Lee et al. BMC Genomics 2011, 12:197 http://www.biomedcentral.com/1471-2164/12/197 R E S E A R C H A R T I C L E Open Access First complete genome sequence of infectious laryngotracheitis virus Sang-Won Lee1*, Philip F Markham1, John F Markham3, Ivonne Petermann2, Amir H Noormohammadi1, Glenn F Browning1, Nino P Ficorilli1, Carol A Hartley1 and Joanne M Devlin1 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. Background Infectious laryngotracheitis virus (ILTV) is an alphaher- pesvirus that causes acute respiratory disease in chick- ens. This disease causes economic loss in poultry industries worldwide and is a significant concern for animal health and welfare [1]. The virus contains a lin- ear, double-stranded DNA genome in a herpesvirus type D arrangement. This genome arrangement consists of a unique long region and a unique short region flanked by identical internal and terminal repeat sequences [2,3], with the short region able to invert with respect to the long region. In previous studies, several regions of the ILTV genome of different strains have been sequenced and annotated [3-12]. Recently, a full genomic sequence * Correspondence: leesw@unimelb.edu.au 1Asia-Pacific Centre for Animal Health, School of Veterinary Science, The University of Melbourne, Parkville, Victoria, 3010, Australia Full list of author information is available at the end of the article of ILTV was assembled by concatenating partial sequences of six different ILTV strains [13]. However, the whole genomic sequence of a single strain of ILTV has not been reported. In this study, the whole genome sequence of a commercial live attenuated vaccine strain of ILTV was examined using high-throughput sequen- cing technology. Results and Discussion Sequencing and coverage Genomic sequencing using the SOLiD™ system gener- ated 526.69 Mb of sequence and 12,046,726 reads. A total of 230 contigs were mapped to the virus genome after de novo assembly. A consensus sequence of 137,693 bp (without the terminal repeat region) was generated after assembly of contigs using the concate- nated reference sequence. The depth of coverage against the concatenated ILTV sequence was greater than 150- © 2011 Lee et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.