Comparative analysis of codon usage in the genomes of SARS-CoV-2 and SARS virus(PDF)
《中国医学物理学杂志》[ISSN:1005-202X/CN:44-1351/R]
- Issue:
- 2023年第11期
- Page:
- 1402-1407
- Research Field:
- 医学生物物理
- Publishing date:
Info
- Title:
- Comparative analysis of codon usage in the genomes of SARS-CoV-2 and SARS virus
- Author(s):
- WANG Fangping1; WANG Zhijian1; SUN Yongping2; AN Zhanhai3
- 1.Department of Physics, School of Electronic Information and Electrical Engineering, Tianshui Normal University, Tianshui 741001, China 2. College of Physics and Electronic Information, Inner Mongolia Normal University, Hohhot 010021, China 3. Tianshui Tianjiabing Middle School, Tianshui 741000, China
- Keywords:
- Keywords: SARS-CoV-2 SARS virus dinucleotide GC content codon adaption index
- PACS:
- R318；R373
- DOI:
- DOI:10.3969/j.issn.1005-202X.2023.11.014
- Abstract:
- Abstract: Objective To analyze the genetic evolution and variation of coronavirus. Methods The codon usage bias and the codon context in the genes of SARS-CoV-2 and SARS virus were compared and analyzed using bioinformatics methods and biometric methods. Results The codon usage bias was observed in the two kinds of virus, with RSCU value varying from 0.10 to 2.67, and the codons preferred (preferred codons) and avoided (rare codons) were basically the same. The correlation analysis showed that the codon adaption index (CAI) was negatively correlated with the GC content at the third site of the codon (GC3) in the two viruses, and that the negative correlation in SARS-CoV-2 was higher than that in SARS (SARS-CoV-2: R2=0.76, P<0.001 SARS: R2=0.48, P<0.001). GC3 decreased with the increase of CAI which reflected the level of gene expression, suggesting highly expressed genes preferred the synonymous codons with low GC3. Though the analysis on the codon context between preferred codons and rare codons, it was found that there were significant differences in the nucleotide composition between preferred codons and rare codons, which were manifested as differences in GC and AT in different codon sites, reflecting the constraints of GC content on the synonymous codon usage bias. Conclusion GC content, codon context, nucleotide composition and gene expression level of SARS-CoV-2 and SARS virus are important factors affecting codon usage bias. The study has reference significance for the study on the genetic evolution and variation of SARS-CoV-2 and SARS virus.
Last Update: 2023-11-24