天山雪莲叶绿体基因组密码子偏好性分析  

Preference analysis of codon usage in the chloroplast genome of Saussurea involucrate

作　　者：何亚玲 彭业军 李锦[1] 冯斌 秦玉杰 王爱英[1] 祝建波[1] HE Yaling;PENG Yejun;LI Jin;FENG Bin;QING Yujie;WANG Aiying;ZHU Jianbo(College of life Sciences,Shihezi University,Shihezi,Xinjiang 832003,China)

机构地区：[1]石河子大学生命科学学院,新疆石河子832003

出　　处：《石河子大学学报（自然科学版）》2022年第1期84-92,共9页Journal of Shihezi University(Natural Science)

基　　金：国家自然科学基金项目(31360053,KZ0016)。

摘　　要：分析天山雪莲叶绿体(cp)基因组密码子使用偏倚的一般模式和影响因素,为提高转基因植物外源基因的表达效率以及了解药用植物雪莲的基因功能研究提供了理论基础。利用生物信息学方法从雪莲叶绿体基因组中筛选出50条长度大于300 bp且以ATG为起始的蛋白编码基因为对象,找出导致密码子偏倚的影响因素。结果表明:第三位的GC平均含量为27.70%,有效密码子数(ENC)变化范围35.59~57.43之间;同义密码子相对使用度(RSCU)>1的密码子有30个,其中29个以A/U结尾;中性绘图显示GC_(3)和GC_(12)的相关系数为0.062,相关性不显著,回归曲线斜率为0.094 6;ENC-plot分析显示ENC比值位于-0.1~0.1区间的基因有37个,大部分基因沿抛物线轨迹分布,但也有几个低ENC的基因分布于曲线下方;奇偶偏好图(PR2-plot)分析显示,第3个碱基的密码子使用不平衡;对应分析结果表明,第1轴贡献率为17.61%,第2、3、4轴贡献率分别为11.59%、7.97%和5.8%,且第1轴与密码子适应指数(CAI)、密码子偏爱指数(CBI)呈负显著相关;最终确定了22个最优密码子,且均以A/U结尾。Analysis the general patterns and influencing factors of codon usage bias in chloroplast(cp) genome of Saussurea involucrate(S.involucrate),can provide a theoretical basis for improving the expression efficiency of exogenous genes in transgenic plants and understanding the gene function of the medicinal plant.In this study, 50 genes with the ATG as initiation codon and the sequence length being more than 300 bp being selected from the chloroplast genome of S.involucrate through bioinformatics method, was to find out the influencing factors of codon bias.The results showed that, the average of GC content in the third position was 27.70% and the range of Effective Number Codon(ENC) was from 35.59 to 57.43.The Relative Synonymous Codon Usage(RSCU) analysis found that 30 codons had a high RSCU value(>1),and 29 out of these 30 preferred A/U as the ending of the codon.The correlation coefficient between GC_(12)and GC_(3)showed no significant different through neutrality analysis, which the value of correlation coefficient was 0.062 and the regressive coefficient was 0.094 6.ENC-plot analysis revealed that the number of genes with the ENC ratio from-0.1 to 0.1 was 37,and most of genes were distributed as the parabolic trajectory.However, several candidate genes with low ENC value were below the expected curve.Parity Rule 2-plot(PR2-plot) analysis showed the unbalanced usage of the codon in third position.The contribution rate of 1 st axis was 17.61%,and the 2 st, 3 st, and 4 st axis contribution rates were 11.59%,7.97%,and 5.8% respectively.Moreover, the 1 st axis showed significant negative correlation with Codon Adaptation Index(CAI) and Codon Bias Index(CBI).Ultimately, 22 codons were identified as the optimal candidates with the end of A/U.

关 键 词：天山雪莲 叶绿体 基因组 密码子偏好性 最优密码子 

分 类 号：R282[医药卫生—中药学]