Abstract
Riemerella anatipestifer is a well-described pathogenic bacterium, which is reported worldwide as the cause of epizootic infectious polyserositis of waterfowl and other avian species. Here, we present the complete genome sequence of R. anatipestifer strain CH3, the serotype 1 prevalent in China.
GENOME ANNOUNCEMENT
Riemerella anatipestifer is a Gram-negative rod-shaped bacterium which was first reported by Riemer as a pathogen of geese (1). It has been isolated from all kinds of avian hosts, including ducks, turkeys, chickens, and other birds (2, 3). In domestic ducks, R. anatipestifer causes epizootic infectious polyserositis, characterized by lethargy, diarrhea, and respiratory and nervous symptoms, which lead to high mortality and consequently to great economic losses (4). Currently, 21 serotypes of R. anatipestifer have been identified, and no significant cross-protection has been reported (5). Infections by R. anatipestifer serotype 1, 2, 3, 5, 6, 7, 8, 10, 11, 13, 14, and 15 strains have been reported in China, with serotypes 1, 2, and 10 responsible for most of the major outbreaks (6). There have been several genomic resources available for R. anatipestifer (7, 8). Here, we report another complete genome sequence of R. anatipestifer serotype 1 strain CH3.
The complete genomic sequencing was conducted using a Roche GS FLX system (9). A total of 186,353 reads totaling 70,430,692 bases (average read length, 377 bp) was obtained, resulting in 11-fold genome coverage. Newbler software (version 2.3) (Roche) was used for sequence assembly. Sequence gaps were filled in by first determining the order of contigs using multiplex PCR (10) and then sequencing the PCR products using ABI 3730xl capillary sequencers. Low-quality regions of the genome were resequenced to obtain the complete linear genome sequence. The final sequencing accuracy was 99.99%. Putative coding sequences (CDS) were identified by Glimmer 3.02 (11) and the Z-Curve program (12). Transfer RNA genes were predicted by tRNAscan-SE (13), while rRNAs were predicted by RNAmmer (14). Functional annotation of CDSs was performed through searching against the nr protein database using BLASTP (15). Clusters of orthologous group (COG) function classifications were performed using the CDD database (http://www.ncbi.nlm.nih.gov/cdd) (16). Orthologs and paralogs were defined as proteins with greater than 30% similarity. The metabolic pathways were constructed using the KEGG database (http://www.genome.jp/kegg/).
R. anatipestifer strain CH3 possesses a single circular chromosome of 2,234,477 bp with a coding percentage of 90.0%. The genome contains 2,186 putative open reading frames (ORFs) with an average length of 920 bp, 9 rRNA operons, and 41 tRNA genes. Of the ORFs, 2,041 were protein-coding genes. The majority of the protein-coding genes (1,359 [66.59%]) were classified into the COG families comprising 20 functional categories. Using KEGG, 908 ORFs (44.49%) were assigned to 30 pathways.
Among all proteins, 16 proteins involved in peptidoglycan biosynthesis and 12 proteins involved in lipopolysaccharide (LPS) biosynthesis were identified. LPS, which functions as an endotoxin, an adhesin, and a modulator of the immune response, is an important virulence factor for numerous bacteria (17–19). The genome sequence provides essential information on understanding the molecular pathogenesis and protective mechanism of R. anatipestifer.
Nucleotide sequence accession number.
This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession no. CP006649. The version described in this paper is the first version.
ACKNOWLEDGMENT
This work was supported by the National Natural Science Foundation of China (31272591).
Footnotes
Citation Wang X, Ding C, Han X, Wang S, Yue J, Hou W, Cao S, Zou J, Yu S. 2015. Complete genome sequence of Riemerella anatipestifer serotype 1 strain CH3. Genome Announc 3(1):e01594-14. doi:10.1128/genomeA.01594-14.
REFERENCES
- 1.Riemer O. 1904. Short communication about an exudative septicaemia observed in geese and its causative agent. Zentralblatt Bakteriologie Originale 37:641–648. [Google Scholar]
- 2.Helfer DH, Helmboldt CF. 1977. Pasteurella anatipestifer infection in turkeys. Avian Dis 21:712–715. doi: 10.2307/1589432. [DOI] [PubMed] [Google Scholar]
- 3.Leavitt S, Ayroud M. 1997. Riemerella anatipestifer infection of domestic ducklings. Can Vet J 38:113. [PMC free article] [PubMed] [Google Scholar]
- 4.Sandhu TS. 1986. Important diseases of ducks, p 111-134. In Farrell DJ, Stapleton P (ed), Duck production science and world practice. University of New England, Armidale, Australia. [Google Scholar]
- 5.Pathanasophon P, Phuektes P, Tanticharoenyos T, Narongsak W, Sawada T. 2002. A potential new serotype of Riemerella anatipestifer isolated from ducks in Thailand. Avian Pathol 31:267–270. doi: 10.1080/03079450220136576. [DOI] [PubMed] [Google Scholar]
- 6.Hu Q, Zhang Z, Miao J, Liu Y, Liu X, Ding S. 2001. The epidemiology study of Riemerella anatipestifer infection in Jiangsu and Anhui provinces. Chinese J Vet Sci Technol 31:12–13. doi: 10.3969/j.issn.1673-4696.2001.08.005. [DOI] [Google Scholar]
- 7.Mavromatis K, Lu M, Misra M, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng J-F, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K. 2011. Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845). Stand Genomic Sci 4:144–153. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Yuan J, Liu W, Sun M, Song S, Cai J, Hu S. 2011. Complete genome sequence of the pathogenic bacterium Riemerella anatipestifer strain RA-GD. J Bacteriol 193:2896–2897. doi: 10.1128/JB.00301-11. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen Y-J, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Ho CH, Irzyk GP. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380. doi: 10.1038/nature03959. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Tettelin H, Radune D, Kasif S, Khouri H, Salzberg SL. 1999. Optimized multiplex PCR: efficiently closing a whole-genome shotgun sequencing project. Genomics 62:500–507. doi: 10.1006/geno.1999.6048. [DOI] [PubMed] [Google Scholar]
- 11.Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. BioInformatics 23:673–679. doi: 10.1093/bioinformatics/btm009. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Guo FB, Ou HY, Zhang CT. 2003. ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes. Nucleic Acids Res 31:1780–1789. doi: 10.1093/nar/gkg254. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Schattner P, Brooks AN, Lowe TM. 2005. The tRNAscan-SE, snoscan and snoGPS Web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 33:W686–W689. doi: 10.1093/nar/gki366. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Lagesen K, Hallin P, Rødland EA, Stærfeldt H-H, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108. doi: 10.1093/nar/gkm160. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15.Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402. doi: 10.1093/nar/25.17.3389. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 16.Marchler-Bauer A, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, Gwadz M, Hao L, He S, Hurwitz DI, Jackson JD, Ke Z, Krylov D, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS. 2007. CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res 35:D237–D240. doi: 10.1093/nar/gkl951. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17.Morona R, Daniels C, Van Den Bosch L. 2003. Genetic modulation of Shigella flexneri 2a lipopolysaccharide O antigen modal chain length reveals that it has been optimized for virulence. Microbiology 149:925–939. doi: 10.1099/mic.0.26141-0. [DOI] [PubMed] [Google Scholar]
- 18.Schaeffer LM, McCormack FX, Wu H, Weiss AA. 2004. Bordetella pertussis lipopolysaccharide resists the bactericidal effects of pulmonary surfactant protein A. J Immunol 173:1959–1965. doi: 10.4049/jimmunol.173.3.1959. [DOI] [PubMed] [Google Scholar]
- 19.Lüneberg E, Mayer B, Daryab N, Kooistra O, Zähringer U, Rohde M, Swanson J, Frosch M. 2001. Chromosomal insertion and excision of a 30 kb unstable genetic element is responsible for phase variation of lipopolysaccharide and other virulence determinants in Legionella pneumophila. Mol Microbiol 39:1259–1271. doi: 10.1111/j.1365-2958.2001.02314.x. [DOI] [PubMed] [Google Scholar]