title: Sequence characteristics of T4-like bacteriophage IME08 benome termini revealed by high throughput sequencing.
abstract: BACKGROUND
  T4 phage is a model species that has contributed broadly to our understanding of molecular biology. T4 DNA replication and packaging share various mechanisms with human double-stranded DNA viruses such as herpes virus. The literature indicates that T4-like phage genomes have permuted terminal sequences, and are generated by a DNA terminase in a sequence-independent manner;
  
  
  METHODS
  genomic DNA of T4-like bacteriophage IME08 was subjected to high throughput sequencing, and the read sequences with extraordinarily high occurrences were analyzed;
  
  
  RESULTS
  we demonstrate that both the 5' and 3' termini of the IME08 genome starts with base G or A. The presence of a consensus sequence TTGGA|G around the breakpoint of the high frequency read sequences suggests that the terminase cuts the branched pre-genome in a sequence-preferred manner. Our analysis also shows that terminal cleavage is asymmetric, with one end cut at a consensus sequence, and the other end generated randomly. The sequence-preferred cleavage may produce sticky-ends, but with each end being packaged with different efficiencies;
  
  
  CONCLUSIONS
  this study illustrates how high throughput sequencing can be used to probe replication and packaging mechanisms in bacteriophages and/or viruses.
authors.affiliation: Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
authors.forename: Xiaofang
authors.initials: X
authors.lastname: Jiang
authors.forename: Huanhuan
authors.initials: H
authors.lastname: Jiang
authors.forename: Cun
authors.initials: C
authors.lastname: Li
authors.forename: Sheng
authors.initials: S
authors.lastname: Wang
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Mi
authors.forename: Xiaoping
authors.initials: X
authors.lastname: An
authors.forename: Jiankui
authors.initials: J
authors.lastname: Chen
authors.forename: Yigang
authors.initials: Y
authors.lastname: Tong
mesh_terms: D001435:Bacteriophages / Q000235:genetics* / Q000502:physiology; D004279:DNA, Viral / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D004706:Endodeoxyribonucleases / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008969:Molecular Sequence Data; D017900:Myoviridae / Q000235:genetics / Q000502:physiology; D014764:Viral Proteins / Q000378:metabolism; D019065:Virus Assembly
chemical_list: D004279:DNA, Viral; D014764:Viral Proteins; D004706:Endodeoxyribonucleases; C030894:terminase