Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Latest Articles
    • Archive
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Microbiology Resource Announcements
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Latest Articles
    • Archive
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
Prokaryotes

Genome Sequence of Chlamydia psittaci Strain 01DC12 Originating from Swine

Helena M. B. Seth-Smith, Michelle Sait, Konrad Sachse, Wolfgang Gaede, David Longbottom, Nicholas R. Thomson
Helena M. B. Seth-Smith
Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Michelle Sait
Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Konrad Sachse
Friedrich-Loeffler-Institute (Federal Research Institute for Animal Health), Institute of Molecular Pathogenesis, Jena, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Wolfgang Gaede
State Institute for Consumer Protection of Saxony-Anhalt, Dept. for Veterinary Medicine, Stendal, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
David Longbottom
Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nicholas R. Thomson
Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/genomeA.00078-12
  • Article
  • Info & Metrics
  • PDF
Loading

ABSTRACT

Chlamydia psittaci is the etiological agent of psittacosis and is a zoonotic pathogen infecting birds and a variety of mammalian hosts. Here we report the genome sequence of the porcine strain 01DC12 which is representative of a novel clade of C. psittaci belonging to ompA genotype E.

GENOME ANNOUNCEMENT

Chlamydia psittaci is a Gram-negative, obligate intracellular bacterium and is the etiological agent of psittacosis, causing disease primarily in birds but also infecting a variety of mammals, including humans. C. psittaci has been isolated from the lungs (1), genital tract (2), and semen (3) of pigs. At least 15 different genotypes have been defined on the basis of the ompA gene sequence variation (4). Here we report the genome sequence of 01DC12, a strain that was isolated from a pig in Saxony-Anhalt, Germany.

The C. psittaci 01DC12 genome was sequenced using the Illumina HiSeq platform with 75-bp paired-end reads, resulting in a mean genome coverage of 248×. Reads were assembled using Velvet v1.0.12 (5) to produce 8 contigs, which were ordered against the C. psittaci strain RD1 genome (6). These were finished manually and using GapFiller (7), resulting in an improved high-quality draft genome sequence (8) consisting of 2 contigs. The chromosome of C. psittaci 01DC12 comprises 1,171,011 bp, with G+C content of 39.0%. Annotation was transferred from strain RD1 using annotations_update (https://github.com/sanger-pathogens/annotations_update) on the basis of BLASTN similarity using the default settings, and manually curated using Artemis (9). Comparative analysis with closely related C. psittaci strains (10–12) was performed using ACT (13). The remaining gap, estimated at 2599 bp, is predicted to encode C and N termini of repetitive pmp genes. This region plus the gaps filled using GapFiller are marked in the genome annotation.

The genome contains 963 predicted coding sequences (CDSs), a single rRNA operon, and 38 tRNA genes. Analysis of the ompA gene confirms that C. psittaci 01DC12 belongs to genotype E. Sequence analysis of the 7 loci used for multilocus sequence typing (MLST) (14) assigned gatA, hemN, and hflX to allele 11, enoA and fumC to allele 13, and gidA and oppA to allele 14, indicating that C. psittaci 01DC12 is a novel MLST sequence type. Comparison with the genome of type strain 6BC (10, 11) shows that the 01DC12 chromosome contains deletions of 360 bp and 144 bp, respectively, in two putative membrane proteins (BN356_2661 and BN356_4221) and a deletion of an 802-bp repeat at the C terminus of an incA/TMH-family membrane protein (BN356_7881). Comparative mapping against strain 6BC revealed 6,262 single-nucleotide polymorphisms (SNPs), suggesting that strain 01DC12 represents a new lineage within C. psittaci. A total of 11 pseudogenes were identified in the genome of 01DC12, including those predicted to encode an aldolase (BN356_2651), Pmp8G (BN356_2811), 6 membrane proteins (BN356_3711, BN356_5531, BN356_5541, BN356_5601, BN356_5741, and BN356_6271), a Mycobacterium avium complex (MAC)/perforin-domain protein (BN356_5611), and an IncA-family protein (BN356_7871). The genome of strain 01DC12 includes a single plasmid of 7553 bp with G+C content of 32.8%, predicted to encode 8 CDSs. Plasmid p01DC12 is differentiated from the plasmid carried by strain 6BC by 2 SNPs (10, 11): one synonymous SNP in a putative helicase (BN356_p003) and one nonsynonymous SNP resulting in a T-I change in hypothetical protein BN356_p008.

Nucleotide sequence accession numbers.The genome and plasmid sequences of C. psittaci 01DC12 have been deposited in EMBL under accession numbers HF545614 and HF545615.

ACKNOWLEDGMENTS

This work was supported by the Wellcome Trust (grant number 098051), by the Biotechnology and Biological Sciences Research Council (BBSRC) (grant number BB/E018939/1), and by the Scottish Government Rural and Environment Research and Analysis Directorate (RERAD).

FOOTNOTES

    • Received 30 October 2012.
    • Accepted 7 November 2012.
    • Published 15 January 2013.
  • Copyright © 2013 Seth-Smith et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.

REFERENCES

  1. 1.↵
    1. Vanrompay D,
    2. Geens T,
    3. Desplanques A,
    4. Hoang TQ,
    5. De Vos L,
    6. Van Loock M,
    7. Huyck E,
    8. Cox E,
    9. Cox E
    . 2004. Immunoblotting, ELISA and culture evidence for Chlamydiaceae in sows on 258 Belgian farms. Vet. Microbiol. 99(1):56–66.
    OpenUrl
  2. 2.↵
    1. Busch M,
    2. Thoma R,
    3. Schiller I,
    4. Corboz L,
    5. Pospischil A
    . 2000. Occurrence of chlamydiae in the genital tracts of sows at slaughter and their possible significance for reproductive failure. J. Vet. Med. B Infect. Dis. Vet. Public Health 47(6):471–480.
    OpenUrlPubMedWeb of Science
  3. 3.↵
    1. Kauffold J,
    2. Melzer F,
    3. Henning K,
    4. Schulze K,
    5. Leiding C,
    6. Sachse K
    . 2006. Prevalence of chlamydiae in boars and semen used for artificial insemination. Theriogenology 65(9):1750–1758.
    OpenUrlCrossRefPubMedWeb of Science
  4. 4.↵
    1. Sachse K,
    2. Laroucau K,
    3. Hotzel H,
    4. Schubert E,
    5. Ehricht R,
    6. Slickers P
    . 2008. Genotyping of Chlamydophila psittaci using a new DNA microarray assay based on sequence analysis of ompA genes. BMC Microbiol. 8:63.
    OpenUrlCrossRefPubMed
  5. 5.↵
    1. Zerbino DR,
    2. Birney E
    . 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18(5):821–829.
    OpenUrlAbstract/FREE Full Text
  6. 6.↵
    1. Seth-Smith HM,
    2. Harris SR,
    3. Range R,
    4. West AP,
    5. Severin JA,
    6. Ossewaarde JM,
    7. Cutcliffe LT,
    8. Skilton RJ,
    9. Marsh P,
    10. Parkhill J,
    11. Clarke IN,
    12. Thomson NR
    . 2011. Genome sequence of the zoonotic pathogen Chlamydophila psittaci. J. Bacteriol. 193(5):1282–1283.
    OpenUrlAbstract/FREE Full Text
  7. 7.↵
    1. Boetzer M,
    2. Pirovano W
    . 2012. Toward almost closed genomes with GapFiller. Genome Biol. 13(6):R56.
    OpenUrlCrossRefPubMed
  8. 8.↵
    1. Chain PSG,
    2. Grafham DV,
    3. Fulton RS,
    4. FitzGerald MG,
    5. Hostetler J,
    6. Muzny D,
    7. Ali J,
    8. Birren B,
    9. Bruce DC,
    10. Buhay C,
    11. Cole JR,
    12. Ding Y,
    13. Dugan S,
    14. Field D,
    15. Garrity GM,
    16. Gibbs R,
    17. Graves T,
    18. Han S,
    19. Harrison SH,
    20. Highlander S,
    21. Hugenholtz P,
    22. Khouri HM,
    23. Kodira CD,
    24. Kolker E,
    25. Kyrpides NC,
    26. Lang D,
    27. Lapidus A,
    28. Malfatti SA,
    29. Markowitz V,
    30. Metha T,
    31. Nelson KEKE,
    32. Parkhill J,
    33. Pitluck S,
    34. Qin X,
    35. Read TD,
    36. Schmutz J,
    37. Sozhamannan S,
    38. Sterk P,
    39. Strausberg RL,
    40. Sutton G,
    41. Thomson NR,
    42. Tiedje JM,
    43. Weinstock G,
    44. Wollam A,
    45. Genomic Standards Consortium Human Microbiome Project Jumpstart Consortium
    46. Detter JC
    . 2009. Genome project standards in a new era of sequencing. Science 326:236–237.
    OpenUrlAbstract/FREE Full Text
  9. 9.↵
    1. Rutherford K,
    2. Parkhill J,
    3. Crook J,
    4. Horsnell T,
    5. Rice P,
    6. Rajandream MA,
    7. Barrell B
    . 2000. Artemis: sequence visualization and annotation. Bioinformatics 16(10):944–945.
    OpenUrlCrossRefPubMedWeb of Science
  10. 10.↵
    1. Voigt A,
    2. Schöfl G,
    3. Heidrich A,
    4. Sachse K,
    5. Saluz HP
    . 2011. Full-length de novo sequence of the Chlamydophila psittaci type strain 6 bc. J. Bacteriol. 193(10):2662–2663.
    OpenUrlAbstract/FREE Full Text
  11. 11.↵
    1. Grinblat-Huse V,
    2. Drabek EF,
    3. Huot Creasy H,
    4. Daugherty SC,
    5. Jones KM,
    6. Santana-Cruz I,
    7. Tallon LJ,
    8. Read TD,
    9. Hatch TP,
    10. Bavoil P,
    11. Myers GSA
    . 2011. Genome sequences of the zoonotic pathogens Chlamydia psittaci 6 bc and Cal10. J. Bacteriol. 193(15):4039–4040.
    OpenUrlAbstract/FREE Full Text
  12. 12.↵
    1. Schöfl G,
    2. Voigt A,
    3. Litsche K,
    4. Sachse K,
    5. Saluz HP
    . 2011. Complete genome sequences of four mammalian isolates of Chlamydophila psittaci. J. Bacteriol. 193(16):4258.
    OpenUrlAbstract/FREE Full Text
  13. 13.↵
    1. Carver TJ,
    2. Rutherford KM,
    3. Berriman M,
    4. Rajandream MA,
    5. Barrell BG,
    6. Parkhill J
    . 2005. ACT: the Artemis comparison tool. Bioinformatics 21(16):3422–3423.
    OpenUrlCrossRefPubMedWeb of Science
  14. 14.↵
    1. Pannekoek Y,
    2. Dickx V,
    3. Beeckman DSA,
    4. Jolley KA,
    5. Keijzers WC,
    6. Vretou E,
    7. Maiden MCJ,
    8. Vanrompay D,
    9. van der Ende A
    . 2010. Multi locus sequence typing of chlamydia reveals an association between Chlamydia psittaci genotypes and host species. PLoS One 5(12):e14179.
    OpenUrlCrossRefPubMed
View Abstract
PreviousNext
Back to top
Download PDF
Citation Tools
Genome Sequence of Chlamydia psittaci Strain 01DC12 Originating from Swine
Helena M. B. Seth-Smith, Michelle Sait, Konrad Sachse, Wolfgang Gaede, David Longbottom, Nicholas R. Thomson
Genome Announcements Jan 2013, 1 (1) e00078-12; DOI: 10.1128/genomeA.00078-12

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Print
Alerts
Sign In to Email Alerts with your Email Address
Email

Thank you for sharing this Microbiology Resource Announcements article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
Genome Sequence of Chlamydia psittaci Strain 01DC12 Originating from Swine
(Your Name) has forwarded a page to you from Microbiology Resource Announcements
(Your Name) thought you would be interested in this article in Microbiology Resource Announcements.
Share
Genome Sequence of Chlamydia psittaci Strain 01DC12 Originating from Swine
Helena M. B. Seth-Smith, Michelle Sait, Konrad Sachse, Wolfgang Gaede, David Longbottom, Nicholas R. Thomson
Genome Announcements Jan 2013, 1 (1) e00078-12; DOI: 10.1128/genomeA.00078-12
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • GENOME ANNOUNCEMENT
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • Info & Metrics
  • PDF

Related Articles

Cited By...

About

  • About MRA
  • Editor in Chief
  • Board of Editors
  • Policies
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • Getting Started
  • Submit a Manuscript
  • Author Warranty
  • Ethics
  • Contact Us
  • ASM Author Center

Follow #MRAJournal

@ASMicrobiology

       

ASM Journals

ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.

About ASM | Contact Us | Press Room

 

ASM is a member of

Scientific Society Publisher Alliance

Copyright © 2019 American Society for Microbiology | Privacy Policy | Website feedback

Online ISSN: 2576-098X