1. Codon usage bias in the N gene of rabies virus
- Author
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Hongyu Zhang, Sijia Lu, Chang Liu, Yuchen Zhang, Pengkun Yuan, Wanting He, Shuo Su, Yanjie Ji, and Ruyi Wang
- Subjects
0301 basic medicine ,Microbiology (medical) ,Biology ,medicine.disease_cause ,Microbiology ,Evolution, Molecular ,03 medical and health sciences ,Mutation Rate ,Genetics ,medicine ,Selection, Genetic ,Clade ,Codon ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Natural selection ,Phylogenetic tree ,Nucleotides ,Rabies virus ,Nucleoprotein ,030104 developmental biology ,Infectious Diseases ,Genetic typing ,Ribonucleoproteins ,Codon usage bias ,Mutation (genetic algorithm) ,Mutation - Abstract
Since its emergence, rabies virus (RABV) has been a major worldwide concern especially in developing countries. The nucleoprotein (N) of RABV is highly conserved and key for genetic typing, thus a better understanding of the N gene evolutionary trajectory can assist the development of control measures. We found that the N gene of RABV has a low codon usage bias with a mean effective number of codons (ENC) value of 56.33 influenced by both mutation pressure and natural selection. However, neutrality analysis indicated that natural selection dominates over mutation pressure. Additionally, we found that dinucleotide bias partly contributed to RABV codon usage bias. On the other hand, based on the clades of phylogenetic tree, we found that the evolutionary rate of the Africa 2 clade was the highest with a mean value of 3.75 × 10− 3 substitutions per site per year. Above all, our results regarding N gene of RABV codon usage will serve future RABV evolution research.
- Published
- 2017