原晓龙 李云琴 张劲峰 王毅

摘 要： 为了解降香黄檀叶绿体基因组密码子使用模式，该文利用Codon W 1.4.2和在线软件CUSP对降香黄檀叶绿体基因组中的52条基因编码序列密码子进行中性绘图、ENC-plot和PR2-plot分析。结果表明：降香黄檀叶绿体基因组密码子的3个位置上GC含量依次为GC1（46.01%）>GC2（38.98%）>GC3（27.80%）。有效密码子数（ENC）范围为37.66～54.43，及ENC值>45的有37个;RSCU>1的密码子有29个，其中16个以U结尾、12个以A结尾。这些说明其偏好以A和U结尾，且偏性较弱。中性绘图分析显示GC12与GC3的相关系数为0.250，相关性不显著，回归系数为0.394;ENC-plot分析显示ENC比值位于-0.05～0.05区间外的基因有38个;PR2-plot分析说明在碱基的使用频率方面，U>A、G>C，说明降香黄檀叶绿体基因组密码子偏好性主要受选择的影响;19个密码子被确定为最优密码子。该研究为降香黄檀叶绿体基因工程、遗传多样性分析等研究提供了科学参考依据。

关键词： 降香黄檀， 叶绿体基因组， 密码子偏好性， 选择

中图分类号： Q755

文献标识码： A

文章编号： 1000-3142（2021）04-0622-09

Abstract： To comprehend the codon usage pattern of chloroplast genome in Dalbergia odorifera， the 52 coding DNA sequences were analyzed to obtain to the results of neutrality plot， ENC-plot and PR2-plot analysis using Codon W 1.4.2 and online software CUSP in the present study. The results were as follows： The GC content in the three positions of codons from the chloroplast genome of D. odorifera was GC1 （46.01%）>GC2 （38.98%）>GC3 （27.80%） successively. The range of effective number codon was from 37.66 to 54.43， and there were 37 genes when ENC value was greater than 45， and there were 29 genes when RSCU value was greater than 1， including 16 genes ending with U and 12 genes ending with A. These suggest that the codons prefer ends with A and U， and have a weak bias. The neutrality plot showed that there was no significant correlation between GC3 and GC12， the correlation coefficient was 0.250， and the regression coefficient was 0.394; ENC-plot analysis revealed that there were 38 genes which ENC ratio located beyond the section from -0.05 to 0.05; PR2-plot analysis showed that U>A and G>C in the base usage frequency. These all illustrated that the codon usage bias in the chloroplast genome of D. odorifera was mainly affected by mutation; 19 codons were identified as the optimal codon. The present study could be useful in the chloroplast genetic engineering and genetic diversity analysis of D. odorifera.

Key words： Dalbergia odorifera， chloroplast genome， codon usage bias， selection

在生物體传递遗传信息的过程中，作为联结核酸和蛋白质的密码子扮演着重要的角色（Zhang et al.， 2019），构成基因组的4种核苷酸可形成64种密码子，各密码子与氨基酸相对应，除甲硫氨酸和色氨酸外，其余18种氨基酸均有2～6个密码子，这些编码同一氨基酸的不同密码子被称为同义密码子（synonymous codon）（Duret， 2002）。在翻译过程中，每个氨基酸相对应同义密码子的使用频率存在差异，即有的同义密码子使用频率高于其他同义密码子，这种现象被称为密码子偏好性（codon usage bias）（Romero et al.， 2000）。密码子偏好性广泛存在于不同生物中，是物种在长期进化过程中受……