multocida. In another recent review, Boyce et al. [32] speculated that the combination of additional P. multocida genome sequences and advances in our ability to genetically manipulate the organism will facilitate PXD101 order major advances in our understanding of disease pathogenesis. To that end, we undertook a detailed comparative genome analysis of two virulent strains (X73 and P1059) and avirulent strain Pm70 of P. multocida. The goal of this study

is to enable narrowed identification of a repertoire of unique genes present in the highly pathogenic avian strains that may play a role in virulence. This information will also facilitate the design of improved modified live vaccine candidates with defined mutations that can be evaluated as immunoprophylactic agent(s) to control P. multocida-caused disease in avian and other host SHP099 mw species. Methods Bacterial strains The strains sequenced in this study included P. multocida strains P1059 (ATCC# 15742) and X73 (ATCC# 11039). Strain P1059 is a well characterized pathogenic strain APO866 molecular weight isolated from the liver of a turkey that died of fowl cholera [30]. Strain X73 is also a well characterized pathogenic strain

isolated from the liver of a chicken that died of fowl cholera [30]. For comparative purposes, the avirulent Pm70 strain was used [15]. There are several reasons why we selected strains P1059 and X73 in this study. First, both strains are highly virulent to chickens, turkeys and other poultry species. Second, they are of different serotypes (P1059 = A:3; and X73 = A:1) and different immunologic types [30]. Thirdly, they are reference serotype strains that are readily available to investigators and there is abundant literature on the biology of these two strains [1, 11, 30, Regorafenib research buy 33–35]. Genome sequencing and annotation Sequencing of strains P1059 and X73 was performed using 454 Life Sciences pyrosequencing at the National Animal Disease Center in

Ames, Iowa. The following data sets were generated for each strain: GS- FLX, with 270,010 shotgun reads of average length 240 bp yielding 64,827,159 bp for P1059; and GS-FLX, with 227,030 shotgun reads of average length of 240 bp, yielding 54,398,540 bp for X73. Reads were de novo assembled into scaffolds using Newbler 2.3 [36]. The draft sequences of these genomes are deposited under the following accession numbers: P1059 [Genbank:AMBQ01000000] and X73 [Genbank:AMBP01000000]. Comparative genomics Annotation of P1059 and X73 was performed using publicly available tools. Putative coding regions were predicted using GeneMarkS [37]. Gene function was assigned using HMMER3 against Pfam-A 24.0, RPS-BLASTp against CDD, and BLASTp against all microbial proteins [38, 39]. tRNA genes were identified using tRNAscan-SE [40]. rRNA genes were identified using RNAmmer [41]. For analysis of the shared and unique proteins in the P.