大豆花叶病毒CP基因密码子使用偏性分析

大豆花叶病毒(soybean mosaic virus,SMV)外壳蛋白(coat protein,CP)是SMV基因组的结构蛋白,在SMV侵染大豆的过程中发挥着重要的作用。运用CUSP和Codon W等软件分析了大豆花叶病毒外壳蛋白的密码子的偏性,并与SMV基因组的密码子偏性进行了比较。结果表明,SMV CP偏好于以A/T结尾的密码子;与SMV基因组密码子偏性相比,发现只有8种氨基酸密码子偏性完全一致。ENC与GC3的相关性分析结果显示,CP的密码子使用偏好性受碱基组成等多种因素共同影响。聚类分析显示基于基因CDS序列的聚类结果与基于密码子偏性参数相对密码子使用度(RSCU)的聚类结果基本一致。通过分析CP密码子使用特性,为进一步研究其功能奠定基础。

Analysis on codon usage of CP gene in soybean mosaic virus

The coat protein (CP) of Soybean mosaic virus (SMV) is the SMV genome structural proteins, it plays an important role in the process of SMV infection soybean. In this study the coding sequence of the CP in SMV was analyzed with Codon W and CUSP（Create a codon usage table）programs while compared with the genome of SMV. The results showed that CP of SMV was biased toward the synonymous codons with A and T. Compared with the codon usage of SMV genome, Codon Usage bias of the CP is the same as eight amino acid codon in the genome of SMV. The correlation analysis between ENC and GC3 indicated that the codon usage of CP gene was affected by many factors including the nucleotide composition. The cluster analysis results based on the gene CDS sequences showed codon usage bias of the CP gene were similar to the bias on the relative synonymous codon usage（RSCU）. The analyzing of the CP codon usage characteristics provided a foundation for further study its functionality.