基于相对密码子频率的芜菁花叶病毒基因组序列的进化分析

现有92株芜菁花叶病毒(TuMV)的全基因组序列已在GenBank报道,据分析报道其中58株不含重组序列。利用系统聚类法对92株TuMV的全基因组序列和58株TuMV全基因组序列的相对密码子频率RSCU值进行聚类分析。同时利用系统发育分析方法分析了这92株和58株TuMV全基因组序列。结果发现,92株芜菁花叶病毒株的密码子偏性聚类树与其系统进化树的一致度很低;而不含重组序列的58株芜菁花叶病毒株的密码子偏性聚类树与其系统进化树的一致度却非常高,且与寄生宿主类型基本对应。这表明在不存在重组的情况下,TuMV密码子频率的偏性可能是宿主内的一种选择压力,影响TuMV基因组的点突变进化方向,促使TuMV适应宿主内环境。

Evolutionary analysis of turnip mosaic virus genomic sequences based on synonymous codon usage

Full genome sequences of 92 Turnip mosaic virus （TuMV） isolates have been reported in the GenBank, 58 out of which were reported to be non - recombinants. The Codon usage bias has been investigated on these 92 and 58 TuMV isolates using the method of hierarcial cluster analysis. The phylogenetic relationships based on nucleotide sequences of these 92 and 58 TuMV isolates were ana- lyzed too. Results show that the codon usage patterns of those 58 TuMV isolates are found to be significantly phylogenetically conserved and almost consistent with the host type. These results suggested that in the condition of no recombination codon usage bias may be one of the host selective pressures affecting the point mutation of TuMV genome in its adaptation to the niche in their host.