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

Draft Genome Sequences of 38 Serratia marcescens Isolates Associated with Acroporid Serratiosis

Nicole C. Elledge, Ron I. Eytan, Lee J. Pinnell, Reavelyn Pray, Jessica L. Joyner, John P. Wares, Kathryn P. Sutherland, Erin K. Lipp, Jeffrey W. Turner
J. Cameron Thrash, Editor
Nicole C. Elledge
aDepartment of Life Sciences, Texas A&M University at Corpus Christi, Corpus Christi, Texas, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ron I. Eytan
bDepartment of Marine Biology, Texas A&M University at Galveston, Galveston, Texas, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Lee J. Pinnell
aDepartment of Life Sciences, Texas A&M University at Corpus Christi, Corpus Christi, Texas, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Reavelyn Pray
aDepartment of Life Sciences, Texas A&M University at Corpus Christi, Corpus Christi, Texas, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jessica L. Joyner
cOdum School of Ecology, University of Georgia, Athens, Georgia, USA
dDepartment of Environmental Health Science, University of Georgia, Athens, Georgia, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
John P. Wares
cOdum School of Ecology, University of Georgia, Athens, Georgia, USA
eDepartment of Genetics, University of Georgia, Athens, Georgia, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kathryn P. Sutherland
fDepartment of Biology, Rollins College, Winter Park, Florida, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Erin K. Lipp
dDepartment of Environmental Health Science, University of Georgia, Athens, Georgia, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jeffrey W. Turner
aDepartment of Life Sciences, Texas A&M University at Corpus Christi, Corpus Christi, Texas, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
J. Cameron Thrash
University of Southern California
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/MRA.00194-19
  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

ABSTRACT

Serratia marcescens is a Gram-negative bacterium causally linked to acroporid serratiosis, a form of white pox disease implicated in the decline of elkhorn corals. We report draft genomes of 38 S. marcescens isolates collected from host and nonhost sources. The availability of these genomes will aid future analyses of acroporid serratiosis.

ANNOUNCEMENT

Serratia marcescens is a widely distributed Gram-negative bacillus within the Enterobacteriaceae family (1). The species has long been recognized as an important pathogen of humans (1, 2), insects (3–5), and plants (6). Two ecotypes (pulsed-field gel electrophoresis [PFGE] types PDL100 and PDR60) were identified as causative agents of acroporid serratiosis (a form of white pox disease) in reef-building Acropora palmata corals (7, 8). Given the ecological importance of A. palmata, it is imperative to gain a better understanding of the genetic mechanisms underlying acroporid serratiosis and what sets the PDL100 and PDR60 ecotypes apart from other pathogenic strains.

Thirty-five S. marcescens PDR60 isolates were collected from a range of host (A. palmata) and nonhost (Siderastrea siderea and Solenastrea bournoni corals, corallivorous snail Coralliophila abbreviata, and wastewater) sources throughout the Florida Keys National Marine Sanctuary (Table 1) (8–10). The WWI31 isolate (obtained from wastewater influent) was virulent against A. palmata but had a novel PFGE pattern (8). The PDL100 isolate was obtained previously from diseased A. palmata in 1999 (7), and the ATCC 13880 isolate was obtained by others from pond water in the Czech Republic and deposited to ATCC in 1961. Starting with glycerol stocks, each isolate was streaked onto Trypticase soy agar plates (37°C overnight), and isolated colonies were grown in lysogeny broth (37°C overnight with shaking). Total DNA for Illumina sequencing was isolated using a Qiagen DNeasy blood and tissue kit (Qiagen, Valencia, CA, USA) per the manufacturer’s instructions. Genomic DNA for PacBio sequencing was isolated using a cetyltrimethylammonium bromide protocol (11). Illumina sequencing libraries were prepared using a PCR-free TrueSeq DNA kit (Illumina, San Diego, CA, USA) and sequenced at Hudson Alpha Institute for Biotechnology (Huntsville, AL, USA) using paired-end chemistry with 250-bp (EL1 and EL119), 150-bp (EL1, EL119, and KS10), or 100-bp (remaining 35 isolates) read lengths. Additionally, six isolates (EL1, EL116, EL119, EL41, EL60, and KS10) were also sequenced on three PacBio single-molecule real-time (SMRT) cells at the Interdisciplinary Center for Biotechnology Research (University of Florida, Gainesville, FL, USA). Adapter sequences and low-quality bases were removed from Illumina reads with TrimGalore! version 0.4.0 (options, -paired and -retain_unpaired) (12). The processed reads were assembled de novo with Velvet version 1.2.10 (options -scaffolding, no; -exp_cov, 80; -cov_cutoff, 10; -min_contig_lgth, 500) (13) using the k-mer sizes listed in Table 1. Hybrid assemblies were constructed with MaSuRCA version 3.2.1 (options, default) (14) using the mean insert sizes and insert size standard deviations calculated with BWA (15). Assembly metrics were determined using QUAST version 5.0.2 (options, default) (16). All genomes were annotated using the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline (PGAP) (17).

View this table:
  • View inline
  • View popup
TABLE 1

Accession numbers, genome assembly metrics, and sources for the 38 S. marcescens isolatesa

Table 1 shows summaries of the 38 draft genome assemblies. The availability of these genomes will aid in more comprehensive analyses of S. marcescens and acroporid serratiosis.

Data availability.This whole-genome shotgun project has been deposited in GenBank under the accession numbers listed in Table 1. The raw sequence reads were deposited in the Sequence Read Archive under the BioProject accession numbers PRJNA494152 (nonhybrid assemblies) and PRJNA438529 (hybrid assemblies).

ACKNOWLEDGMENT

This project was funded by NSF-NIH Ecology of Infectious Disease program grants EF1015342 (awarded to Erin K. Lipp and John P. Wares) and EF1015032 (awarded to Kathryn P. Sutherland).

FOOTNOTES

    • Received 19 February 2019.
    • Accepted 4 March 2019.
    • Published 4 April 2019.
  • Copyright © 2019 Elledge 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. Grimont PAD,
    2. Grimont F
    . 1978. The genus Serratia. Annu Rev Microbiol 32:221–248. doi:10.1146/annurev.mi.32.100178.001253.
    OpenUrlCrossRefPubMedWeb of Science
  2. 2.↵
    1. Hejazi A,
    2. Falkiner FR
    . 1997. Serratia marcescens. J Med Microbiol 46:903–912. doi:10.1099/00222615-46-11-903.
    OpenUrlCrossRefPubMedWeb of Science
  3. 3.↵
    1. Bell JV,
    2. King EG,
    3. Hamalle RJ
    . 1974. Interactions between bollworms, a braconid parasite, and the bacterium Serratia marcescens. Ann Entomol Soc Am 67:712–714. doi:10.1093/aesa/67.4.712.
    OpenUrlCrossRef
  4. 4.↵
    1. Lysenko O
    . 1985. Non-sporeforming bacteria pathogenic to insects: incidence and mechanisms. Annu Rev Microbiol 39:673–695. doi:10.1146/annurev.mi.39.100185.003325.
    OpenUrlCrossRefPubMedWeb of Science
  5. 5.↵
    1. Burritt NL,
    2. Foss NJ,
    3. Neeno-Eckwall EC,
    4. Church JO,
    5. Hilger AM,
    6. Hildebrand JA,
    7. Warshauer DM,
    8. Perna NT,
    9. Burritt JB
    . 2016. Sepsis and hemocyte loss in honey bees (Apis mellifera) infected with Serratia marcescens strain sicaria. PLoS One 11:e0167752. doi:10.1371/journal.pone.0167752.
    OpenUrlCrossRef
  6. 6.↵
    1. Bruton BD,
    2. Mitchell F,
    3. Fletcher J,
    4. Pair SD,
    5. Wayadande A,
    6. Melcher U,
    7. Brady J,
    8. Bextine B,
    9. Popham TW
    . 2003. Serratia marcescens, a phloem-colonizing, squash bug-transmitted bacterium: causal agent of cucurbit yellow vine disease. Plant Dis 87:937–944. doi:10.1094/PDIS.2003.87.8.937.
    OpenUrlCrossRef
  7. 7.↵
    1. Patterson KL,
    2. Porter JW,
    3. Ritchie KB,
    4. Polson SW,
    5. Mueller E,
    6. Peters EC,
    7. Santavy DL,
    8. Smith GW
    . 2002. The etiology of white pox, a lethal disease of the Caribbean elkhorn coral, Acropora palmata. Proc Natl Acad Sci U S A 99:8725–8730. doi:10.1073/pnas.092260099.
    OpenUrlAbstract/FREE Full Text
  8. 8.↵
    1. Sutherland KP,
    2. Shaban S,
    3. Joyner JL,
    4. Porter JW,
    5. Lipp EK
    . 2011. Human pathogen shown to cause disease in the threatened elkhorn coral Acropora palmata. PLoS One 6:e23468. doi:10.1371/journal.pone.0023468.
    OpenUrlCrossRef
  9. 9.↵
    1. Sutherland KP,
    2. Porter JW,
    3. Turner JW,
    4. Thomas BJ,
    5. Looney EE,
    6. Luna TP,
    7. Meyers MK,
    8. Futch JC,
    9. Lipp EK
    . 2010. Human sewage identified as likely source of white pox disease of the threatened Caribbean elkhorn coral, Acropora palmata. Environ Microbiol 12:1122–1131. doi:10.1111/j.1462-2920.2010.02152.x.
    OpenUrlCrossRefPubMedWeb of Science
  10. 10.↵
    1. Joyner JL,
    2. Sutherland KP,
    3. Kemp DW,
    4. Berry B,
    5. Griffin A,
    6. Porter JW,
    7. Amador MHB,
    8. Noren HKG,
    9. Lipp EK
    . 2015. Systematic analysis of white pox disease in Acropora palmata of the Florida Keys and the role of Serratia marcescens. Appl Environ Microbiol 81:4451–4457. doi:10.1128/AEM.00116-15.
    OpenUrlAbstract/FREE Full Text
  11. 11.↵
    1. Wilson K
    . 2001. Preparation of genomic DNA from bacteria. Curr Protoc Mol Biol 56:2.4.1–2.4.5. doi:10.1002/0471142727.mb0204s56.
    OpenUrlCrossRef
  12. 12.↵
    1. Krueger F
    . 2015. Trim galore. A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files. http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/.
  13. 13.↵
    1. Zerbino D,
    2. Birney E
    . 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829. doi:10.1101/gr.074492.107.
    OpenUrlAbstract/FREE Full Text
  14. 14.↵
    1. Zimin AV,
    2. Marçais G,
    3. Puiu D,
    4. Roberts M,
    5. Salzberg SL,
    6. Yorke JA
    . 2013. The MaSuRCA genome assembler. Bioinformatics 29:2669–2677. doi:10.1093/bioinformatics/btt476.
    OpenUrlCrossRefPubMedWeb of Science
  15. 15.↵
    1. Li H,
    2. Durbin R
    . 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760. doi:10.1093/bioinformatics/btp324.
    OpenUrlCrossRefPubMedWeb of Science
  16. 16.↵
    1. Gurevich A,
    2. Saveliev V,
    3. Vyahhi N,
    4. Tesler G
    . 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. doi:10.1093/bioinformatics/btt086.
    OpenUrlCrossRefPubMedWeb of Science
  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
View Abstract
PreviousNext
Back to top
Download PDF
Citation Tools
Draft Genome Sequences of 38 Serratia marcescens Isolates Associated with Acroporid Serratiosis
Nicole C. Elledge, Ron I. Eytan, Lee J. Pinnell, Reavelyn Pray, Jessica L. Joyner, John P. Wares, Kathryn P. Sutherland, Erin K. Lipp, Jeffrey W. Turner
Microbiology Resource Announcements Apr 2019, 8 (14) e00194-19; DOI: 10.1128/MRA.00194-19

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 Sequences of 38 Serratia marcescens Isolates Associated with Acroporid Serratiosis
(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 Sequences of 38 Serratia marcescens Isolates Associated with Acroporid Serratiosis
Nicole C. Elledge, Ron I. Eytan, Lee J. Pinnell, Reavelyn Pray, Jessica L. Joyner, John P. Wares, Kathryn P. Sutherland, Erin K. Lipp, Jeffrey W. Turner
Microbiology Resource Announcements Apr 2019, 8 (14) e00194-19; DOI: 10.1128/MRA.00194-19
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • ANNOUNCEMENT
    • ACKNOWLEDGMENT
    • FOOTNOTES
    • REFERENCES
  • Figures & Data
  • 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