5种家蚕病毒的密码子及密码对使用模式分析

通过分析5种家蚕病毒基因组密码子和密码对使用模式,初步探讨5种家蚕病毒的基因组进化和对宿主的适应策略。采用生物信息学方法对碱基含量(GCall、GC1、GC2、GC3、GC3s)、有效密码子数(ENc)、相对同义密码子使用度(RSCU)、密码对(codon-pair)等进行统计分析的结果表明:5种家蚕病毒的密码子偏好性均较低,病毒间的碱基组成及ENc值差异较小,碱基组成对密码子使用模式影响较小;不同病毒选择不同的偏好性密码子,不同病毒的密码对偏好性程度不同,其中,家蚕类葡萄斑点病毒(Bombyx mori macula-like virus,BmMLV)密码对偏好性最强,家蚕质型多角体病毒(Bombyx mori cypovirus,BmCPV)和家蚕核型多角体病毒(Bombyx mori nucleopolyhedrovirus,BmNPV)密码对偏好性最弱。聚类分析表明BmCPV和家蚕浓核病毒(Bombyx mori densovirus,BmDNV)的密码子使用模式相似,BmNPV和家蚕传染性软化病病毒(Bombyx mori infec-tious flacherie virus,BmIFV)的密码子使用模式相似;BmMLV、BmNPV和BmDNV的密码对使用模式相似,BmIFV和BmCPV的密码对使用模式相似。5种病毒的偏好性密码子和偏好性密码对不同,显示不同病毒的密码子和密码对的进化路径不同,对宿主的适应策略不同。

Analysis on Codon and Codon-pair Usage Pattern in Five Silkworm Viruses

Genomic evolution and adaptive strategy to their hosts of five silkworm(Bombyx mori) viruses were preliminary studied through analysis on genomic codon and codon-pair usage patterns.Base contents(GCall,GC1,GC2,GC3 and GC3s),effective number of codons(ENc),relative synonymous codon usage(RSCU) and codon-pair were calculated and analyzed using a bioinformatic approach.A generally weak codon bias was found in the five silkworm viruses.Base composition and ENc value ranges varied slightly between the five viruses while base composition had little influence on codon usage pattern.Different viruses used different preferred codons,and differed in the degree of preferred codon-pairs.Among them,Bombyx mori macula-like virus(BmMLV) had the highest codon-pair bias,while B.mori cypovirus(BmCPV) and B.mori nucleopolyhedrovirus(BmNPV) had the lowest codon-pair bias.Cluster analysis showed that the codon usage patterns were similar between BmCPV and B.mori densovirus(BmDNV),between BmNPV and B.mori infectious flacherie virus(BmIFV).The codon-pair usage patterns were similar among BmMLV,BmNPV and BmDNV,and between BmIFV and BmCPV.Different preferred codons and codon-pairs used by these five silkworm viruses indicated that different viruses had various evolutionary paths and various adaptive strategies against hosts.