Analysis on Codon Usage Bias of Chloroplast Genome in Ampelopsis grossedentata

Abstract

【Objective】Ampelopsis grossedentata belongs to Ampelopsis of the Vitaceae family and it has great medicinal value. The chloroplast genome codon usage bias of A. grossedentata and its main influencing factors are analyzed with a view to providing a reference for chloroplast genomics research, species protection and germplasm innovation of A. grossedentata.【Method】The complete genome sequence of A. grossedentata chloroplast was downloaded from the NCBI online database, and the protein coding sequence was screened. The effective number of codons (ENC), the relative synonymous codons usage (RSCU), and the GC content of the three codons of each gene were calculated by using CodonW software. The correlation between the parameters was calculated and mapped by R software.【Result】A total of 59 protein coding sequences are screened from the chloroplast genome of A. grossedentata. The total average GC content and average GC content of the third base of the codon are 37.98% and 29.45%, respectively. The ENC value ranges from 37.39 to 57.12, suggesting that the chloroplast genome codon use of A. grossedentata has a weak bias. ENC-plot analysis, PR2-plot analysis and neutral plot analysis reveal that natural selection is the most important factor affecting the codon usage bias of the A. grossedentata chloroplast genome. In addition, 13 optimal codons are recognized, including UUU, CUA, AUA, UCA, CCA, ACA, GCA, CAU, GAU, UGA, AGA, GGA and GGG.【Conclusion】The study results provide references for phylogeny and evolution of chloroplast genome codon in A. grossedentata.

Keywords

• chloroplast
• genetic evolution
• codon usage bias
• ampelopsis grossedentata