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
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • 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
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • 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
Genome Sequences

Complete Genome Assembly of Yersinia pseudotuberculosis IP2666pIB1

Adam Zoubeidi, Leah Schwiesow, Victoria Auerbuch, Hanh N. Lam
Vincent Bruno, Editor
Adam Zoubeidi
aDepartment of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Leah Schwiesow
bDepartment of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Victoria Auerbuch
aDepartment of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Hanh N. Lam
aDepartment of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Vincent Bruno
University of Maryland School of Medicine
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/MRA.01592-18
  • Article
  • Info & Metrics
  • PDF
Loading

ABSTRACT

Yersinia pseudotuberculosis, closely related to Yersinia pestis, is a human pathogen and model organism for studying bacterial pathogenesis. To aid in genomic analysis and understanding bacterial virulence, we sequenced and assembled the complete genome of the human pathogen Yersinia pseudotuberculosis IP2666pIB1.

ANNOUNCEMENT

Three species within the Yersinia genus are human pathogens, Yersinia pestis, Yersinia pseudotuberculosis, and Yersinia enterocolitica. All three pathogenic Yersinia species harbor a 70-kb virulence plasmid referred to as pYV, which encodes a type III secretion system critical for virulence (1 – 5). Three mouse virulent Y. pseudotuberculosis strains, YPIII, IP32953, and IP2666, are commonly used for analysis of Y. pseudotuberculosis pathogenicity. The IP2666pIB1 strain, which has been used as the basis for a number of studies (6 – 8), was generated by the Bliska lab (9) by curing the IP2666 strain of its native virulence plasmid and inserting the well-characterized pYV virulence plasmid from YPIII, called pIB1. Although many bacterial genome sequences were released, the IP2666pIB1 genome sequence was not available. Here, we present a complete sequence of the chromosome and pIB1 plasmid of Y. pseudotuberculosis IP2666pIB1.

Y. pseudotuberculosis IP2666pIB1 was grown in 2xYT (yeast extract-tryptone) at 26°C, shaken overnight. The culture was diluted to an optical density (OD600) of 0.1 and grown at 26°C, and cells were pelleted when the culture reached an OD600 of 0.8. Genomic DNA was extracted with a DNeasy blood and tissue kit (Qiagen). The samples were sent to the DNA Technologies Core at the University of California, Davis, for library preparation with the DNA sequencing kit 4.0 v2 with C4 chemistry, PacBio RS II sequencing (library preparation followed by size selection of 15 kb with Blue Pippin), and MiSeq paired-end sequencing with a 300-bp read length.

Trimmomatic version 0.36 (10) was used to trim off low-quality bases and adapter sequences from MiSeq reads. The trimmed, paired-end reads were used to assemble the genome. PacBio sequences were trimmed with Canu 1.7 (11) during assembly. The average PacBio sequence length is 20 kb. The genome sequence was assembled from two data sets from PacBio long reads (161,000 reads) and MiSeq paired-end reads (2,956,000 reads), resulting in more than 50× coverage. The two data sets were assembled together with SPAdes v3.11.1 (12), and PacBio reads were assembled with Canu 1.7 using default parameters (11). Outputs from the two programs were aligned and visualized in SeaView v4.5.2 (13). The assembled genome was manually inspected and curated in Artemis 16.0.0 (14) to a high-quality completion (15). Briefly, at positions where there were differences between the two assembled sequences aligned and visualized in SeaView, the high-quality sequence reads aligned to the genome were inspected in Artemis to reconcile the disagreements. The genome sequence was annotated with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (16, 17).

The chromosome size is 4,614,856 bp, with 47.5% GC content, 4,115 predicted coding sequences, 102 ribosomal and transfer RNAs, and 182 pseudogenes. The pIB1 virulence plasmid showed 44.8% GC content and 96 coding sequences. It is important to note that, unlike Y. pestis CO92 (GenBank accession number NC_003143) and Y. pseudotuberculosis IP32953 (GenBank accession number NZ_CP009712), the entire high-pathogenicity island on the pgm locus (18) containing yersiniabactin biosynthetic genes is absent in this strain, which is similar to Y. pseudotuberculosis YPIII (GenBank accession number CP009792) (19).

Data availability.The Yersinia pseudotuberculosis IP2666pIB1 project has been deposited in the National Center of Biotechnology Information (NCBI) under the accession numbers CP032566 and CP032567 (BioProject number PRJNA475632). The raw sequencing reads have also been submitted to the Sequence Read Archive (SRA) under accession numbers SRR8061175, SRR8061176, and SRR8061177.

ACKNOWLEDGMENTS

Research reported in this publication was supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under award number R01AI119082 (to V.A.).

We thank Jim Bliska for his gift of Yersinia pseudotuberculosis IP2666pIB1 for our study.

FOOTNOTES

    • Received 30 November 2018.
    • Accepted 22 January 2019.
    • Published 14 February 2019.
  • Copyright © 2019 Zoubeidi et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

REFERENCES

  1. 1.↵
    1. Portnoy DA,
    2. Wolf-Watz H,
    3. Bolin I,
    4. Beeder AB,
    5. Falkow S
    . 1984. Characterization of common virulence plasmids in Yersinia species and their role in the expression of outer membrane proteins. Infect Immun 43:108–114.
    OpenUrlAbstract/FREE Full Text
  2. 2.↵
    1. Ben-Gurion R,
    2. Shafferman A
    . 1981. Essential virulence determinants of different Yersinia species are carried on a common plasmid. Plasmid 5:183–187. doi:10.1016/0147-619X(81)90019-6.
    OpenUrlCrossRefPubMedWeb of Science
  3. 3.↵
    1. Gemski P,
    2. Lazere JR,
    3. Casey T
    . 1980. Plasmid associated with pathogenicity and calcium dependency of Yersinia enterocolitica. Infect Immun 27:682–685.
    OpenUrlAbstract/FREE Full Text
  4. 4.↵
    1. Ferber DM,
    2. Brubaker RR
    . 1981. Plasmids in Yersinia pestis. Infect Immun 31:839–841.
    OpenUrlAbstract/FREE Full Text
  5. 5.↵
    1. Gemski P,
    2. Lazere JR,
    3. Casey T,
    4. Wohlhieter JA
    . 1980. Presence of a virulence-associated plasmid in Yersinia pseudotuberculosis. Infect Immun 28:1044–1047.
    OpenUrlAbstract/FREE Full Text
  6. 6.↵
    1. Garrity-Ryan LK,
    2. Kim OK,
    3. Balada-Llasat J-M,
    4. Bartlett VJ,
    5. Verma AK,
    6. Fisher ML,
    7. Castillo C,
    8. Songsungthong W,
    9. Tanaka SK,
    10. Levy SB,
    11. Mecsas J,
    12. Alekshun MN
    . 2010. Small molecule inhibitors of LcrF, a Yersinia pseudotuberculosis transcription factor, attenuate virulence and limit infection in a murine pneumonia model. Infect Immun 78:4683–4690. doi:10.1128/IAI.01305-09.
    OpenUrlAbstract/FREE Full Text
  7. 7.↵
    1. Fisher ML,
    2. Castillo C,
    3. Mecsas J
    . 2007. Intranasal inoculation of mice with Yersinia pseudotuberculosis causes a lethal lung infection that is dependent on Yersinia outer proteins and PhoP. Infect Immun 75:429–442. doi:10.1128/IAI.01287-06.
    OpenUrlAbstract/FREE Full Text
  8. 8.↵
    1. Auerbuch V,
    2. Isberg RR
    . 2007. Growth of Yersinia pseudotuberculosis in mice occurs independently of Toll-like receptor 2 expression and induction of interleukin-10. Infect Immun 75:3561–3570. doi:10.1128/IAI.01497-06.
    OpenUrlAbstract/FREE Full Text
  9. 9.↵
    1. Bliska JB,
    2. Guan KL,
    3. Dixon JE,
    4. Falkow S
    . 1991. Tyrosine phosphate hydrolysis of host proteins by an essential Yersinia virulence determinant. Proc Natl Acad Sci USA 88:1187–1191. doi:10.1073/pnas.88.4.1187.
    OpenUrlAbstract/FREE Full Text
  10. 10.↵
    1. Bolger AM,
    2. Lohse M,
    3. Usadel B
    . 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi:10.1093/bioinformatics/btu170.
    OpenUrlCrossRefPubMedWeb of Science
  11. 11.↵
    1. Koren S,
    2. Walenz BP,
    3. Berlin K,
    4. Miller JR,
    5. Bergman NH,
    6. Phillippy AM
    . 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27:722–736. doi:10.1101/gr.215087.116.
    OpenUrlAbstract/FREE Full Text
  12. 12.↵
    1. Bankevich A,
    2. Nurk S,
    3. Antipov D,
    4. Gurevich AA,
    5. Dvorkin M,
    6. Kulikov AS,
    7. Lesin VM,
    8. Nikolenko SI,
    9. Pham S,
    10. Prjibelski AD,
    11. Pyshkin AV,
    12. Sirotkin AV,
    13. Vyahhi N,
    14. Tesler G,
    15. Alekseyev MA,
    16. Pevzner PA
    . 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi:10.1089/cmb.2012.0021.
    OpenUrlCrossRefPubMed
  13. 13.↵
    1. Gouy M,
    2. Guindon S,
    3. Gascuel O
    . 2010. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27:221–224. doi:10.1093/molbev/msp259.
    OpenUrlCrossRefPubMedWeb of Science
  14. 14.↵
    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 16:944–945. doi:10.1093/bioinformatics/16.10.944.
    OpenUrlCrossRefPubMedWeb of Science
  15. 15.↵
    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 CS,
    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 KE,
    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, Genomic Standards Consortium Human Microbiome Project Jumpstart Consortium
    , Detter JC. 2009. Genome project standards in a new era of sequencing. Science 326:236–237. doi:10.1126/science.1180614.
    OpenUrlAbstract/FREE Full Text
  16. 16.↵
    1. Haft DH,
    2. DiCuccio M,
    3. Badretdin A,
    4. Brover V,
    5. Chetvernin V,
    6. O’Neill K,
    7. Li W,
    8. Chitsaz F,
    9. Derbyshire MK,
    10. Gonzales NR,
    11. Gwadz M,
    12. Lu F,
    13. Marchler GH,
    14. Song JS,
    15. Thanki N,
    16. Yamashita RA,
    17. Zheng C,
    18. Thibaud-Nissen F,
    19. Geer LY,
    20. Marchler-Bauer A,
    21. Pruitt KD
    . 2018. RefSeq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res 46:D851–D860. doi:10.1093/nar/gkx1068.
    OpenUrlCrossRefPubMed
  17. 17.↵
    1. Tatusova T,
    2. DiCuccio M,
    3. Badretdin A,
    4. Chetvernin V,
    5. Nawrocki EP,
    6. Zaslavsky L,
    7. Lomsadze A,
    8. Pruitt KD,
    9. Borodovsky M,
    10. Ostell J
    . 2016. NCBI Prokaryotic Genome Annotation Pipeline. Nucleic Acids Res 44:6614–6624. doi:10.1093/nar/gkw569.
    OpenUrlCrossRefPubMed
  18. 18.↵
    1. Buchrieser C,
    2. Rusniok C,
    3. Frangeul L,
    4. Couve E,
    5. Billault A,
    6. Kunst F,
    7. Carniel E,
    8. Glaser P
    . 1999. The 102-kilobase pgm locus of Yersinia pestis: sequence analysis and comparison of selected regions among different Yersinia pestis and Yersinia pseudotuberculosis strains. Infect Immun 67:4851–4861.
    OpenUrlAbstract/FREE Full Text
  19. 19.↵
    1. Rakin A,
    2. Schneider L,
    3. Podladchikova O
    . 2012. Hunger for iron: the alternative siderophore iron scavenging systems in highly virulent Yersinia. Front Cell Infect Microbiol 2:151. doi:10.3389/fcimb.2012.00151.
    OpenUrlCrossRefPubMed
View Abstract
PreviousNext
Back to top
Download PDF
Citation Tools
Complete Genome Assembly of Yersinia pseudotuberculosis IP2666pIB1
Adam Zoubeidi, Leah Schwiesow, Victoria Auerbuch, Hanh N. Lam
Microbiology Resource Announcements Feb 2019, 8 (7) e01592-18; DOI: 10.1128/MRA.01592-18

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.
Complete Genome Assembly of Yersinia pseudotuberculosis IP2666pIB1
(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.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Complete Genome Assembly of Yersinia pseudotuberculosis IP2666pIB1
Adam Zoubeidi, Leah Schwiesow, Victoria Auerbuch, Hanh N. Lam
Microbiology Resource Announcements Feb 2019, 8 (7) e01592-18; DOI: 10.1128/MRA.01592-18
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • 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

 

American Society for Microbiology
1752 N St. NW
Washington, DC 20036
Phone: (202) 737-3600

Copyright © 2021 American Society for Microbiology | Privacy Policy | Website feedback

Online ISSN: 2576-098X