噬菌体基因组PaP1的鸟枪法测序及其生物信息学分析

目的对分离的铜绿假单胞菌噬菌体PaP1进行全基因组测序，并进行初步的生物信息学分析，为噬菌体的改造及其治疗奠定基础。方法采用鸟枪法随机测序和重叠群组装的策略对PaP1进行基因组测序，并通过EditSeq、开放读码框架（ORF）finder、GeneMark^TM、BPROM、FindTerm、Palindromes、Equicktandem及FAStRNA等软件对所获得的基因组序列的一般特征、蛋白质同源性序列及tRNA基因等进行分析和预测。结果PaP1基因组约为90000bp，其中最大重叠群为28249bp。在已获得序列中预测出120个ORFs、41个推定基因及9个簇集在5’末端的tRNA基因。在41个推定基因中，预测出编码DNA末端酶大亚单位、DNA解旋酶B亚单位、肽聚糖结合蛋白及3个尾丝蛋白等6个基因的功能。结论鸟枪法只能测出噬菌体基因组PaP1的部分序列，重复序列的存在是该基因组测序困难的原因。

Sequencing of bacteriophage genome PaP1 with shot-gun library and analysis of its bioinformatics

Objective To sequence Pseudomonas aeruginosa phage genome PaP1 with shot-gun library, and to analyze its bioinformatics, so as to lay a foundation of the genome remodeling and phage-therapy. Methods Shot-gun library and contig package strategy were carried out for sequencing PaP1 genome, and the characteristics of the acquired genomic sequence, the homologous protein sequence, and tRNA gene were analyzed and predicted with software of EditSeq, ORF finder, GeneMarkTM , BPROM and FindTerm, Palindromes and Equcktandem, PSIBLAST and FAStRNA. Results The whole genome PaP1 was about 90kb, and the acquired biggest contig was 28 249 bp. There were 120 ORFs, 41 putative genes and 9 tRNA genes predicted from acquired sequence. Among 41 predicted genes, 6 genes which encode terminase large subunit, including DNA Gyrase B subunit, peptidoglycan binding protein and 3 tail fiber proteins, were functionally known by analysis of bioinformatics. Conclusion Only a part of sequence from genome PaP1 can be obtained with shot-gun library strategy. The difficulty for sequencing this genome is due to the presence of multiple repetitions.