title: On genome annotation of Brucellaphage Gadvasu (BpG): discovery of ORFans for integrated systems biology approaches.
abstract: Brucellaphage Gadvasu (BpG) is a lytic phage infecting Brucella spp. Brucellaphages contain dsDNA as genetic material and are short-tailed particles with host-specificity. Here, we report the challenges on annotation in the complete genome sequence of BpG when compared with that of a recent broad host-range brucellaphage Pr, an original reference genome. The extracted DNA was subjected to genome sequencing with Illumina technology and assembled using SSAKE/Velvet. A significant number of genes were found to be similar between the phages with sequence analysis revealing conserved open reading frames that correspond to 33 gene ontology classifiers, transcriptional terminators and a few putative transcriptional promoters. The analyses revealed that the genome constitutes 1269 contigs and 275 genes encoding 260 proteins. The sequence comparison from the reference data indicated that the genome shares an approximately 70 % nucleotide similarity and differs mainly in the region encoding proteins. We bring this commentary providing an overview of how this exemplar genome can allow us to understand these known unknown regions in brucellaphages.
authors.affiliation: Department of Veterinary Microbiology, College of Veterinary Science, GADVASU, Ludhiana, Punjab 141004 India.
authors.forename: Deepti
authors.initials: D
authors.lastname: Chachra
authors.affiliation: Department of Veterinary Microbiology, College of Veterinary Science, GADVASU, Ludhiana, Punjab 141004 India ; Food and Agricultural Products Center, Oklahoma State University, Stillwater, OK 74078-6055 USA.
authors.forename: Pushpinder
authors.initials: P
authors.lastname: Kaur
authors.affiliation: Bioclues.org, Kukatpally, Hyderabad, 500 072 India.
authors.forename: Prasad
authors.initials: P
authors.lastname: Siddavatam
authors.affiliation: Bioclues.org, Kukatpally, Hyderabad, 500 072 India ; Bioinformatics Organization, 28 Pope St, Hudson, MA 01749 USA ; Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark.
authors.forename: Prashanth
authors.identifier: 0000-0002-8535-278X
authors.initials: P
authors.lastname: Suravajhala
authors.affiliation: Department of Veterinary Microbiology, College of Veterinary Science, GADVASU, Ludhiana, Punjab 141004 India.
authors.forename: Hari Mohan
authors.initials: HM
authors.lastname: Saxena
keywords: Annotation; Brucellaphage; De novo assembly; Genome mapping; Next generation sequencing; Whole genome sequence