扁蓿豆叶绿体基因组密码子偏好性分析

为阐明扁蓿豆（Medicago ruthenica）叶绿体基因组密码子使用模式，以其50条蛋白编码序列（CDS）为对象，利用软件CodonW 1.4.2、Excel以及在线程序对其ENC，RSCU，GC含量、中性绘图、PR2-plot、最优密码子等进行分析得到以下结果：基因组平均GC含量为40.58%，其中GC1>GC2>GC3；ENC的取值介于35.77～56.62之间，表明密码子使用偏好性较弱；基因组中共有30个密码子RSCU>1，其中29个以A/U结尾；ENC-plot绘图分析结果中多数基因分布于标准曲线下方，22个基因ENC比值在—0.05～0.05之间，密码子偏好性主要受选择影响；PR2-plot分析表明碱基T的使用频率大于A，G大于C，说明密码子偏好性还受其他因素影响；该基因组中共有UUU，UUA，ACU等11个最优密码子并均以A/U结尾。以上研究结果可为扁蓿豆叶绿体基因组优良基因利用提供理论与基础。

Codon Usage Bias of Chloroplast Genome in Medicago ruthenica

In order to elucidate the codon usage pattern of the chloroplast genome of Medicago ruthenica,a series of analyses such as the value range of the ENC,RSCU,GC content,neutral mapping,PR2-plot,and optimal codon were performed using the software CodonW 1.4.2,Excel,and online programs 50 protein-coding sequences (CDS). The results showed that the average GC content of the genome was 40.58%,with GC1 > GC2 > GC3;the values of ENC ranged from 35.77～56.62,indicating a weak preference for codon usage in M ruthenica;The correlation analysis showed that the correlation coefficient between GC₁₂ and GC₃ was 0.1685,which was not significant;the analysis showed that there were 30 codons in the chloroplast genome in M ruthenica with RSCU>1,29 of which ended in A/U;the ENC-plot analysis showed that most of the genes were distributed below the standard curve,and the ENC ratios of 22 genes were between —0.05 and 0.05,indicating that the codon M ruthenica of lucerne was mainly influenced by selection. PR2-plot analysis showed that base T was used more frequently than A,and G was used more frequently than C,indicating that the codon preference of the chloroplast genome was also influenced by other factors;11 optimal codons,including UUU,UUA,CUU,and ACU,were analyzed in the chloroplast genome and all ended with A/U. The results of the above study can provide some theory and basis for the utilization of excellent genes in the chloroplast genome of M ruthenica.