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J Bacteriol. May 2011; 193(10): 2662–2663.
PMCID: PMC3133153
Full-Length De Novo Sequence of the Chlamydophila psittaci Type Strain, 6BC [down-pointing small open triangle]
Anja Voigt,1 Gerhard Schöfl,1 Alexander Heidrich,1 Konrad Sachse,2 and Hans Peter Saluz1,3*
1Department of Cell and Molecular Biology, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
2Friedrich-Löffler-Institute (Federal Research Institute for Animal Health), Institute of Molecular Pathogenesis, Jena, Germany
3Friedrich Schiller University, Jena, Germany
*Corresponding author. Mailing address: Department of Cell and Molecular Biology, Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstrasse 11a, Jena D-07745, Germany. Phone: 493 641 532 1201. Fax: 493 641 532 2361. E-mail: Hanspeter.Saluz/at/hki-jena.de.
Received February 18, 2011; Accepted March 11, 2011.
Abstract
Chlamydophila psittaci is an obligate intracellular zoonotic pathogen, mainly of birds. It is the causative agent of psittacosis in birds and humans. Here we report the full-length de novo genome sequence of the avian isolate 6BC, the type strain of the species C. psittaci.
Chlamydophila psittaci, the pathogenic agent of psittacosis (parrot disease or ornithosis) (14), is an obligate intracellular Gram-negative bacterium reported to infect a wide range of primarily avian, but also other vertebrate hosts: e.g., cattle, goats, horses, or crocodiles (12, 17). Transmissions from birds to humans occur (7, 10, 18).
The avian isolate 6BC was the original type strain of the former species Chlamydia psittaci (16) and has been retained as the type strain of the emended species Chlamydophila psittaci (5).
Strain 6BC was isolated originally from a parakeet in California in 1941 (ATCC no. VR-125). This sample was donated to K.S. by D. Vanrompay (University of Ghent, Belgium) in 2004 and has been passaged in BGMK (Buffalo green monkey kidney) cells on a regular basis.
To facilitate discrimination between chlamydial DNA and contaminant host DNA, C. psittaci 6BC cells were proliferated in human HeLa cells (ATCC no. CCL-2) prior to DNA extraction. We used a combination of Roche 454 pyrosequencing, Illumina, and Sanger sequencing to determine the complete genomic sequence of C. psittaci 6BC. Approximately 28 million 40-bp reads were obtained on an Illumina Genome analyzer II, and 47,000 reads of an average length of 386 bp were obtained on a Roche Genome sequencer FLX.
A backbone sequence was constructed by assembling all reads with MIRA3 (2). Gaps were closed with Gap 4.10 (1), and contig order was verified by PCR and Sanger sequencing. To locate areas of low (<10-fold) coverage and potential ambiguities, all Illumina reads were remapped against the completed sequence backbone. On average, a 487-fold sequence coverage was achieved. Sections of low coverage were confirmed by subsequent Sanger sequencing.
The DNA sequence was annotated by using the ISGA pipeline (11), available at http://isga.cgb.indiana.edu/. Briefly, potential protein-, rRNA-, and tRNA-coding genes were predicted by Glimmer3 (3), RNAmmer (13), and tRNAscan-SE (15), respectively. The predicted protein sequences were searched against nonredundant protein databases (NCBI, SwissProt, and Protein Data Bank) with AB-BLASTp (8). The predicted proteins were compared against the PFAM (6) and TIGRFAM (9) databases with HMMPFAM (4). The results from these analyses were combined into a gene function prediction that informed a manual annotation of the sequence and predicted proteins.
The genome is composed of a circular 1,171,660-bp chromosome containing 967 predicted protein-coding genes and a 7,553-bp plasmid containing 8 protein-coding sequences.
Comparison of C. psittaci 6BC, Chlamydophila abortus S26/3 (accession no. NC_004552), Chlamydophila felis Fe/C-56 (NC_007899), and Chlamydophila caviae GPIC (NC_003361) revealed high colinearity. The C. psittaci genome contains 38 tRNA genes and one rRNA operon containing three (5S, 23S, and 16S) rRNAs. The bacterial chromosome has a GC content of 39.06%, similar to other Chlamydiaceae. A total of 89.39% of the C. psittaci genome is predicted to be coding sequences.
Nucleotide sequence accession numbers.
The genome sequence of C. psittaci strain 6BC has been deposited in GenBank and assigned accession no. CP002549 (chromosome) and CP002550 (plasmid).
Acknowledgments
We are grateful to Daisy Vanrompay for sharing C. psittaci 6BC with us. We thank Melanie Grigsby for proofreading the manuscript. We are indebted to Mathias Platzer for providing computer facilities and GATC Biotech AG (Konstanz, Germany) for the prompt delivery of sequencing data.
This study was supported by BMBF, Germany (grant 01KI0724 to H.P.S.), and by the Graduate School of Excellence Jena School for Microbial Communication (JSMC).
Footnotes
[down-pointing small open triangle]Published ahead of print on 25 March 2011.
1. Bonfield J. K., Smith K. F., Staden R. 1995. A new DNA sequence assembly program. Nucleic Acids Res. 23:4992–4999. [PMC free article] [PubMed]
2. Chevreux B., Pfisterer T., Suhai S. 2000. Automatic assembly and editing of genomic sequences, p. 51–65 In Suhai S., editor. (ed.), Genomics and proteomics—functional and computational aspects. Kluwer Academic/Plenum Publishers, New York, NY.
3. Delcher A. L., Harmon D., Kasif S., White O., Salzberg S. L. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27:4636–4641. [PMC free article] [PubMed]
4. Eddy S. R. 1998. Profile hidden Markov models. Bioinformatics 14:755–763. [PubMed]
5. Everett K. D., Bush R. M., Andersen A. A. 1999. Emended description of the order Chlamydiales, proposal of Parachlamydiaceae fam. nov. and Simkaniaceae fam. nov., each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae, including a new genus and five new species, and standards. Int. J. Syst. Bacteriol. 49:415–440. [PubMed]
6. Finn R. D., et al. 2010. The Pfam protein families database. Nucleic Acids Res. 38:D211–D222. [PMC free article] [PubMed]
7. Gaede W., et al. 2008. Chlamydophila psittaci infections in humans during an outbreak of psittacosis from poultry in Germany. Zoonoses Public Health 55:184–188. [PubMed]
8. Gish W. 2009. AB-BLASTp. Advanced Biocomputing LLC. St. Louis, MO.
9. Haft D. H., et al. 2001. TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res. 29:41–43. [PMC free article] [PubMed]
10. Harkinezhad T., et al. 2009. Prevalence of Chlamydophila psittaci infections in a human population in contact with domestic and companion birds. J. Med. Microbiol. 58:1207–1212. [PubMed]
11. Hemmerich C., Buechlein A., Podicheti R., Revanna K. V., Dong Q. 2010. An Ergatis-based prokaryotic genome annotation web server. Bioinformatics 26:1122–1124. [PubMed]
12. Horn M. 2008. Chlamydiae as symbionts in eukaryotes. Annu. Rev. Microbiol. 62:113–131. [PubMed]
13. Lagesen K., et al. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100–3108. [PMC free article] [PubMed]
14. Longbottom D., Coulter L. J. 2003. Animal chlamydioses and zoonotic implications. J. Comp. Pathol. 128:217–244. [PubMed]
15. Lowe T. M., Eddy S. R. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955–964. [PMC free article] [PubMed]
16. Moulder J. W., Hatch T. P., Kuo C.-C., Schachter J., Storz J. 1984. Genus Chlamydia, p. 729–739 In Krieg N. R., editor. (ed.), Bergey's manual of systematic bacteriology. Williams & Wilkins, Baltimore, MD.
17. Pantchev A., Sting R., Bauerfeind R., Tyczka J., Sachse K. 2010. Detection of all Chlamydophila and Chlamydia spp. of veterinary interest using species-specific real-time PCR assays. Comp. Immunol. Microbiol. Infect. Dis. 33:473–484. [PubMed]
18. Van Droogenbroeck C., et al. 2009. Simultaneous zoonotic transmission of Chlamydophila psittaci genotypes D, F and E/B to a veterinary scientist. Vet. Microbiol. 135:78–81. [PubMed]
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