点地梅属10种植物叶绿体基因组密码子偏好性分析  

Analysis of codon bias in chloroplast genomes of ten plants in Androsace

作　　者：郭玉朋 史明伟 马虎 马彦军[2] 姚步青[3] GUO Yupeng;SHI Mingwei;MA Hu;MA Yanjun;YAO Buqing(Qinghai Provincial Key Laboratory of High Value Utilization of Characteristic Economic Plants,Qinghai Tibet Plateau Potentilla anserine Industry Research Institute,College of Ecological Environment and Resources,Qinghai Minzu University,Xining 810007,China;College of Forestry,Gansu Agricultural University,Lanzhou 730070,China;Key Laboratory of Restoration Ecology of Cold Area in Qinghai Province,Northwest Institute of Plateau Biology,Chinese Academy of Sciences,Xining 810008,China)

机构地区：[1]青海民族大学生态环境与资源学院,青海省特色经济植物高值化利用重点实验室,青海省蕨麻产业研究院,青海西宁810007 [2]甘肃农业大学林学院,甘肃兰州730070 [3]中国科学院西北高原生物研究所,青海省寒区恢复生态学重点实验室,青海西宁810008

出　　处：《中草药》2025年第4期1355-1365,共11页Chinese Traditional and Herbal Drugs

基　　金：青海民族大学研究生专业示范思政课程建设项目(SK-2022-09)。

摘　　要：目的研究点地梅属Androsace L.物种叶绿体基因组蛋白编码基因密码子的偏好性及其影响因素。方法测序了点地梅属1个物种(西藏点地梅)的叶绿体基因组,其他9物种的序列从NCBI下载。根据序列筛选条件,共得到41条共有序列。用CodonW 1.4.2计算相关参数,Python整理数据,R做相关性分析并绘图。结果点地梅属各物种密码子第1、2、3位置碱基组成GC含量表现为GC1>GC2>GC3,其中第3位GC含量最小。各位点GC含量相关性为GC1、GC2极显著,而两者与GC3相关性都不显著,说明3个位置GC含量变化机制不同。3个位置GC含量都小于50%,表明密码子倾向于使用A/U碱基,尤其是第3位。从10个物种中共鉴定到13~17个最优密码子。所有基因的有效密码子数(effective number of codons,ENC)均大于35,说明密码子使用整体偏性较弱。中性绘图、ENC-plot及PR2-plot分析显示,造成密码子使用偏性的主要因素是自然选择,但突变压对大部分基因的密码子偏性也有重要影响。系统发育及聚类分析显示密码子偏性在物种间是保守的。结论点地梅属叶绿体基因组蛋白编码基因倾向于使用A/U碱基编码的密码子,自然选择是影响密码子偏好性的主要因素。研究结果能为点地梅属的分子进化、系统发育及叶绿体基因工程提供基础。Objective To study the codon preference of chloroplast genome protein encoding genes and influencing factors in Androsac.Methods The chloroplast genome of Androsace mariae was sequenced,and the sequences of the other nine species were downloaded from NCBI.According to the sequence screening conditions,a total of 41 common sequences were obtained.CodonW 1.4.2 was used to calculate the relevant parameters,Python was used to process the data,R was used for correlation analysis and drawing figures.Results The GC content at the first,second and third positions of the codon was GC1>GC2>GC3,and the GC content at the third position was the minimum.The correlation of GC content between GC1 and GC2 was extremely significant,but not significant for GC3 between GC1 or GC2,indicating that the change mechanism of GC content at the three sites was different.The GC content of all three sites was less than 50%,indicating that the codons tended to use A/U bases,especially the third position.A total of 13—17 optimal codons were identified from 10 species.Effective number of codons(ENC)of all genes were greater than 35,indicating that the overall bias was weak.Neutral-plot,ENC-plot and PR2-plot analysis showed that the main factor causing codon bias was natural selection,but mutation pressure also had an important influence on the codon bias of most genes.Phylogenetic and cluster analysis showed that codon bias was conserved in species.Conclusion The protein coding genes of the chloroplast genome tend to use codons encoded by A/U bases,and natural selection is the main factor affecting codon preference.The results of this study can provide the basis for molecular evolution,phylogeny and chloroplast genetic engineering.

关 键 词：点地梅属 密码子偏性 最优密码子 突变压 自然选择 

分 类 号：R286.12[医药卫生—中药学]