Objective:To clarify the codon usage preference in the chloroplast genome of two orchids of the Ponerorchis and explore the influencing factors of codon preference.Methods:The codon selec-tion in the chloroplast genomes of two medicinal species of orchids was analyzed by CodonW,CUSP and SPSS.Results:Through the analysis of two species of medicinal plants of the Ponerorchis of the Orchidaceae,the content of GC codons in the chloroplast genomes of both species was found to be 35.8%to 37.3%,and the number of effective number of codons was 47.10%to 47.79%,indicating a weak codon preference.The results of neutral mapping,ENC-plot,PR2-plot and other studies showed that selection and mutation were the main factors affecting the codon usage preference of chlo-roplast genomes of two Ponerorchis medicinal plants.The relative synonymous codon usage(RSCU)values and effective number of codon(ENC)values were compared to obtain 65 optimal codons.The codon preference was the A/T ending,indicating that the codon usage bias was largely determined by natural selection.The usage bias of chloroplast genome was analyzed and verified by the clustering method.The key factors were GUU,UCA,CCA,ACA,UAA,GAU,UGU,AGA and AGG.Con-clusion:This study could provide a theoretical basis for the construction and optimization of a heterolo-gous protein expression vector in the chloroplast genome of Ponerorchis.
维普
万方数据
