1株3型鸭甲肝病毒的VP1和VP3基因的密码子使用偏性分析

Codon-bias Analysis of VP1 and VP3 Genes of one Type 3 Duck Hepatitis A Virus

为了解临床分离的1株3型鸭甲肝病毒的结构蛋白VP1和VP3基因的密码子使用特性,本文对该毒株的VP1和VP3基因与从NCBI下载的同源性较高的3型鸭甲肝病毒进行了密码子偏性分析。结果表明,该毒株的VP1和VP3与所比对的5株3型鸭甲肝病毒VP1和VP3基因密码子使用模式基本一致,分别确定了12种和13种高频密码子,且偏爱以A或U结尾。通过6株3型鸭甲肝病毒的VP1和VP3基因的密码子偏性比较和聚类分析发现,其中4株分类地位相近。

In order to understand the codon characteristics of VP1 and VP3 genes of an isolated clinical type 3 Duck Hepatitis A Virus(DHAV), codon-bias analysis of the VP1 and VP3 genes were analyzed with the highly homologous Type 3 DHAV downloaded from Genbank in present study. Results showed that the codon–bias patterns of VP1 and VP3 genes of the isolated strain were almost the same as those of the 5 strains downloaded from Genbank. 12 and 13 high frequency codons were identified respectively, and were preferable to use A or U as ending codon. Codon-bias comparison and cluster analysis of VP1 and VP3 genes of type 3 DHAV from 6 strains indicated that 4 of them have similar taxonomic position. This study provides a theoretical basis for future protein expression study.