甘草属7种植物叶绿体基因组密码子使用偏好性分析  

Analysis of codon usage bias of chloroplast genome in seven Glycyrrhiza species

作　　者：代江鹏 蔡一鸣 刘巧珍 高晓霞 朱爽[1] DAI Jiang-peng;CAI Yi-ming;LIU Qiao-zhen;GAO Xiao-xia;ZHU Shuang(Guangdong Province Key Laboratory for Biotechnology Drug Candidates,School of Biopharmaceutics,Guangdong Pharmaceutical University,Guangzhou 510006,China;School of Pharmacy,Guangdong Pharmaceutical University,Guangzhou 510006,China)

机构地区：[1]广东药科大学、生命科学与生物制药学院广东省生物技术候选药物研究重点实验室,广东广州510006 [2]广东药科大学药学院,广东广州510006

出　　处：《中草药》2023年第9期2907-2916,共10页Chinese Traditional and Herbal Drugs

基　　金：广东省省级科技计划项目(2017A020213014)。

摘　　要：目的探究甘草属7种植物叶绿体基因组密码子使用模式及影响因素。方法从NCBI获取国内已有的7种甘草属植物叶绿体全基因组,筛选得到49条共有蛋白编码序列,使用codonW 1.44、EMBOSS、SPSS 26.0等分析密码子偏好性相关参数。结果7种甘草属物种叶绿体基因组密码子不同位置的GC含量均小于50%,共得到了29个高频密码子,其中有28个密码子第3位碱基为A/U,筛选得到的17个最优密码子第3位碱基均为A/U。7种甘草属植物叶绿体蛋白编码基因的ENC值均大于35,密码子偏好性较弱。PR2-plot分析、ENC-plot分析和中性绘图分析结果显示突变压力和自然选择均为这7种甘草属物种叶绿体基因组密码子偏好性形成的重要影响因素,但自然选择对密码子偏好性形成的贡献更大。基于叶绿体编码序列构建的系统发育树与基于RSCU的聚类分析结果具有一定的相似性,叶绿体基因组密码子偏好性与物种的系统发育关系存在一定的联系。结论7种甘草属植物叶绿体基因组密码子第3位倾向于使用A/U碱基,自然选择是密码子偏好性形成的主要影响因素。Objective To explore codon usage patterns and affecting factors of chloroplast genome in seven Glycyrrhiza species.Methods A total of 49 common protein coding sequences were screened from the complete chloroplast genomes of seven Glycyrrhiza species in China downloaded from the NCBI database.The relative parameters of codon usage bias were analyzed by codonW 1.44,EMBOSS,SPSS 26.0.Results All of the GC content of different codon positions in seven Glycyrrhiza species were less than 50%.The third base of 28 codons were A/U among 29 high-frequency codons,and all the third base of 17 optimal codons were A/U.The ENC values of all the chloroplast genomic protein coding genes in seven Glycyrrhiza species were more than 35,showing the weak codon usage bias.The analysis of PR2-plot,ENC-plot and neutral plot analysis revealed that both of mutation pressure and natural selection were the important factors influencing the formation of codon usage preference,but natural selection contributed more in the process.The similarity between phylogenetic tree based on the chloroplast coding sequences and RSCU cluster analysis indicated that the codon usage preference was associated with the phylogenetic relationship.Conclusion The third position of codon tends to use A/U base in seven Glycyrrhiza chloroplast genome,and natural selection is the main factor affecting the formation of codon usage bias.

关 键 词：叶绿体基因组 甘草属 密码子偏好性 最优密码子 粗毛甘草 光果甘草 胀果甘草 刺果甘草 圆果甘草 甘草 云南甘草 

分 类 号：R286.12[医药卫生—中药学]