7种昆虫质型多角体病毒基因组密码对的使用模式分析

An Analysis on Codon Pair Usage Pattern in Seven Cypovirus Genomes of Insect

质型多角体病毒(cypoviruses,CPV)是昆虫常见病原微生物。采用生物信息学方法对7种昆虫CPV基因组编码序列进行密码对使用模式分析,探究昆虫CPV基因组特征。分析结果表明:昆虫CPV基因组中密码对的使用是非随机的,密码对组合NNA→ANN、NNG→GNN、NNU→CNN、NNU→UNN中的多数密码对是CPV负偏好性密码对,密码对组合NNA→CNN、NNA→UNN、NNG→CNN、NNU→GNN中的多数密码对是CPV正偏好性密码对;残值最高的10个密码对与残值最低的10个密码对中有4个共用密码子(AAA、AAG、GAU、UAU),进一步说明密码对使用的偏好性;不同CPV间的基因组密码对使用偏好性程度相近,但极端偏好性密码对种类不同。同一电泳型CPV在聚类分析中的距离较近,说明同一电泳型CPV的基因组密码对使用模式相似,并且系统发育分析结果与基于密码对使用模式的聚类分析结果一致,说明CPV基因组密码对使用模式分析可用于研究其基因组进化。昆虫CPV基因组密码对使用具有偏好性,这种偏好性是其基因组特征的一种表现。

Cypoviruses （CPVs） are common pathogenic microorganism of insect. We analyzed the codon-pair usage patterns of seven insect CPV genomes through bioinformatic methods to explore the genomic characterization of insect CPVs. The results showed that the codon-pair usage of insect CPVs was non-random. Most codon-pairs of the codon-pair combinations such as NNA→ANN, NNG→GNN, NNU→CNN and NNU→UNN were CPV negatively biased codon- pairs, while most codon-pairs of the codon-pair combinations such as NNA→CNN, NNA→UNN, NNG→CNN and NNU→GNN were CPV positively biased codon-pairs. The 10 codon-pairs with the highest residual values and 10 codon-pairs with the lowest residual values shared four identical codons （AAA, AAG, GAU and UAU）, further explaining the biased usage of codon-pairs. Different CPVs possessed similar degree of codon-pair usage bias but different species of extremely biased codon-pairs. CPVs of the same electrophoretic type displayed close distance in cluster analysis, implying that they possessed similar codon-pair usage patterns. Moreover, the result of phylogenetic analysis was in accordance with that of cluster analysis, indicating that CPVs codon-pair usage pattern analysis can be used to infer genome evolution of CPVs. Codon-pair usage of insect CPVs is biased and the biased codon-pair usage is a representation of its genomic characteristics.