Clonorchis sinensis: codon usage in nuclear genes.
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.
Tang
Yi
Y
Department of Parasitology, Chung-Ang University College of Medicine, Tongjak-gu, Seoul 156-756, Republic of Korea.
Cho
Pyo Yun
PY
Kim
Tae Im
TI
Hong
Sung-Jong
SJ
D000596:Amino Acids / Q000235:genetics; D000818:Animals; D001482:Base Composition / Q000502:physiology; D002467:Cell Nucleus / Q000235:genetics; D003004:Clonorchis sinensis / Q000737:chemistry / Q000235:genetics*; D003062:Codon / Q000737:chemistry / Q000502:physiology*
D000596:Amino Acids; D003062:Codon