Mutation and selection cause codon usage and bias in mitochondrial genomes of ribbon worms (Nemertea)

Abstract

The phenomenon of codon usage bias is known to exist in many genomes and it is mainly determined by mutation and selection. To understand the patterns of codon usage in nemertean mitochondrial genomes, we use bioinformatic approaches to analyze the protein-coding sequences of eight nemertean species. Neutrality analysis did not find a significant correlation between GC12 and GC3. ENc-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENc values are below it. ENc-plot suggested that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally and we propose that codons containing A or U at third position are used preferentially in nemertean species, regardless of whether corresponding tRNAs are encoded in the mitochondrial DNA. Context-dependent analysis indicated that the nucleotide at the second codon position slightly affects synonymous codon choices. These results suggested that mutational and selection forces are probably acting to codon usage bias in nemertean mitochondrial genomes.

Figure 1. Neutrality plot (GC12 against GC3).

Cephalothrix hongkongiensis; the regression line is y = −1.0593x+0.4625, R² = 0.2862. Cephalothrix sp.; the regression line is y = −0.4401x+0.3755, R² = 0.0857. Lineus alborostratus; the regression line is y = 0.4684x+0.2799, R² = 0.1746. Lineus virids; the regression line is y = 0.4684x+0.2799, R² = 0.1746. Zygeupolia rubens; the regression line is y = −0.6239x+0.5701, R² = 0.1583. Emplectonema gracile, the regression line is y = 0.3281x+0.1697, R² = 0.0173. Nectonemertes cf. mirabilis; the regression line is y = 0.4506x+0.2396, R² = 0.0968. Paranemertes cf. peregrina; the regression line is y = 0.0422x+0.3429, R² = 0.0008.

Figure 2. Relation between GC3 and ENc (ENc-plot).

ENc were plotted against GC content at the third codon position. The expected ENc from GC3 are shown as a standard curve.

Figure 3. PR2-bias plot [A3/(A3 + T3) against G3/(G3+ C3)].

Cephalothrix hongkongiensis; average position is x = 0.2396±0.0951, y = 0.5503±0.2980. Cephalothrix sp.; average position is x = 0.2941±0.0632, y = 0.4821±0.2900. Lineus alborostratus; average position is x = 0.2729±0.0435, y = 0.7299±0.0588. Lineus virids; average position is x = 0.1800±0.0533, y = 0.7734±0.1243. Zygeupolia rubens; average position is x = 0.1902±0.0597, y = 0.9176±0.0701. Emplectonema gracile, average position is x = 0.2288±0.0430, y = 0.7031±0.1273. Nectonemertes cf. mirabilis; average position is x = 0.1433±0.0432, y = 0.7752±0.1114. Paranemertes cf. peregrina; average position is x = 0.2270±0.0695, y = 0.8814±0.0814.

Figure 4. Frequency ratios [R(YZ)] of 12 dinucleotides at second and third codon positions.

Values are averaged from eight nemertean species.