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
Prokaryotes

Draft Genome Sequence of Curtobacterium sp. Strain UCD-KPL2560 (Phylum Actinobacteria)

Brian A. Klein, Katherine P. Lemon, Lina L. Faller, Guillaume Jospin, Jonathan A. Eisen, David A. Coil
Brian A. Klein
aDepartment of Microbiology, The Forsyth Institute, Cambridge, Massachusetts, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Katherine P. Lemon
aDepartment of Microbiology, The Forsyth Institute, Cambridge, Massachusetts, USA
bDivision of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Lina L. Faller
aDepartment of Microbiology, The Forsyth Institute, Cambridge, Massachusetts, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Guillaume Jospin
cGenome Center, University of California Davis, Davis, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jonathan A. Eisen
cGenome Center, University of California Davis, Davis, California, USA
dDepartment of Evolution and Ecology and Department of Medical Microbiology and Immunology, University of California Davis, Davis, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
David A. Coil
cGenome Center, University of California Davis, Davis, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/genomeA.01040-16
  • Article
  • Info & Metrics
  • PDF
Loading

ABSTRACT

Here, we present the draft genome sequence of the actinobacterium Curtobacterium sp. strain UCD-KPL2560, which was isolated from the running surface of an indoor track field house in Medford, MA, USA (42.409716°N, -71.115169°W). The genome assembly contains 3,480,487 bp in 156 contigs.

GENOME ANNOUNCEMENT

Members of the genus Curtobacterium, which was accepted as a genus in 1972 and refined in 1986 (1, 2), have been previously isolated from soil (3, 4), plants (5), cheese-processing equipment (6), and residential carpet (7). Curtobacterium spp. are characterized as Gram-positive aerobic bacilli that frequently demonstrate yellow-orange pigment when grown in vitro (2). Curtobacterium spp. are not common pathogens of humans; however, Curtobacterium spp. are recognized plant pathogens (8), and rare plant-to-human infections, as well as occasional human host isolation, are reported (9, 10).

We isolated Curtobacterium sp. strain UCD-KPL2560 from the flooring of an indoor track facility in Medford, MA, on 15 October 2015 as part of a project to produce reference genomes for microorganisms residing in the built environment. A nylon-flocked swab (Copan) dipped in sterile buffer (0.1 M NaCl and 0.1% Tween) was rubbed over the track surface starting block area (5 cm2) for 1 min, inoculated onto brain heart infusion agar containing fosfomycin (20 µg/ml), and incubated aerobically at 37°C for five days. A small round orange colony was selected from the original isolation plate and subcultured for purity. For 16S rRNA identification, an initial DNA extraction was performed with the DNeasy purification kit (Qiagen). A putative genus name was assigned to the isolate following PCR amplification (primers 27F and 1492R) and subsequent Sanger sequencing of the 16S rRNA gene. Genomic DNA for whole-genome sequencing was extracted using the MasterPure complete DNA/RNA purification kit (Epicentre).

Illumina paired-end libraries were generated using a Nextera DNA sample prep kit (Illumina). We selected 600- to 900-bp fragments using a Pippin Prep (Sage Science). Resultant libraries were sequenced on an Illumina MiSeq, with a read length of 300 bp. This produced a total of 3,920,338 paired-end reads. Quality trimming and error correction of the reads resulted in 3,506,299 high-quality reads using the A5-MiSeq assembly pipeline (version 05/22/2015) (11, 12). The resulting assembly contained 156 scaffolds (minimum, 598 bp; maximum, 215,854 bp; N50, 36,322 bp). The final assembly contained 3,480,487 bp, with a G+C content of 72% and a coverage estimate of 114% (EC value). Genome completeness was assessed using PhyloSift and CheckM (13, 14); all 37 PhyloSift marker genes were present, with 36 in single copy, and the ribosomal subunit L14 present in four copies. CheckM gave a 99% completeness estimation.

Annotation was performed using the RAST server (default settings on 14 April 2016) (15). Curtobacterium sp. strain UCD-KPL2560 contains 3,201 predicted coding sequences (CDSs), four predicted rRNAS, and 53 predicted tRNAs. It has 12 type IV pilus genes, 34 motility genes, and four auxin biosynthesis genes. At least two partial phages are predicted, and no clustered regularly interspaced short palindromic repeat (CRISPR) systems were identified (15–17).

We attempted to assign a putative species designation to Curtobacterium sp. UCD-KPL2560 using PhyloPhlAn and by generating a 16S-rRNA-gene-based phylogeny of Curtobacterium species curated by the Ribosomal Database Project (18, 19). However, neither yielded an assignment. PhyloPhlAn generated “Clavibacter michiganensis” taxonomic assignments for 16 of 17 Curtobacterium spp., with available NCBI sequencing data (one reclassified as Rothia). Additionally, Curtobacterium sp. UCD-KPL2560 did not fall within a well-supported clade of a single species within the genus Curtobacterium using 16S rRNA alone.

Accession number(s).This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession no. MCIG00000000. The version described in this paper is version MCIG01000000.

ACKNOWLEDGMENTS

We thank Tufts University for access to the Gantcher Indoor Track Center facility and promotion of facilities and microbial research. Sequencing was performed at the DNA Technologies Core facility in the Genome Center at the UC Davis, Davis, CA.

This work was funded in part by a grant (to J.A.E.) and postdoctoral fellowship (to B.A.K.) from the Alfred P. Sloan Foundation as part of their program on the Microbiology of the Built Environment.

FOOTNOTES

    • Received 9 August 2016.
    • Accepted 17 August 2016.
    • Published 6 October 2016.
  • Copyright © 2016 Klein 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. Yamada K,
    2. Komagata K
    . 1972. Taxonomic studies on coryneform bacteria V. Classification of coryneform bacteria. J Gen Appl Microbiol 18:417–431. doi:10.2323/jgam.18.417.
    OpenUrlCrossRef
  2. 2.↵
    1. Komagta K,
    2. Suzuki K
    . 1986. Genus Curtobacterium, p 1313–1317. In Bergey's manual of systematic bacteriology. Williams & Wilkins, Philadelphia, PA.
  3. 3.↵
    1. Kim MK,
    2. Kim YJ,
    3. Kim HB,
    4. Kim SY,
    5. Yi TH,
    6. Yang DC
    . 2008. Curtobacterium ginsengisoli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 58:2393–2397. doi:10.1099/ijs.0.65591-0.
    OpenUrlCrossRefPubMed
  4. 4.↵
    1. Mariita RM,
    2. Bhatnagar S,
    3. Hanselmann K,
    4. Hossain MJ,
    5. Korlach J,
    6. Boitano M,
    7. Roberts RJ,
    8. Liles MR,
    9. Moss AG,
    10. Leadbetter JR,
    11. Newman DK,
    12. Dawson SC
    . 2015. Complete genome sequence of Curtobacterium sp. strain MR_MD2014, isolated from topsoil in Woods Hole, Massachusetts. Genome Announc 3(6):e01504-15. doi:10.1128/genomeA.01504-15.
    OpenUrlAbstract/FREE Full Text
  5. 5.↵
    1. Bulgari D,
    2. Minio A,
    3. Casati P,
    4. Quaglino F,
    5. Delledonne M,
    6. Bianco PA
    . 2014. Curtobacterium sp. genome sequencing underlines plant growth promotion-related traits. Genome Announc 2(4):e00592-14. doi:10.1128/genomeA.00592-14.
    OpenUrlAbstract/FREE Full Text
  6. 6.↵
    1. Didienne R,
    2. Defargues C,
    3. Callon C,
    4. Meylheuc T,
    5. Hulin S,
    6. Montel MC
    . 2012. Characteristics of microbial biofilm on wooden vats (“gerles”) in PDO Salers cheese. Int J Food Microbiol 156:91–101. doi:10.1016/j.ijfoodmicro.2012.03.007.
    OpenUrlCrossRefPubMed
  7. 7.↵
    1. Flanagan JC,
    2. Lang JM,
    3. Darling AE,
    4. Eisen JA,
    5. Coil DA
    . 2013. Draft genome sequence of Curtobacterium flaccumfaciens strain UCD-AKU (phylum Actinobacteria). Genome Announc 1(3):e00244-13. doi:10.1128/genomeA.00244-13.
    OpenUrlAbstract/FREE Full Text
  8. 8.↵
    1. Agarkova IV,
    2. Lambrecht PA,
    3. Vidaver AK,
    4. Harveson RM
    . 2012. Genetic diversity among Curtobacterium flaccumfaciens pv. flaccumfaciens populations in the American high plains. Can J Microbiol 58:788–801. doi:10.1139/w2012-052.
    OpenUrlCrossRefPubMed
  9. 9.↵
    1. Francis MJ,
    2. Doherty RR,
    3. Patel M,
    4. Hamblin JF,
    5. Ojaimi S,
    6. Korman TM
    . 2011. Curtobacterium flaccumfaciens septic arthritis following puncture with a Coxspur hawthorn thorn. J Clin Microbiol 49:2759–2760. doi:10.1128/JCM.00340-11.
    OpenUrlAbstract/FREE Full Text
  10. 10.↵
    1. Funke G,
    2. Aravena-Roman M,
    3. Frodl R
    . 2005. First description of Curtobacterium spp. isolated from human clinical specimens. J Clin Microbiol 43:1032–1036. doi:10.1128/JCM.43.3.1032-1036.2005.
    OpenUrlAbstract/FREE Full Text
  11. 11.↵
    1. Tritt A,
    2. Eisen JA,
    3. Facciotti MT,
    4. Darling AE
    . 2012. An integrated pipeline for de novo assembly of microbial genomes. PLoS One 7:e42304. doi:10.1371/journal.pone.0042304.
    OpenUrlCrossRefPubMed
  12. 12.↵
    1. Coil D,
    2. Jospin G,
    3. Darling AE
    . 2015. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 31:587–589. doi:10.1093/bioinformatics/btu661.
    OpenUrlCrossRefPubMed
  13. 13.↵
    1. Darling AE,
    2. Jospin G,
    3. Lowe E,
    4. Matsen FA,
    5. Bik HM,
    6. Eisen JA
    . 2014. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2:e243. doi:10.7717/peerj.243.
    OpenUrlCrossRef
  14. 14.↵
    1. Parks DH,
    2. Imelfort M,
    3. Skennerton CT,
    4. Hugenholtz P,
    5. Tyson GW
    . 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Genome Res 25:1043–1055. doi:10.1101/gr.186072.114.
    OpenUrlAbstract/FREE Full Text
  15. 15.↵
    1. Overbeek R,
    2. Olson R,
    3. Pusch GD,
    4. Olsen GJ,
    5. Davis JJ,
    6. Disz T,
    7. Edwards RA,
    8. Gerdes S,
    9. Parrello B,
    10. Shukla M,
    11. Vonstein V,
    12. Wattam AR,
    13. Xia F,
    14. Stevens R
    . 2014. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42:D206–D214. doi:10.1093/nar/gkt1226.
    OpenUrlCrossRefPubMedWeb of Science
  16. 16.↵
    1. Arndt D,
    2. Grant JR,
    3. Marcu A,
    4. Sajed T,
    5. Pon A,
    6. Liang Y,
    7. Wishart DS
    . 2016. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 44:W16–W21. doi:10.1093/nar/gkw387.
    OpenUrlCrossRefPubMed
  17. 17.↵
    1. Grissa I,
    2. Vergnaud G,
    3. Pourcel C
    . 2007. CRISPRFinder: a Web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35:W52–W57. doi:10.1093/nar/gkm360.
    OpenUrlCrossRefPubMedWeb of Science
  18. 18.↵
    1. Segata N,
    2. Börnigen D,
    3. Morgan XC,
    4. Huttenhower C
    . 2013. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun 4:2304. doi:10.1038/ncomms3304.
    OpenUrlCrossRefPubMed
  19. 19.↵
    1. Cole JR,
    2. Wang Q,
    3. Cardenas E,
    4. Fish J,
    5. Chai B,
    6. Farris RJ,
    7. Kulam-Syed-Mohideen AS,
    8. McGarrell DM,
    9. Marsh T,
    10. Garrity GM,
    11. Tiedje JM
    . 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37:D141–D145. doi:10.1093/nar/gkn879.
    OpenUrlCrossRefPubMedWeb of Science
PreviousNext
Back to top
Download PDF
Citation Tools
Draft Genome Sequence of Curtobacterium sp. Strain UCD-KPL2560 (Phylum Actinobacteria)
Brian A. Klein, Katherine P. Lemon, Lina L. Faller, Guillaume Jospin, Jonathan A. Eisen, David A. Coil
Genome Announcements Oct 2016, 4 (5) e01040-16; DOI: 10.1128/genomeA.01040-16

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.
Draft Genome Sequence of Curtobacterium sp. Strain UCD-KPL2560 (Phylum Actinobacteria)
(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
Draft Genome Sequence of Curtobacterium sp. Strain UCD-KPL2560 (Phylum Actinobacteria)
Brian A. Klein, Katherine P. Lemon, Lina L. Faller, Guillaume Jospin, Jonathan A. Eisen, David A. Coil
Genome Announcements Oct 2016, 4 (5) e01040-16; DOI: 10.1128/genomeA.01040-16
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

 

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