Genome Structural Characteristics Of The Different Serotypes Riemerella Anatipestifer

Duck infectious serositis is a contagious disease of ducks, turkeys and birds, the pathogen is the Riemerella Anatipestifer. The mortality rate of this disease is about90%,1-8weeks ducks are the main infected ducks, the general course of acute or chronic sepsis. Lesions mainly for the cellulose pericarditis, perihepatitis, the air sac inflammation, meningitis, and in some cases also appear arthritis. Officially established as a separate branch in1993, and renamed Riemerella Anatipestifer. Riemerella Anatipestifer have25serotypes, but on cross protection between serotypes. The genomic information Riemerella Anatipestifer only five complete genome sequence and an incomplete sequence fragments present in the NCBI genome database. Wherein three completed by the sequencing of this laboratory:the standard strains ATCC11845, RA-CH-1(serotype Type Ⅰ) and RA-CH-2(serotype Type II). Due to the scarcity of genome sequence data, the structure of the genome Riemerella Anatipestifer study more scarce, therefore, through our research, we hope to be able to provide basis for Riemerella Anatipestifer research.Isolated from clinical the two Riemerella Anatipestifer (RA-CH-1and RA-CH-2), and buy ATCC11845. Then we have three Riemerella Anatipestifer sequencing and annotation. We conducted a comparative analysis of ATCC11845, RA-CH-1, RA-CH-2and RA-GD in the NCBI database. The analysis results show that the ATCC11845, RA-GD and RA-CH-2three genomes only have a little difference in number of genes, GC content of about35%. RA-CH-1appeared relatively large differences. Genome length is more than three out of140,000bp. RA-CH-1GC content is also slightly higher than the other strains, and the gene number more than100. With the difference rather than the different serotypes of the RA-CH-2greater than the same serotype RA-GD.Riemerella Anatipestifer contains a large number of functional proteins. Mainly the following:Iron transport protein TonB family. The main function of this family is the iron-transport system of the bacteria. Iron absorption is a critical part of the growth of bacteria and iron also has a great influence on bacterial virulence factors, iron transport pathway is very important for maintaining bacterial survival. The capsular exopolysaccharide is important pathogenic factor for many bacteria to the class protein not only be able to suppress many bacterial biofilm formations, but also has the characteristics of the destruction that has been generated biofilms. And in some bacteria there to enhance the effects of some antibiotics destroy the cell’s outer membrane. Two types of efflux systems in Riemerella Anatipestifer genome, which is a Small Multidrug Resistant protein (SMR) family, the other is major facilitator super family (MFS-1). In addition to the above two active efflux system composed of protein, there are still several other antibiotic resistance genes, for example:vanz family proteins, the main function for the vancomycin resistance gene; the penicillinase repressor; acriflavin resistance protein; camphor resistance protein crcb; multiple antibiotic resistances (marc)-related protein.The repetitive sequence is a nucleotide sequence repeated in the genome. These sequences are generally does not encode a polypeptide; can be divided into the interspersed repetitive sequences and tandem repeat sequence. The interspersed repetitive sequences are also known transposable element. Include three kinds:the long terminal repeated, the short interspersed nuclear elements, the long interspersed nuclear elements. The main functions of the long terminal repeat (LTR) are regulating the transcription of viral genes, replication, and integration of the viral gene. Short interspersed nuclear elements (SINE) and long interspersed nuclear elements (LINE) widespread in the eukaryotic genome and occupy a large portion. They are in the form of retrotrans-position inserted into the genome chromosomal new location. They are considered to study the species taxa phylogenetic relationship and population genetics excellent mark, because retrotrans-position are irreversible and independence. Repeat analysis results show that, the four Riemerella Anatipestifers tandem repeat sequence both in copy number or repeat a consistent sequence unit is highly consistent. We do enrichment analysis of between the repeat sequence region and gene overlap region COG function. The results show that, ATCC-11845, RA-CH-2, RA-the GD of the repeat sequence gene, in the folded, recombinant and modified aspects of the function significantly with significant enrichment, while in other functions, did not appear significant enrichment (significant level=0.05). Strain RA-CH-1all the functionality demonstrated significant enrichment.Bacteriophage is a virus infection of microorganisms such as bacteria, fungi, actinomycetes and spirochetes. Bacteriophage integrated in the genome of host bacteria is called prophage. According to the results of previous studies, the prophage in the growth and reproduction of bacteria and the evolutionary process plays an important role. And containing a prophage in the bacterial chromosome is a very common phenomenon. The prophage integration can increase the chance of bacteria obtain foreign useful sequence, enhanced pathogenicity, or to improve their ability to adapt to the living environment. However, the insertion of the prophage may cause the bacteria are cleaved death. By our detection, four genomes failed to identify the presence of a complete prophage. only some fragments of sequence similarity with the phage or prophage.Genomic Island (GI) is the lateral origin evidence characteristic part of the genome. Depending on the kind of carrying the gene, but also can be divided into the pathogenicity island (PAls), the xenobiotic degradation Islands, the metabolic Island, the resistance Island, fitness Islands. Genomic Island has a symbiotic or pathogenic mechanisms or biocompatibility clustering of gene collection, and they have specific structural features. The GC content, nucleotide bias, and the codon usage of the Genomic Island with respect to the level of the chromosome will exhibit differences. The many genes Island also contains part of the exogenous gene, for example, phages and plasmids movable element, can be achieved to parallel move use the self-splicing to other suitable bacteria. This capability is part of the virulence genes or resistance gene is one important way to move between different bacteria, one of the reasons is caused by bacterial multi-drug resistant. Our results show that, RA-CH-1has10genes Island, but have not been able to find similar Genomic Island in the other three Riemerella Anatipestifers. Have a very high similarity to the DNA sequence of these two genes Islands RGL4and RGL9with Ornithobacterium rhinolracheale DSM15997DNA sequence. ATCC11845. RA-GD and RA-CH-2three genomic island between high similarity. Each strain has unique genetic Island.The genes in genes family have a common ancestor, after multiplication and mutation, to form a collection of genes. From the results of analysis of the gene family as well as homologous gene, RA-CH-1has the most distinctive gene family, and up to16, while the other three is only1-2. The630gene familys are the four Riemerella Anatipestifer have, these gene familys account for about half of the number of all the gene familys.This shows that the gene family types of Riemerella Anatipestifers have high commonality; their complexity of the gene family may have an impact on the biological characteristics.We were the four Riemerella Anatipestifer build a phylogenetic tree. At the same time, the conservative element and non-conservative element also constructed a phylogenetic tree. Found through analysis of the conservative element and the non-conservative element topology is consistent, but the branch lengths are not the same. The phylogenetic tree analysis showed strain RA-CH-1, RA-CH-2and ATCC in the same branch nearest. RA-GD belongs to another branch. The analysis showed that of the non-conserved regions and conserved regions, the Riemerella Anatipestifer of non-conserved regions have a higher mutation rate, the mutation rate is about8times the conserved region.