Abstract
Panax ginseng is usually used as a famous plant medicine in many countries. In order to study the codon usage in whole chloroplast genome in Panax ginseng, whole chloroplast genome sequence is analyzed via codonW software and some results such as relationships between the codon adaptation index, frequency of optimal codons, codon bias index, effective number of codons, especially the relative synonymous codon usage are all discussed. Furthermore, PR2-bias plot, histogram GC content, Codon Bias Index are also analyzed for exploring the sequence characteristics of chloroplast genome in Panax ginseng. These results showed that codon usage bias in the chloroplast genome from Panax ginseng is weak, and the relative results could lay a foundation for other further study on the medicinal plant Panax ginseng.
Highlights
Panax ginseng is a commonly used medicinal plant in Traditional Chinese Medicine [1]
When discrimination of ginseng is concerned, Guisheng Li, et al analyzed the differences related mitochondrial from Russian wild ginseng [24], Jong-Hak Kim tended to think that the auxin repressed protein gene could be used to discriminate of Panax ginseng Meyer cultivar Chunpoong and American ginseng [25], Min-Jeong Lee, et al, studied the variation in the ginsenoside profiles of cultivated Panax ginseng C.A
CodonW [34] is used to calculate the Codon Adaptation Index (CAI), Frequency of Optimal Codons (Fop), Codon Bias Index (CBI), Effective Number of Codons (ENC), and so on, the calculated results are further processed for getting the Relative Synonymous Codon Usage (RSCU)
Summary
Panax ginseng is a commonly used medicinal plant in Traditional Chinese Medicine [1]. In this study, based on the previous studies, a genome comprehensive analysis of codon usage on whole chloroplast genome in medicinal plant Panax Ginseng is studied. Whole chloroplast genome in medicinal plant Panax Ginseng is downloaded from GenBank of NCBI, which
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