Clonorchis sinensis: codon usage in nuclear genes |
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Authors: | Tang Yi Cho Pyo Yun Kim Tae Im Hong Sung-Jong |
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Institution: | a Department of Parasitology, Chung-Ang University College of Medicine, Tongjak-gu, Seoul 156-756, Republic of Korea b Institute of Parasitic Diseases, Zhejiang Academy of Medical Sciences, 182 Tian Mu Shan Rd. Hangzhou, Zhejiang 310013, PR China |
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Abstract: | 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. |
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Keywords: | Clonorchis sinensis Trematode Synonymous codons Codon usage Bias Nc Effective number of codons RSCU relative synonymous codon usage GC1 GC2 GC3 frequency of codons with G or C at the first second or third position respectively |
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