Subjects: Biology >> Botany >> Applied botany submitted time 2018-09-07 Cooperative journals: 《广西植物》
Abstract： Synonymous codons are used with different frequencies among both species and genes within the same genome. In order to analyze the codon usage patterns of the chloroplast genome of camphora tree, 53 CDS(Coding DNA Sequences)were selected from the chloroplast genome of camphora tree and analyzed the codon usage pattern and bias by CodonW, EMBOSS, R language and other softwares. The results showed that the effective codon number (ENC) of the chloroplast gene ranged from 36.82 to 59.30, indicating that bias of codons was weak. There were 32 codons with relative codon usage greater than 1, of which 28 were rich in A and U, indicating that the 3rd position of codon prefers A and U genetic bases. Neutral analysis found that the correlation between GC3 and GC12 was not significant, and the slope of the regression curve was 0.049, suggesting that codon bias was mainly affected by natural selection, while the ENC-plot analysis found that most genes fell below and around the curve. It was shown that the mutation also affected the formation of codon bias. Eventually， 9 codons (UUU, CUU, UCA, ACA, UAU, AAU, GAU, UGA, GGA) were identified as the optimal codons for the chloroplast genome of camphora tree.
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