Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: An improved high-quality draft genome sequence of Carnobacterium inhibens subsp. inhibens strain K1T

Abstract

Abstract Despite their ubiquity and their involvement in food spoilage, the genus Carnobacterium remains rather sparsely characterized at the genome level. Carnobacterium inhibens K1 T is a member of the Carnobacteriaceae family within the class Bacilli . This strain is a Gram-positive, rod-shaped bacterium isolated from the intestine of an Atlantic salmon. The present study determined the genome sequence and annotation of Carnobacterium inhibens K1 T . The genome comprised 2,748,608 bp with a G + C content of 34.85 %, which included 2621 protein-coding genes and 116 RNA genes. The strain contained five contigs corresponding to presumptive plasmids of sizes: 19,036; 24,250; 26,581; 65,272; and 65,904 bp.

Authors:
; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1618969
Alternate Identifier(s):
OSTI ID: 1377481
Grant/Contract Number:  
CSP-1165; AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Name: Standards in Genomic Sciences Journal Volume: 11 Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
Springer Science + Business Media
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Nicholson, Wayne L., Davis, Christina L., Shapiro, Nicole, Huntemann, Marcel, Clum, Alicia, Reddy, T. B. K., Pillay, Manoj, Markowitz, Victor, Varghese, Neha, Pati, Amrita, Ivanova, Natalia, Kyrpides, Nikos, and Woyke, Tanja. An improved high-quality draft genome sequence of Carnobacterium inhibens subsp. inhibens strain K1T. United Kingdom: N. p., 2016. Web. doi:10.1186/s40793-016-0193-3.
Copy to clipboard
Nicholson, Wayne L., Davis, Christina L., Shapiro, Nicole, Huntemann, Marcel, Clum, Alicia, Reddy, T. B. K., Pillay, Manoj, Markowitz, Victor, Varghese, Neha, Pati, Amrita, Ivanova, Natalia, Kyrpides, Nikos, & Woyke, Tanja. An improved high-quality draft genome sequence of Carnobacterium inhibens subsp. inhibens strain K1T. United Kingdom. https://doi.org/10.1186/s40793-016-0193-3
Copy to clipboard
Nicholson, Wayne L., Davis, Christina L., Shapiro, Nicole, Huntemann, Marcel, Clum, Alicia, Reddy, T. B. K., Pillay, Manoj, Markowitz, Victor, Varghese, Neha, Pati, Amrita, Ivanova, Natalia, Kyrpides, Nikos, and Woyke, Tanja. Thu . "An improved high-quality draft genome sequence of Carnobacterium inhibens subsp. inhibens strain K1T". United Kingdom. https://doi.org/10.1186/s40793-016-0193-3.
Copy to clipboard
@article{osti_1618969,
title = {An improved high-quality draft genome sequence of Carnobacterium inhibens subsp. inhibens strain K1T},
author = {Nicholson, Wayne L. and Davis, Christina L. and Shapiro, Nicole and Huntemann, Marcel and Clum, Alicia and Reddy, T. B. K. and Pillay, Manoj and Markowitz, Victor and Varghese, Neha and Pati, Amrita and Ivanova, Natalia and Kyrpides, Nikos and Woyke, Tanja},
abstractNote = {Abstract Despite their ubiquity and their involvement in food spoilage, the genus Carnobacterium remains rather sparsely characterized at the genome level. Carnobacterium inhibens K1 T is a member of the Carnobacteriaceae family within the class Bacilli . This strain is a Gram-positive, rod-shaped bacterium isolated from the intestine of an Atlantic salmon. The present study determined the genome sequence and annotation of Carnobacterium inhibens K1 T . The genome comprised 2,748,608 bp with a G + C content of 34.85 %, which included 2621 protein-coding genes and 116 RNA genes. The strain contained five contigs corresponding to presumptive plasmids of sizes: 19,036; 24,250; 26,581; 65,272; and 65,904 bp.},
doi = {10.1186/s40793-016-0193-3},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 11,
place = {United Kingdom},
year = {Thu Sep 08 00:00:00 EDT 2016},
month = {Thu Sep 08 00:00:00 EDT 2016}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1186/s40793-016-0193-3
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 1 work
Citation information provided by
Web of Science
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

The Genera Lactobacillus and Carnobacterium
book, January 2006

Carnobacterium: positive and negative effects in the environment and in foods
journal, September 2007

Carnobacterium iners sp. nov., a psychrophilic, lactic acid-producing bacterium from the littoral zone of an Antarctic pond
journal, July 2012

  • Snauwaert, I.; Hoste, B.; De Bruyne, K.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 4
  • DOI: 10.1099/ijs.0.042861-0

Complete Genome Sequence of Carnobacterium gilichinskyi Strain WN1359T (DSM 27470T)
journal, October 2013

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
journal, November 2007

  • Pruesse, E.; Quast, C.; Knittel, K.
  • Nucleic Acids Research, Vol. 35, Issue 21
  • DOI: 10.1093/nar/gkm864

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification
journal, October 2014

  • Reddy, T. B. K.; Thomas, Alex D.; Stamatis, Dimitri
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku950

Proposals Concerning the Higher Taxa of Bacteria
journal, January 1978

  • Gibbons, N. E.; Murray, R. G. E.
  • International Journal of Systematic Bacteriology, Vol. 28, Issue 1
  • DOI: 10.1099/00207713-28-1-1

Real-Time DNA Sequencing from Single Polymerase Molecules
journal, January 2009

Complete Genome Sequence of Carnobacterium sp. 17-4
journal, May 2011

  • Voget, S.; Klippel, B.; Daniel, R.
  • Journal of Bacteriology, Vol. 193, Issue 13
  • DOI: 10.1128/JB.05113-11

Growth of Carnobacterium spp. from permafrost under low pressure, temperature, and anoxic atmosphere has implications for Earth microbes on Mars
journal, December 2012

  • Nicholson, W. L.; Krivushin, K.; Gilichinsky, D.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 2
  • DOI: 10.1073/pnas.1209793110

The genome sequence of the lactic acid bacterium, Carnobacterium maltaromaticum ATCC 35586 encodes potential virulence factors
journal, January 2012

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
journal, May 2013

  • Chin, Chen-Shan; Alexander, David H.; Marks, Patrick
  • Nature Methods, Vol. 10, Issue 6
  • DOI: 10.1038/nmeth.2474

The genus Carnobacterium
book, January 1995

Genomic and phenotypic analyses of Carnobacterium jeotgali strain MS3T, a lactate-producing candidate biopreservative bacterium isolated from salt-fermented shrimp
journal, April 2015

  • Whon, Tae Woong; Hyun, Dong-Wook; Nam, Young-Do
  • FEMS Microbiology Letters, Vol. 362, Issue 10
  • DOI: 10.1093/femsle/fnv058

Carnobacterium pleistocenium sp. nov., a novel psychrotolerant, facultative anaerobe isolated from permafrost of the Fox Tunnel in Alaska
journal, January 2005

  • Pikuta, E. V.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 55, Issue 1
  • DOI: 10.1099/ijs.0.63384-0

Carnobacterium inhibens sp. nov., isolated from the intestine of Atlantic salmon (Salmo salar)
journal, October 1999

  • Joborn, A.; Dorsch, M.; Olsson, J. C.
  • International Journal of Systematic Bacteriology, Vol. 49, Issue 4
  • DOI: 10.1099/00207713-49-4-1891

The minimum information about a genome sequence (MIGS) specification
journal, May 2008

  • Field, Dawn; Garrity, George; Gray, Tanya
  • Nature Biotechnology, Vol. 26, Issue 5
  • DOI: 10.1038/nbt1360

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997

  • Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A.
  • Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402
  • DOI: 10.1093/nar/25.17.3389

Classification of Lactobacillus divergens, Lactobacillus piscicola, and Some Catalase-Negative, Asporogenous, Rod-Shaped Bacteria from Poultry in a New Genus, Carnobacterium
journal, October 1987

  • Collins, M. D.; Farrow, J. A. E.; Phillips, B. A.
  • International Journal of Systematic Bacteriology, Vol. 37, Issue 4
  • DOI: 10.1099/00207713-37-4-310

Gene Ontology: tool for the unification of biology
journal, May 2000

  • Ashburner, Michael; Ball, Catherine A.; Blake, Judith A.
  • Nature Genetics, Vol. 25, Issue 1
  • DOI: 10.1038/75556

tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997

Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010

Complete Chromosome Sequence of Carnobacterium maltaromaticum LMA 28
journal, January 2013

  • Cailliez-Grimal, C.; Chaillou, S.; Anba-Mondoloni, J.
  • Genome Announcements, Vol. 1, Issue 1
  • DOI: 10.1128/genomeA.00115-12

IMG ER: a system for microbial genome annotation expert review and curation
journal, June 2009

GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes
journal, May 2010

  • Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia
  • Nature Methods, Vol. 7, Issue 6
  • DOI: 10.1038/nmeth.1457
    Sort by:
    [ × clear filter / sort ]

    Similar Records in DOE PAGES and OSTI.GOV collections: