Analysis of Codon Usage Bias in the Chloroplast Genome of A.heterotro-poides Fr.Schmidt var.mandshuricum(Maxim.)Kitag.
To determine codon usage bias and the causes in chloroplast genome of Asarum heterotropoides Fr.Schmidt var.mandshuricum(Maxim.)Kitag..The Codon W 1.4.2 software and CUSP program were employed to analyze the codon usage characteristics of 50 CDS sequences after screening,and the optimal codon was determined by neutral plotting,ENC-plot and PR2-plot.The results showed that the general trend of GC content in different positions of the chloroplast genome codon was GC1(47.60％)＞GC2(40.25％)＞GC3(30.96％),significant correlation was found between ENC and GC3.There were 31 codons with RSCU value greater than 1,of which 30 codons ended with A/U,and only 1 codon ended in G.It proved that the third base of codon tend to use the codons ending with A/U.The range of ENC from 38.10 to 58.19,and the average content was 48.77,which indicated that codons bias was weaker.Further analysis showed that the codon preference of chloroplast genome of A.heterotropoides Fr.Schmidt var.mandshuricum(Maxim.)Kitag.was mainly influenced by natural selection.Taking ENC value and RSCU value as reference,a total of 18 optimal codons were screened out,there are 17 codons that all ended in A/U except for UUG.The study can provided a basis for the chloroplast genetic engineering,environmental adaptation and phylogenetic of A.heterotropoides Fr.Schmidt var.mandshuricum(Maxim.)Kitag..
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