大肠埃希氏菌噬菌体Bp38全基因组测序及生物信息学分析

Whole Genome Sequencing and Bioinformatics Analysis of E.coli Bacteriophage Bp38

为了解命名为Bp38的裂解性大肠埃希氏菌噬菌体的遗传背景及基因功能,对其进行全基因组测序和拼接,并采用EditSeq、tRNAscan-SE、tRNAdb、ORF finder、SnapGene、MEGA和Datamonkey等软件对其基因组的基本特性、功能基因预测及注释、遗传进化关系及溶菌酶基因的选择压力进行生物信息学分析。结果表明,噬菌体Bp38基因组全长170004 bp,核酸类型为dsDNA,平均G+C含量为37.60%,有140个功能基因,根据预测的功能可将其分为裂解模块、DNA包装模块、结构组成模块、假性蛋白模块和核酸复制与调控模块,有2个tRNA,分别转运精氨酸(Arg)和蛋氨酸(Met);以末端酶大亚基核酸序列构建系统进化树,分析出Bp38为有尾噬菌体目、肌尾噬菌体科、Tevenvirinae亚科、Mosigvirus属;Bp38溶菌酶基因的选择压力分析结果显示,其共有173个氨基酸位点,其中有2个正向选择位点、10个负向选择位点,分析后可知其溶菌酶基因既受外界环境选择压力的影响,又受自身进化压力的影响,且自身进化压力强于外界环境选择压力。研究结果阐明了大肠埃希氏菌噬菌体Bp38的分子特征,为进一步利用该噬菌体提供了理论依据。

In order to understand the genetic background and gene function of a lytic Escherichia coli phage named Bp38,the genome of E.coli bacteriophage Bp38 was sequenced and the whole genome was spliced.The general characteristics,functional gene prediction and annotation,genetic evolution and selection pressure of lysozyme gene were analyzed by EditSeq,tRNAscan-SE,tRNAdb,ORF finder,SnapGene,MEGA and Datamonkey.The results showed that the total genome length of phage Bp38 was 170004 bps.According to the predicted function,it can be divided into cleavage module,DNA packaging module,structure composition module,pseudoprotein module and nucleic acid replication and regulation module.There are two tRNAs,which transport arginine(Arg)and methionine(Met),respectively.The phylogenetic tree was constructed based on the nucleic acid sequence of terminal enzyme large subunit.The results showed that Bp38 belonged to tailed phages,Myococcidae,Tevenvirinae subfamily and Mosigvirus genus.The selection pressure analysis of bp38 lysozyme gene showed that there were 173 amino acid sites,including 2 positive selection sites and 10 negative selection sites.The analysis showed that the lysozyme gene was affected by both the selection pressure of external environment and its own evolutionary pressure,and the pressure of itself evolution is stronger than that of external environment selection.[Conclusion]This study illuminated the genetic characteristics of E.coli bacteriophage Bp38 and laid the theoretical foundation for making use of it.