Genome sequence and comparative analysis of <i>Avibacterium paragallinarum</i>

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Title	Genome sequence and comparative analysis of Avibacterium paragallinarum
Authors	David Requena^{1, 2}, Ana Chumbe¹, Michael Torres^{1, 2}, Ofelia Alzamora¹, Manuel Ramirez1, 2, Hugo Valdivia-Olarte^{1, 2}, Andres Hazaet Gutierrez^{1, 2, 3}, Ray Izquierdo-Lara¹, Luis Tataje-Lavanda¹, Milagros Zavaleta¹, Luis Tataje-Lavanda¹, Ivan Best¹, Manolo Fernández-Sánchez¹, Eliana Icochea^{1, 4}, Mirko Zimic^{1, 2} & Manolo Fernández-Díaz¹*-FARVET Research Group
Affiliation	¹FARVET S.A.C. Carretera Panamericana Sur Nº 766 Km 198.5, Chincha Alta. Ica – Peru; ²Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia. Av. Honorio Delgado 430, San Martin de Porres Lima –Peru; ³Institute for Immunology and Informatics, University of Rhode Island, 292 Morris Ave. Providence, RI – USA, ZIP: 02906-2611; ⁴Laboratorio de Patología Aviar. Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos. Lima, Peru. Av. Circunvalación Cdra. 28 s/n, San Borja. Lima - Perú.
Email	farvet@farvet.com; *Corresponding author
Article Type	Hypothesis
Date	Received May 18, 2013; Accepted May 27, 2013; Published June 08, 2013
Abstract	Background: Avibacterium paragallinarum, the causative agent of infectious coryza, is a highly contagious respiratory acute disease of poultry, which affects commercial chickens, laying hens and broilers worldwide. Methodology: In this study, we performed the whole genome sequencing, assembly and annotation of a Peruvian isolate of A. paragallinarum. Genome was sequenced in a 454 GS FLX Titanium system. De novo assembly was performed and annotation was completed with GS De Novo Assembler 2.6 using the H. influenzae str. F3031 gene model. Manual curation of the genome was performed with Artemis. Putative function of genes was predicted with Blast2GO. Virulence factors were identified by comparison with the Virulence Factor Database. Results: The genome obtained has a length of 2.47 Mb with 40.66% of GC content. Seventy five large contigs (>500 nt) were obtained, which comprised 1,204 predicted genes. All the contigs are available in Genbank [GenBank: PRJNA64665]. A total of 103 virulence factors, reported in the Virulence Factor Database, were found in A. paragallinarum. Forty four of them are present in 7 species of Haemophilus, which are related with pathogenesis, virulence and host immune system evasion. A tetracycline-resistance associated transposon (Tn10), was found in A. paragallinarum, possibly acting as a defense mechanism. Discussion and conclusion: The availability of A. paragallinarum genome represents an important source of information for the development of diagnostic tests, genotyping, and novel antigens for potential vaccines against infectious coryza. Identification of virulence factors contributes to better understanding the pathogenesis, and planning efforts for prevention and control of the disease.
Keywords	Infectious coryza, genome sequencing, virulence factors, syntenic homology, Tn10 transposon.
Citation	Requena et al. Bioinformation 9(10): 528-536 (2013)
Edited by	P Kangueane
ISSN	0973-2063
Publisher	Biomedical Informatics
License	This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.