摘要
为了解萝卜ICE1密码子的使用特性,运用CUSP和Codon W软件程序分析萝卜ICE1密码子的使用偏好性,并与芜菁等10种植物ICE1、萝卜基因组样本及拟南芥等基因组密码子偏性进行比较。结果表明,萝卜ICE1密码子偏好以A/T结尾;根据RSCU值,确定萝卜ICE1高频密码子有12个;与萝卜基因组密码子相比,19个密码子的偏好性相同;与其他物种同源基因相比,密码子选择偏性存在差异;聚类分析中,基于ICE1编码序列的聚类结果比密码子使用偏性分析更能准确地反映物种间的亲缘关系;与其他物种基因组密码子使用频率比较发现,同科物种(拟南芥、甘蓝)差异较小,与水稻差异较大,预示着萝卜ICE1在异源表达时尚需进行适当的改造和优化。萝卜ICE1密码子偏性分析为萝卜ICE1的异源表达及分子遗传研究提供了一定的理论依据。
To understand codon usage features of ICE1 gene in radish,the sequence of ICE1 was analyzed via programs of CUSP and Codon W,and it was also compared with other 10 plant species and genomes. The results showed that ICE1 in radish was bias towards the synonymous codons with A and T at third codon position. According to the RSCU（ Relative Synonymous Codon Usage）,12 codons were high-frequency. Compared with the codon usages of other radish genes,bias towards of 19 codons were the same. There were some differences in codon bias of ICE1 among different species. The cluster tree of ICE1 based on CDS revealed a better evolutionary relationship among different species than the result analyzed by RSCU. The differences of codon usage between ICE1 and rice genome was larger than that between ICE1 and some cruciferae plant genomes（ Arabidopsis,cabbage）. This means something should be done to ICE1 to heterologous expression of ICE1. This study not only preliminarily reveals the codon usage pattern of ICE1 of radish,but also provides a certain theoretical basis to further molecular genetic study.
出处
《核农学报》
CAS
CSCD
北大核心
2018年第3期477-485,共9页
Journal of Nuclear Agricultural Sciences
基金
国家大宗蔬菜农业产业技术体系(CARS-25-37)
山东省农业良种工程重点课题-十字花科名产蔬菜新品种选育
潍坊市科学技术发展项目(2016ZJ1061)
