title: Codon Usage Bias and Determining Forces in Taenia solium Genome.
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.
authors.affiliation: College of Veterinary Medicine, Jilin University, Changchun, 130000, P. R. China ; State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, P. R. China.
authors.forename: Xing
authors.initials: X
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, P. R. China.
authors.forename: Xusheng
authors.initials: X
authors.lastname: Ma
authors.affiliation: College of Veterinary Medicine, Jilin University, Changchun, 130000, P. R. China.
authors.forename: Xuenong
authors.initials: X
authors.lastname: Luo
authors.affiliation: College of Veterinary Medicine, Jilin University, Changchun, 130000, P. R. China.
authors.forename: Houjun
authors.initials: H
authors.lastname: Ling
authors.affiliation: College of Veterinary Medicine, Jilin University, Changchun, 130000, P. R. China.
authors.forename: Xichen
authors.initials: X
authors.lastname: Zhang
authors.affiliation: College of Veterinary Medicine, Jilin University, Changchun, 130000, P. R. China.|State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, P. R. China.
authors.forename: Xuepeng
authors.initials: X
authors.lastname: Cai
mesh_terms: D000818:Animals; D001483:Base Sequence; D003062:Codon / Q000235:genetics*; D019143:Evolution, Molecular; D049751:Genome, Helminth; D015801:Helminth Proteins / Q000235:genetics*; D008969:Molecular Sequence Data; D041201:Taenia solium / Q000235:genetics*
chemical_list: D003062:Codon; D015801:Helminth Proteins
keywords: Taenia solium; codon usage bias; intron number; mutation bias; translation selection