Objective Davidia involucrata is the only existing tertiary relict plant of genus Davidia in the family Nyssaceae. It is a unique endangered tree species under first-class protection in China. The synonymous codon usage bias (SCUB) of chloroplast genome and its main influencing factors were analyzed to provide a reference for further research at the molecular level, species conservation and germplasm innovation of the D. involucrata.
Method The complete chloroplast genome of D. involucrata was downloaded from the NCBI online database and the protein-coding sequences were screened. The effective number of codon (ENC), codon adaptation index (CAI), the relative synonymous codon usage (RSCU), and the contents of four bases, A, T, C, and G in the codon were calculated by CodonW software. Finally, the correlation between the parameters were calculated and the plots were maken using R software.
Result (1) A total of 59 protein-coding sequences were screened from the chloroplast genome of D. involucrata. The average guanine and cytosine bases (GC) content and the average GC content of the third base of the codons were 38.33% and 30.68%, respectively. The average CAI was 0.16 and the average ENC was 46.55, indicating that the chloroplast genome gene expression level of D. involucrata was low and the codon use bias was weak. (2) Enc-plot, PR2-plot, neutral plot and correspondence analysis revealed that selection pressure was the most important factor affecting SCUB of D. involucrata chloroplast genome. (3) A total of 12 optimal codons were selected.
Conclusion The SCUB of chloroplast genome in D. involucrata is weak, and its SCUB is not only mainly affected by selection pressure, but also affected by factors such as mutation pressure, base composition and gene expression level. Meanwhile, a total of 12 optimal codons are selected, which can be used in future genetic improvement and germplasm innovation research of D. involucrate.
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