Analysis on bias of functional gene codon of Eleutherococcus senticosus
10.7501/j.issn.0253-2670.2013.05.020
- Author:
Zhao-Bin XING
1
Author Information
1. College of Life Science
- Publication Type:Journal Article
- Keywords:
Bias index;
Codon usage;
Eleutherococcus senticosus (Rupr. et Maxim.) Maxim.;
Functional genes;
GC content;
Optimized codon
- From:
Chinese Traditional and Herbal Drugs
2013;44(5):598-603
- CountryChina
- Language:Chinese
-
Abstract:
Objective: To analyze the codon usage of functional genes in Eleutherococcus senticosus and their influencing factors. Methods: The multivariate statistical analysis and correspondence analysis were carried out using CodonW and SPSS software with codon of 17 genes selected from the functional genes of E. senticosus. Results: GC contents at the three positions of functional gene codons in E. senticosus was 51.03%, 41.23%, and 40.04%, all of which had a significant correlation coefficient (P < 0.05). The correlation coefficients with GC12 and GC3 were 0.262, and both were insignificant. The relative synonymous codon usage of 27 codons was greater than 1, among which 22 codons ended with A or T base. In the corresponding analysis, the first axis showed the variation of 22.78%, and there were significant correlation coefficients in codon adaptation, codon bias index, and GC3 (P < 0.01). The correlation coefficients were 0.686, 0.617, and 0.786, respectively, but they were insignificantly related with the effective number of codons (ENC). The second axis showed the variation of 19.28% and it was only significantly related with ENC (r = 0.635). Seventeen optimized codons in functional genes of E. senticosus were defined. Conclusion: All codons of functional genes in E. senticosus prefer to ending with A or T base. The codon usage bias is formed under the effects of mutation and selection.
