 35.77/ 108x 207 19/ 0.72 316 11892 2.75/ 71 97.7
Schizochytrium 40.85/ 72x 283 15/ 0.64 1953 10612 1.5/ 345 97
Aurantiochytrium 60.93/ 31x 101 10/ 2.46 937 14859 1.5/ 494 96

 

Figure 1. Boxplots of (A) Relative synonymous codon usage and (B) codon frequencies across three labyrinthulomycetes in comparison to other species. Outliers are labeled. CLICK IMAGE TO ENLARGE.

We calculated the genome-wide relative synonymous codon usage (RSCU; Fig. 1A), codon frequencies (Fig. 1B) and GC content (Table 2) for predicted coding sequences from each of the three species.

We compared these to other stramenopiles: the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana, and the oomycete Phytophthora sojae, as well as to the ascomycete fungus Saccharomyces cerevisiae. We found:

  • The stramenopiles have distinctly different patterns of codon usage than the yeast Saccharomyces.
  • The thraustochytrid Schizochytrium has codon usage more similar to the oomycete Phytophthora than to the other labyrinthulomycetes (Aplanochytrium and the thraustochytrid Aurantiochytrium).
  • In general Schizochytrium shows underutilization of codons ending in A or T, and overutilization for codons ending in G or C, with the divergence reaching significance as an outlier for some threonine, alanine, leucine, and arginine codons.
  • Although never indicated as an outlier, Phytophthora shows a similar codon use pattern as Schizochytrium.
  • The differences in codon usage are broadly consistent with the greater GC content of CDS in Schizochytrium (~63%) and Phytophthora (~59%) than the other genomes (~40 to 51%).

However, these comparisons also show that GC content is not the only factor associated with variations in codon usage patterns.

Table 2. GC content of coding sequences.

Aplanochytrium kerguelense 0.424
Aurantiochytrium limacinum 0.489
Phaeodactylum tricornutum 0.509
Phytophthora sojae   0.584
Saccharomyces cerevisiae   0.396
Schizochytrium aggregatum 0.628
Thalassiosira pseudonana 0.479

Analysis code for results presented above is available at protocols.io. The codon tables are available at Academic Commons.

This data was generated by Collier, Rest, et al. as part of a grant from the Gordon and Betty Moore Foundation.