Department of Biological and Environmental Sciences, University of Gothenburg, Sweden.
Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China.
PLoS One. 2014 Jan 15;9(1):e85631. doi: 10.1371/journal.pone.0085631. eCollection 2014.
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.
密码子使用偏性现象存在于许多基因组中，主要由突变和选择决定。为了了解纽形动物线粒体基因组中密码子的使用模式，我们使用生物信息学方法分析了 8 种纽形动物的蛋白质编码序列。中性分析没有发现 GC12 和 GC3 之间有显著的相关性。ENc 图显示了一些处于或接近预期曲线的基因，但大多数低 ENc 值的点都在曲线下方。ENc 图表明，突变偏向在塑造密码子使用中起主要作用。奇偶校验规则 2 图（PR2）分析表明，GC 和 AT 没有按比例使用，我们提出在纽形动物中，无论线粒体 DNA 是否编码相应的 tRNA，第三位置含有 A 或 U 的密码子都被优先使用。上下文相关分析表明，第二密码子位置的核苷酸会略微影响同义密码子的选择。这些结果表明，突变和选择压力可能对纽形动物线粒体基因组的密码子使用偏性起作用。
