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

Complete Genome Sequence of Magnetospirillum sp. Strain XM-1, Isolated from the Xi'an City Moat, China

Yinzhao Wang, Tongwei Zhang, Wei Lin, Bingfang Zhang, Yao Cai, Caiyun Yang, Jinhua Li, Huangtao Xu, Yongxin Pan
Yinzhao Wang
aPGL, Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
bFrance-China Bio-Mineralization and Nano-Structures Laboratory, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
cUniversity of Chinese Academy of Sciences, Beijing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Tongwei Zhang
aPGL, Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
bFrance-China Bio-Mineralization and Nano-Structures Laboratory, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Wei Lin
aPGL, Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
bFrance-China Bio-Mineralization and Nano-Structures Laboratory, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Bingfang Zhang
aPGL, Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
bFrance-China Bio-Mineralization and Nano-Structures Laboratory, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yao Cai
aPGL, Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
bFrance-China Bio-Mineralization and Nano-Structures Laboratory, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Caiyun Yang
aPGL, Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
bFrance-China Bio-Mineralization and Nano-Structures Laboratory, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jinhua Li
aPGL, Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
bFrance-China Bio-Mineralization and Nano-Structures Laboratory, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Huangtao Xu
aPGL, Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
bFrance-China Bio-Mineralization and Nano-Structures Laboratory, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yongxin Pan
aPGL, Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
bFrance-China Bio-Mineralization and Nano-Structures Laboratory, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
cUniversity of Chinese Academy of Sciences, Beijing, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/genomeA.01171-16
  • Article
  • Info & Metrics
  • PDF
Loading

ABSTRACT

The magnetotactic bacterium Magnetospirillum sp. strain XM-1 was recently isolated from the Xi'an City moat, China. It belongs to the Rhodospirillaceae family in the Alphaproteobacteria class. Here, we report the complete genome sequence of XM-1. The genome contains a single circular chromosome of 4,825,187 bp and a plasmid of 167,290 bp.

GENOME ANNOUNCEMENT

Magnetotactic bacteria are able to synthesize intracellular nanosized magnetic crystals (Fe3O4/Fe3S4) usually arranged into a chain structure, known as magnetosomes, that help the cells navigate along the geomagnetic field in aquatic environments (1, 2). Magnetospirillum sp. strain XM-1, belonging to the Alphaproteobacteria was isolated from the eutrophic city moat in Xi'an, China (3), and synthesizes about 10 magnetite magnetosomes per cell (4).

The complete genome of Magnetospirillum sp. strain XM-1 was sequenced using Illumina HiSeq 2000 sequencing platforms (BGI, China). Short-insert (~500-bp) and long-insert (~6,000-bp) size DNA libraries were constructed, and a total of 121,032,268 reads were obtained, corresponding to 1,089 Mb of sequence data. De novo and reference-based assemblies were performed by SOAPdenovo version 2.04 (5). Genome of Magnetospirillum magneticum AMB-1 (6) was used as a reference strain. For highly complex region, PCRs were conducted to fill all the gaps.

The complete genome sequence of strain XM-1 comprised one circular chromosome of 4,825,187 bp and one plasmid of 167,290 bp. The G+C contents of the chromosome and plasmid are 65.64% and 66.48%, respectively. Gene annotation and analysis were performed using the MaGe Genoscope Web-based system (7). All predicted open reading frames were manually checked. The chromosome contains 4,766 coding sequences (CDSs), 53 tRNAs, two sets of rRNA operons, and 11 miscellaneous RNAs. The average CDS length is 940 bp. Of 4,766 CDSs, 74.26% could be classified as at least one category of the Clusters of Orthologous Groups (COG), in which genes related to signal transduction mechanisms (10.93%) account for dominant COG categories. Inorganic ion transport and metabolism correspond to 5.6% of the gene products in COGs. The plasmid contains 186 CDSs, and their average length is 817 bp. Compared with the chromosome, only 38.17% of plasmid CDSs could be classified as COG groups. Genes associated with replication, recombination, and repair (8.6%) rank first in COG groups in plasmids while making up only 5.7% in the chromosome.

Magnetosome formation in magnetotactic bacteria is controlled by a cluster of conserved genes (8). In Magnetospirillum sp. strain XM-1, we found that these essential genes are organized in mamGFDC, mms6, mamAB, and mamXY clusters in an approximately 100-kb region. A total of 39 genes are predicted related to magnetosome synthesis, including fur, feoAB, and ftsZ-like genes, and 24 genes were annotated as transposases or mobile elements (9).

Strain XM-1 possesses a megaplasmid containing three clusters of heavy metal efflux genes, one czcD gene, and merR-like heavy metal regulation genes. These outer membrane heavy metal efflux genes can help bacteria export the toxic heavy metal (10). Five DNA methylase-related genes, one putative type II restriction enzyme gene, a resolvase domain-containing protein gene, and a putative DNA topoisomerase are present in the plasmid, which may help bacteria avoid foreign DNA invasion (11, 12).

Accession number(s).The complete genome sequence of Magnetospirillum sp. strain XM-1 has been deposited at DDBJ/ENA/GenBank under the accession numbers LN997848 and LN997849.

FOOTNOTES

    • Received 26 August 2016.
    • Accepted 26 August 2016.
    • Published 20 October 2016.
  • Copyright © 2016 Wang 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. Bazylinski DA,
    2. Lefèvre C,
    3. Schüler D
    . 2013. Magnetotactic bacteria, p 453–494. In Rosenberg E, DeLong E, Lory S, Stackebrandt E, Thompson F (ed), The prokaryotes. Springer Verlag, Berlin, Germany Heidelberg.
  2. 2.↵
    1. Lin W,
    2. Bazylinski DA,
    3. Xiao T,
    4. Wu L-F,
    5. Pan Y
    . 2014. Life with compass: diversity and biogeography of magnetotactic bacteria. Environ Microbiol 16:2646–2658. doi:10.1111/1462-2920.12313.
    OpenUrlCrossRefPubMed
  3. 3.↵
    1. Wang Y,
    2. Lin W,
    3. Li J,
    4. Pan Y
    . 2013. High diversity of magnetotactic Deltaproteobacteria in a freshwater niche. Appl Environ Microbiol 79:2813–2817. doi:10.1128/AEM.03635-12.
    OpenUrlAbstract/FREE Full Text
  4. 4.↵
    1. Wang Y,
    2. Lin W,
    3. Li J,
    4. Zhang T,
    5. Li Y,
    6. Tian J,
    7. Gu L,
    8. Vander Heyden YV,
    9. Pan Y
    . 2015. Characterizing and optimizing magnetosome production of Magnetospirillum sp. XM-1 isolated from Xi'an City Moat, China. FEMS Microbiol Lett 362:fnv167. doi:10.1093/femsle/fnv167.
    OpenUrlCrossRefPubMed
  5. 5.↵
    1. Luo R,
    2. Liu B,
    3. Xie Y,
    4. Li Z,
    5. Huang W,
    6. Yuan J,
    7. He G,
    8. Chen Y,
    9. Pan Q,
    10. Liu Y,
    11. Tang J,
    12. Wu G,
    13. Zhang H,
    14. Shi Y,
    15. Liu Y,
    16. Yu C,
    17. Wang B,
    18. Lu Y,
    19. Han C,
    20. Cheung DW,
    21. Yiu S-M,
    22. Peng S,
    23. Zhu X,
    24. Liu G,
    25. Liao X,
    26. Li Y,
    27. Yang H,
    28. Wang J,
    29. Lam T-W,
    30. Wang J
    . 2012. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1:18. doi:10.1186/2047-217X-1-18.
    OpenUrlCrossRefPubMed
  6. 6.↵
    1. Matsunaga T,
    2. Okamura Y,
    3. Fukuda Y,
    4. Wahyudi AT,
    5. Murase Y,
    6. Takeyama H
    . 2005. Complete genome sequence of the facultative anaerobic magnetotactic bacterium Magnetospirillum sp. strain AMB-1. DNA Res 12:157–166. doi:10.1093/dnares/dsi002.
    OpenUrlCrossRefPubMedWeb of Science
  7. 7.↵
    1. Vallenet D,
    2. Engelen S,
    3. Mornico D,
    4. Cruveiller S,
    5. Fleury L,
    6. Lajus A,
    7. Rouy Z,
    8. Roche D,
    9. Salvignol G,
    10. Scarpelli C,
    11. Médigue C
    . 2009. Microscope: a platform for microbial genome annotation and comparative genomics. Database 2009:bap021. doi:10.1093/database/bap021.
    OpenUrlCrossRefPubMed
  8. 8.↵
    1. Komeili A
    . 2012. Molecular mechanisms of compartmentalization and biomineralization in magnetotactic bacteria. FEMS Microbiol Rev 36:232–255. doi:10.1111/j.1574-6976.2011.00315.x.
    OpenUrlCrossRefPubMedWeb of Science
  9. 9.↵
    1. Kolinko I,
    2. Jogler C,
    3. Katzmann E,
    4. Schüler D
    . 2011. Frequent mutations within the genomic magnetosome island of Magnetospirillum gryphiswaldense are mediated by RecA. J Bacteriol 193:5328–5334. doi:10.1128/JB.05491-11.
    OpenUrlAbstract/FREE Full Text
  10. 10.↵
    1. Delmar JA,
    2. Su C-C,
    3. Yu EW
    . 2014. Bacterial multidrug efflux transporters. Annu Rev Biophys 43:93–117. doi:10.1146/annurev-biophys-051013-022855.
    OpenUrlCrossRefPubMed
  11. 11.↵
    1. Clark TA,
    2. Murray IA,
    3. Morgan RD,
    4. Kislyuk AO,
    5. Spittle KE,
    6. Boitano M,
    7. Fomenkov A,
    8. Roberts RJ,
    9. Korlach J
    . 2012. Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Res 40:e29. doi:10.1093/nar/gkr1146.
    OpenUrlCrossRefPubMed
  12. 12.↵
    1. Dowen RH,
    2. Pelizzola M,
    3. Schmitz RJ,
    4. Lister R,
    5. Dowen JM,
    6. Nery JR,
    7. Dixon JE,
    8. Ecker JR
    . 2012. Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci U S A 109:E2183–E2191. doi:10.1073/pnas.1209329109.
    OpenUrlAbstract/FREE Full Text
View Abstract
PreviousNext
Back to top
Download PDF
Citation Tools
Complete Genome Sequence of Magnetospirillum sp. Strain XM-1, Isolated from the Xi'an City Moat, China
Yinzhao Wang, Tongwei Zhang, Wei Lin, Bingfang Zhang, Yao Cai, Caiyun Yang, Jinhua Li, Huangtao Xu, Yongxin Pan
Genome Announcements Oct 2016, 4 (5) e01171-16; DOI: 10.1128/genomeA.01171-16

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.
Complete Genome Sequence of Magnetospirillum sp. Strain XM-1, Isolated from the Xi'an City Moat, China
(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 Sequence of Magnetospirillum sp. Strain XM-1, Isolated from the Xi'an City Moat, China
Yinzhao Wang, Tongwei Zhang, Wei Lin, Bingfang Zhang, Yao Cai, Caiyun Yang, Jinhua Li, Huangtao Xu, Yongxin Pan
Genome Announcements Oct 2016, 4 (5) e01171-16; DOI: 10.1128/genomeA.01171-16
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • GENOME ANNOUNCEMENT
    • 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