Analysis of the Codon Usage Bias of Chloroplast Genome in Erigeron breviscapus (Vant.) Hand-Mazz

Purpose To understand the usage preference of plastome codons in Erigeron breviscapus (Vant.) Hand-Mazz.

Method47 CDS (coding DNA sequences) were screened using CodonW 1.4.2 software and CUSP program by searching the whole chloroplast genome sequence of E. breviscapus as the research objects; and the mapping analysis of neutral, ENC-plot, and PR2-plot were used in this study.

ResultThe ratio of GC base content at different positions in plastome codons was GC₁>GC₂>GC₃, which indicates that the base bias at the end of codons perfer A/T (U); the average effective number of codons was 47.18, therefore the codon usage bias is weak; through three kinds of mapping analysis, it was found that the main factor affecting the codon preference of plastome in E. breviscapus chloroplast genome was natural selection, other factors (such as mutation) also contributed; in the analysis of optimal codons, 18 optimal codons such as UUU, UUA and UUG were determined. All of these codons end with A and U, expect one was G.

ConclusionThe preference for the third position of the plastome in E. breviscapus prefer ending with A or U base. The codon usage pattern is affected by selection and other factors, among which selection has a greater effect. The results can provide a reference for the subsequent use of genetic engineering methods to modify the foreign gene codon and improve the expression of the transgene in the chloroplast of E. breviscapus.