Codon Usage Bias Analysis of Chloroplast Genome of Zelkove schneideriana
[Objective]The chloroplast genome codon usage bias of precious wood species Zelkove schneideriana and the main factors forming the bias were explored to provide the reference for utilizing excellent gene of chloroplast genetic engineering of Z.schneideriana and improving the gene expression efficiency.[Method]54 coding DNA sequences(CDS)in the chloroplast genome of Z.schneideriana were analyzed by Codon W 1.4.2 and CUSP.[Result]The GC content of the third base in the codons of chloroplast genome in Z.schneideriana was 26.70%,which was significantly lower than the first base of 46.39%and the second base of 38.94%;The ENC value ranged from 35.94 to 61.00,and CDS with ENC value more than 45 had 45,accounting for 83.33%in all testing genes.This showed that the codon usage bias in CDS region of chloroplast genome in Z.schneideriana was relatively weak.The neutrality plot and ENC-plot analysis showed that the natural selection had a significant influence on codon usage bias in the chloroplast genome of Z.schneideriana.PR2-plot analysis showed that most of the genes were located in the third quadrant,and the third base of the gene had a strong preference for T and C;The chloroplast genome with RSCU value greater than 1 had 26 codons,with bias ending with A or U bases,among which ending with U,A and G were 11,12 and 3 codons respectively.[Conclusion]There are many factors affecting codon usage bias of chloroplast genome of Z.schneideriana,among which natural selection is the main influencing factors,the GC content in the third base of chloroplast codon have significant effect on its genome codon bias,and UUG,AUU,UCU,CCU,UGA and AGG are the optimum codons of Z.schneideriana.
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