Codon Usage Bias and Determining Forces in Taenia solium Genome

The Korean Journal of Parasitology
Xing YangXuepeng Cai

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.

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Citations

May 17, 2017·The Korean Journal of Parasitology·Young-An Bae
Jan 28, 2020·Genome Génome / Conseil National De Recherches Canada·Aasim MajeedPankaj Bhardwaj
Aug 17, 2018·International Journal of Molecular Sciences·Xu ZhangJiyong Zhou
Sep 29, 2018·Food Science and Biotechnology·Prosenjit PaulSupriyo Chakraborty
Sep 24, 2019·Frontiers in Genetics·Guillermo LamollePablo Smircich
Aug 7, 2018·Molecular and Biochemical Parasitology·Lucas L MaldonadoLaura Kamenetzky

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Software Mentioned

CodonW
tRNAscan
SPSS
SE

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