title: First complete genome sequence of infectious laryngotracheitis virus.
abstract: BACKGROUND
  Infectious laryngotracheitis virus (ILTV) is an alphaherpesvirus that causes acute respiratory disease in chickens worldwide. To date, only one complete genomic sequence of ILTV has been reported. This sequence was generated by concatenating partial sequences from six different ILTV strains. Thus, the full genomic sequence of a single (individual) strain of ILTV has not been determined previously. This study aimed to use high throughput sequencing technology to determine the complete genomic sequence of a live attenuated vaccine strain of ILTV.
  
  
  RESULTS
  The complete genomic sequence of the Serva vaccine strain of ILTV was determined, annotated and compared to the concatenated ILTV reference sequence. The genome size of the Serva strain was 152,628 bp, with a G + C content of 48%. A total of 80 predicted open reading frames were identified. The Serva strain had 96.5% DNA sequence identity with the concatenated ILTV sequence. Notably, the concatenated ILTV sequence was found to lack four large regions of sequence, including 528 bp and 594 bp of sequence in the UL29 and UL36 genes, respectively, and two copies of a 1,563 bp sequence in the repeat regions. Considerable differences in the size of the predicted translation products of 4 other genes (UL54, UL30, UL37 and UL38) were also identified. More than 530 single-nucleotide polymorphisms (SNPs) were identified. Most SNPs were located within three genomic regions, corresponding to sequence from the SA-2 ILTV vaccine strain in the concatenated ILTV sequence.
  
  
  CONCLUSIONS
  This is the first complete genomic sequence of an individual ILTV strain. This sequence will facilitate future comparative genomic studies of ILTV by providing an appropriate reference sequence for the sequence analysis of other ILTV strains.
authors.affiliation: Asia-Pacific Centre for Animal Health, School of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia. leesw@unimelb.edu.au
authors.forename: Sang-Won
authors.initials: SW
authors.lastname: Lee
authors.forename: Philip F
authors.initials: PF
authors.lastname: Markham
authors.forename: John F
authors.initials: JF
authors.lastname: Markham
authors.forename: Ivonne
authors.initials: I
authors.lastname: Petermann
authors.forename: Amir H
authors.initials: AH
authors.lastname: Noormohammadi
authors.forename: Glenn F
authors.initials: GF
authors.lastname: Browning
authors.forename: Nino P
authors.initials: NP
authors.lastname: Ficorilli
authors.forename: Carol A
authors.initials: CA
authors.lastname: Hartley
authors.forename: Joanne M
authors.initials: JM
authors.lastname: Devlin
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D004279:DNA, Viral / Q000235:genetics; D016679:Genome, Viral / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D025921:Iltovirus / Q000235:genetics*; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA; D014613:Vaccines, Attenuated / Q000235:genetics
chemical_list: D004279:DNA, Viral; D014613:Vaccines, Attenuated