海南2种龙脑香科植物叶绿体基因组密码子偏好性分析

Codon Usage Bias in Chloroplast Genomes of Two Species of Dipterocarpaceae in Hainan

为分析坡垒、青梅叶绿体基因组密码子偏好性使用模式,运用CodonW、R语言等软件对49条坡垒叶绿体基因组密码子和51条青梅叶绿体基因组密码子进行中性绘图、ENC-plot等系统分析。结果表明,坡垒、青梅叶绿体基因组有效密码子数(ENC)均超过50,其密码子偏好性较弱。中性绘图分析发现,坡垒和青梅GC3与GC12相关不显著,回归斜率分别为0.21、0.18,说明密码子偏好性主要受到自然选择的影响。ENC-plot分析结果显示,两者均约有20个基因分布在ENC期望值曲线附近,这部分基因密码子偏性主要受突变影响。相对同义密码子使用度(RSCU)分析发现,坡垒、青梅最优密码子各有17、15个,且多以A/T结尾,但两者中相同的最优密码子仅有11个。其中,坡垒密码子第1位碱基及序列长度对叶绿体基因组密码子偏性影响较大;青梅则是第3位碱基组成对密码子偏性影响较大。综上,坡垒、青梅叶绿体基因组密码子偏性是由选择和突变及其它因素共同作用形成的,但存在一定差异。

In order to analyze the codon usage patterns of the chloroplast genomes of Hopea hainanensis and Vatica mangachapoi,49 and 51 CDS(coding DNA sequences)were selected respectively from the chloroplast genomes of Hopea hainanensis and Vatica mangachapoi to analyze the neutrality plot and ENC-plot based on CodonW,R language and other software.The results showed that the effective codon number(ENC)of the two chloroplast genomes coding sequence were over 50,indicating that the bias of codons was weak.The neutral analysis found that the correlation between GC3 and GC12 of Hopea hainanensis and Vatica mangachapoi was not significant,and the slope of the regression curve were 0.21 and 0.18,suggesting that codon bias was mainly affected by natural selection.The ENC-plot analysis revealed that about 20 genes of chloroplast genome were distributed near the expected value curve of ENC,and their codon bias was mainly affected by mutation.The RSCU analysis showed that there were respectively 17 and 15 optimal codons for Hopea hainanensis and Vatica mangachapoi chloroplast genomes,and the most preferred codons ended with A and T,but only 11 optimal codons were the same.Among them,the first base of codon and sequence length of Hopea hainensis chloroplast genome had great influence on the codon bias of chloroplast genome,while the third base of codon of Vatica mangachapoi chloroplast genome had great influence on the codon bias.To sum up,the codon bias of the chloroplast genomes of Hopea hainensis and Vatica mangachapoi was formed by selection,mutation and other factors,but there were some differences.