title: The complete genome sequence of EC1-UPM, a novel N4-like bacteriophage that infects Escherichia coli O78:K80.
abstract: BACKGROUND
  Bacteriophage EC1-UPM is an N4-like bacteriophage which specifically infects Escherichia coli O78:K80, an avian pathogenic strain that causes colibacillosis in poultry. The complete genome sequence of bacteriophage EC1-UPM was analysed and compared with other closely related N4-like phage groups to assess their genetic similarities and differences.
  
  
  RESULTS
  Bacteriophage EC1-UPM displays a very similar codon usage profile with its host and does not contain any tRNA gene. Comparative genomics analysis reveals close resemblance of bacteriophage EC1-UPM to three N4-like bacteriophages namely vB_EcoP_G7C, IME11 and KBNP21 with a total of 44 protein coding genes shared at 70% identity threshold. The genomic region coding for the tail fiber protein was found to be unique in bacteriophage EC1-UPM. Further annotation of the tail fiber protein using HHpred, a highly sensitive homology detection tool, reveals the presence of protein structure homologous to various polysaccharide processing proteins in its C-terminus. Leveraging on the availability of multiple N4-like bacteriophage genome sequences, the core genes of N4-like bacteriophages were identified and used to perform a multilocus phylogenetic analysis which enabled the construction of a phylogenetic tree with higher confidence than phylogenetic trees based on single genes.
  
  
  CONCLUSIONS
  We report for the first time the complete genome sequence of a N4-like bacteriophage which is lytic against avian pathogenic Escherichia coli O78:K80. A novel 928 amino acid residues tail fiber protein was identified in EC1-UPM which may be useful to further the understanding of phage-host specificity. Multilocus phylogenetic analysis using core genes of sequenced N4-like phages showed that the evolutionary relationship correlated well with the pattern of host specificity.
authors.forename: Han Ming
authors.initials: HM
authors.lastname: Gan
authors.affiliation: Laboratory of Vaccines and Immunotherapeutics, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia. sieo@upm.edu.my.
authors.forename: Chin Chin
authors.initials: CC
authors.lastname: Sieo
authors.forename: Shirley Gee Hoon
authors.initials: SG
authors.lastname: Tang
authors.forename: Abdul Rahman
authors.initials: AR
authors.lastname: Omar
authors.forename: Yin Wan
authors.initials: YW
authors.lastname: Ho
mesh_terms: D000818:Animals; D001717:Birds; D016000:Cluster Analysis; D003090:Coliphages / Q000235:genetics* / Q000302:isolation & purification*; D004279:DNA, Viral / Q000737:chemistry* / Q000235:genetics*; D004926:Escherichia coli / Q000302:isolation & purification / Q000821:virology*; D016679:Genome, Viral; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D014764:Viral Proteins / Q000235:genetics
chemical_list: D004279:DNA, Viral; D014764:Viral Proteins