Tang Yi, Cho Pyo Yun, Kim Tae Im, Hong Sung-Jong
Department of Parasitology, Chung-Ang University College of Medicine, Tongjak-gu, Seoul 156-756, Republic of Korea.
Exp Parasitol. 2007 Feb;115(2):187-91. doi: 10.1016/j.exppara.2006.08.007. Epub 2006 Oct 5.
Codon usage in Clonorchis sinensis was analyzed using 12,515 codons from 38 coding sequences. Total GC content was 49.83%, and GC1, GC2 and GC3 contents were 56.32%, 43.15% and 50.00%, respectively. The effective number of codons converged at 51-53 codons. When plotted against total GC content or GC3, codon usage was distributed in relation to GC3 biases. Relative synonymous codon usage for each codon revealed a single major trend, which was highly correlated with GC content at the third position when codons began with A or U at the first two positions. In codons beginning with G or C base at the first two positions, the G or C base rarely occurred at the third position. These results suggest that codon usage is shaped by a bias towards G or C at the third base, and that this is affected by the first and second bases.
利用来自38个编码序列的12515个密码子对华支睾吸虫的密码子使用情况进行了分析。总GC含量为49.83%，GC1、GC2和GC3含量分别为56.32%、43.15%和50.00%。有效密码子数收敛于51 - 53个密码子。当绘制密码子使用情况与总GC含量或GC3的关系图时，密码子使用情况与GC3偏好相关。每个密码子的相对同义密码子使用情况显示出单一的主要趋势，当密码子的前两个位置以A或U开头时，该趋势与第三位的GC含量高度相关。在前两个位置以G或C碱基开头的密码子中，并第三位很少出现G或C碱基。这些结果表明，密码子使用情况受第三位对G或C的偏好影响，并且这受到第一位和第二位碱基的影响。
