| Riemerella anatipestifer(RA) infection is a contagious disease of domestic ducks,geese,turkeys, andother domestic and wild birds. It also called infectious serositis. It occurs as an acute or chronicsepticemia characterized by fibrinous pericarditis, perihepatitis, airsacculitis, caseous salpingitis, andmeningitis. It accounts for significant economic losses due to high mortality, weight loss,condemnations, downgrading, and salvage. Currently, the whole-genome sequences of five strains ofRA have been released in Gen Bank. There are 2,000 encoding genes in RA genome, few of which havethe known functions. Identification of genetic differences between virulent and attenuated strains isimportant for analyzing genetic evolutionary relationship and virulence difference among differentstrains, and studying the molecular epidemiology. Suppression substractive hybridization andwhole-genome sequencing have been used in this study to analyze the genetic differences between RAvirulent strains HXb2 and attenuated strains NJ-1. The results in this study establish the foundation forscreening new virulence genes.This study laid the groundwork for further identifying new virulence factors, and studying thefunctions of the HXb2- specific proteins.1. Identification of genomic differences between virulent strain HXb2 and attenuated strainNJ-1 using suppression substractive hybridizationSuppression subtractive hybridization(SSH) was performed using the genome of highly pathogenicRiemerella anatipestifer strain HXb2 as tester and the genome of attenuated strain NJ-1 as driver. Afterdetected by the dot-blot and PCR, 52 differential fragments were identified. Sequences analysis withBLAST, DNASTAR and PSORTb softwares showed that 3 differential genes encoded out membraneprotein, and 5 genes encoded cytoplasmic membrane protein, such as phosphate transporter, 1 genesencoded extracellular protein and 11 genes encoded intracellular proteins, such as alaninedehydrogenase, beta-lactamase and some hypothetical protein, the locations of other 25 differentialgenes encoding hypothetical protein, and 7 genes unknown. The proteins encoded by these differentialgenes may be related to the virulence of HXb2, or HXb2-specific proteins, etc.2. Analysis of genomic differences between Riemerella anatipestifer strains HXb2 and NJ-1through genome sequencingIn this study, we obtained the full genome sequence of strains HXb2 and the draft genome sequenceof strain NJ-1.The detailed analysis and functional annotation for this organism was performed. HXb2 genome is a chromosome of 2,425,237 bp containing 2383 predicted genes, and 2274 genes can befound homologous sequence in the NR database. 1068 of them have predicted functions. In addition,there are 9 genomic islands predicted in the genome of HXb2. On the other hand, the draft genomesequence of strain NJ-1 included 42 contigs, and the total nucleotide acids is 2,197,342 bp containing2040 predicted genes, and 1928 genes can be found homologous sequence in the NR database. 1078 ofthem have predicted functions. Comparison of the genome sequences of strains HXb2 and NJ-1 showedthat there are 1837 common genes, 548 HXb2-specific genes and 410 NJ-1-specific genes. The proteinsencoded by these differential genes in both strains HXb2 and NJ-1 are involved in metabolism,membrane protein, information storage and processing, hypothetical protein, and general function. Inaddition, the HXb2-specific genes encoded for toxin-antitoxin system protein, phage tail type measureprotein, and CRISPR-associated protein may be related to the virulence of this strain. |
