栽培大豆和野生大豆线粒体基因组密码子使用偏性的比较分析

为分析栽培大豆和野生大豆线粒体基因组的密码子使用特征差异,该文以其线粒体基因组编码序列为研究对象,比较其密码子偏性形成的影响因素和演化过程。结果表明:(1)栽培大豆和野生大豆线粒体基因组编码区的GC含量分别为44.56%和44.58%,说明栽培大豆和野生大豆线粒体编码基因均富含A/T碱基。(2)栽培大豆和野生大豆线粒体基因组密码子第1位、第2位GC含量平均值与第3位GC含量的相关性均呈极显著水平,说明突变在其密码子偏性形成中的作用不可忽略; PR2-plot分析显示,在同义密码子第3位碱基的使用频率上,嘌呤低于嘧啶; Nc-plot分析中Nc比值位于-0.1～0.2区间的基因数占总基因数的95%以上;突变和选择等多重因素共同作用影响了大豆线粒体基因组编码序列密码子使用偏性的形成。(3)有20、21个密码子分别被确定为栽培大豆和野生大豆线粒体基因组编码序列的最优密码子,其中除丝氨酸TCC密码子外均以A或T结尾。综上结果认为,栽培大豆线粒体密码子偏性的形成受选择的影响要高于野生大豆,这可能是栽培大豆由野生大豆经长期人工栽培驯化的结果。

Comparative analysis on codon usage bias in mitogenome of two species in genus Glycine

The characteristic of codon usage in mitogenome of wild and cultivated soybean was studied and compared to explore the main factors affecting codon usage bias and codon evolution. The results were as follows:(1)The GC content in the coding region of mitochondrial genome of cultivated soybean and wild soybean was 44.56% and 44.58%, respectively, which indicated that the coding sequences of soybean mitogenome was rich in A/T base.(2)PR2-plot analysis showed that the third base of codon usage was biased, where pyrimidine was used more frequently than purine; Nc-plot analysis revealed that the number of genes with Nc ratio in the range of -0.1-0.2 accounts for more than 95% of the total number of genes. The above-mentioned results showed that the multiple factors such as mutation and selection affected the formation of codon usage bias in soybean mitogenome. GC1 and GC2 value was significantly correlated with GC3, suggesting that codon bias in the mitogenome of cultivated and wild soybeans was mainly affected by mutation.(3)In addition, 20 and 21 codons were identified to be the optimal codons for the mitogenome of cultivated and wild soybeans, with most of the preferred synonymous codons ending with A or T base. The formation of mitochondrial codon bias of cultivated soybean was more affected by selection than that of wild soybean, which may be the result of long-term artificial cultivation and domestication of cultivated soybean.