大花香水月季叶绿体基因组密码子使用偏性分析  

An Analysis on Codon Usage Bias of Chloroplast Genome of Rosa odorata var. gigantea

作　　者：牛元 徐琼[1] 王嵛德 代立兰 庄健 赵亚兰 NIU Yuan;XU Qiong;WANG Yu-de;DAI Li-lan;ZHUANG Jian;ZHAO Ya-lan(Lanzhou Agro-technical Research and Popularization Center, Lanzhou,Gansu 730010, China)

机构地区：[1]兰州市农业科技研究推广中心,甘肃兰州730010

出　　处：《西北林学院学报》2018年第3期123-130,共8页Journal of Northwest Forestry University

基　　金：甘肃省科技重大专项(1302NKDA028);兰州市科技攻关计划项目(2010-1-239;2016-3-4);兰州市科技局人才项目(2015-RC-87);甘肃省农科院院地科技合作项目(2017GAAS63)

摘　　要：以大花香水月季叶绿体基因组为研究对象,利用codonW等软件,通过分析大花香水月季叶绿体基因组54个基因密码子的使用偏性,探讨影响密码子偏好性形成的主要因素。结果表明:1)中性绘图分析显示GC3与GC12的相关系数为0.141,不显著相关,说明密码子第1、2位与第3位碱基组成变异无明显关联。2)ENC绘图分析显示,期望值曲线下方分布了大部分基因,偏性较强,而仅少量基因沿曲线分布或在曲线附近,偏性较弱。3)基于RSCU的对应性分析表明,第1轴能够解释基因总变异的10.35%,第1轴与CAI、CBI呈负显著相关。4)PR2-plot分析显示,密码子第3位碱基的使用存在偏性,嘧啶比嘌呤使用更为频繁。5)最终确定了TTT、CTT和TCA等13个最优密码子,且均以A或T结尾。综上所述,大花香水月季叶绿体基因组密码子的使用受突变影响较弱,更多地受到如选择压力等其他因素的影响。Taking chloroplast genome of Rosa odorata var.giganteaas research object,fifty-four genes were analyzed by CodonW and other software to explore the main factors affecting codon usage bias.The results were as follows.1）Neutral mapping analysis showed that the correlation coefficient between GC12 and GC3 was 0.141,and the correlation was not significant,indicating that there was no significant correlation between the first two and the third base composition variation of codon.2）ENCplot analysis showed that only a few genes in the genome were distributed along the expected value curve or near the expected value curve,which bias were weak,while most genes were distributed below the expected value curve,which bias were strong.3）RSCUbased correspondence analysis showed that the first axis explained 10.35% of the total variation of the gene and was negatively related to CAI and CBI.4）PR2-plot analysis showed that the third base of codon usage was biased,where pyrimidine was used more frequently than purine.5）Thirty preferred codon were identified finally,which all ended with A and T.In conclusion,the codon usage bias is formed under less effect of mutation and more effect of other factors such as selection pressure.

关 键 词：大花香水月季 叶绿体基因组 GC含量 密码子使用 最优密码子 

分 类 号：S685.12[农业科学—观赏园艺]