Korean J Parasitol.  2015 Dec;53(6):689-697. 10.3347/kjp.2015.53.6.689.

Codon Usage Bias and Determining Forces in Taenia solium Genome

Affiliations
  • 1College of Veterinary Medicine, Jilin University, Changchun, 130000, P. R. China. caixp@vip.163.com
  • 2State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, P. R. China.

Abstract

The tapeworm Taenia solium is an important human zoonotic parasite that causes great economic loss and also endangers public health. At present, an effective vaccine that will prevent infection and chemotherapy without any side effect remains to be developed. In this study, codon usage patterns in the T. solium genome were examined through 8,484 protein-coding genes. Neutrality analysis showed that T. solium had a narrow GC distribution, and a significant correlation was observed between GC12 and GC3. Examination of an NC (ENC vs GC3s)-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENC (the effective number of codons) values were detected below the expected curve, suggesting 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. We also identified 26 optimal codons in the T. solium genome, all of which ended with either a G or C residue. These optimal codons in the T. solium genome are likely consistent with tRNAs that are highly expressed in the cell, suggesting that mutational and translational selection forces are probably driving factors of codon usage bias in the T. solium genome.

Keyword

Taenia solium; codon usage bias; translation selection; mutation bias; intron number

MeSH Terms

Animals
Base Sequence
Codon/*genetics
Evolution, Molecular
*Genome, Helminth
Helminth Proteins/*genetics
Molecular Sequence Data
Taenia solium/*genetics
Codon
Helminth Proteins
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