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

Title: High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk

Abstract

Chryseobacterium bovis DSM 19482 T (Hantsis-Zacharov et al., Int J Syst Evol Microbiol 58:1024-1028, 2008) is a Gram-negative, rod shaped, non-motile, facultative anaerobe, chemoorganotroph bacterium. C. bovis is a member of the Flavobacteriaceae, a family within the phylum Bacteroidetes. It was isolated when psychrotolerant bacterial communities in raw milk and their proteolytic and lipolytic traits were studied. Here we describe the features of this organism, together with the draft genome sequence and annotation. The DNA G + C content is 38.19%. The chromosome length is 3,346,045 bp. It encodes 3236 proteins and 105 RNA genes. The C. bovis genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes study.

Authors:
 [1];  [2];  [3];  [3];  [3];  [3];  [3];  [3];  [3];  [3];  [3];  [3];  [3];  [3];  [3];  [4];  [3];  [5]
+ Show Author Affiliations
  1. Univ. of Haifa (Israel). Dept. of Evolutionary and Environmental Biology
  2. Leibniz Inst. for German Collection of Microorganisms and Cell Cultures (DSMZ), Braunschweig (Germany)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Newcastle Univ., Tyne (United Kingdom). School of Biology
  5. Univ. of Haifa (Israel). Dept. of Evolutionary and Environmental Biology, Dept. of Biology and Environment
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:
1379843
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; flavobacteriaceae; psychrotolerant; proteolysis; lipolysis; beta-carotene

Citation Formats

Laviad-Shitrit, Sivan, Göker, Markus, Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, T. B. K., Daum, Chris, Shapiro, Nicole, Markowitz, Victor, Ivanova, Natalia, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C., and Halpern, Malka. High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk. United States: N. p., 2017. Web. doi:10.1186/s40793-017-0242-6.
Copy to clipboard
Laviad-Shitrit, Sivan, Göker, Markus, Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, T. B. K., Daum, Chris, Shapiro, Nicole, Markowitz, Victor, Ivanova, Natalia, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C., & Halpern, Malka. High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk. United States. https://doi.org/10.1186/s40793-017-0242-6
Copy to clipboard
Laviad-Shitrit, Sivan, Göker, Markus, Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, T. B. K., Daum, Chris, Shapiro, Nicole, Markowitz, Victor, Ivanova, Natalia, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C., and Halpern, Malka. Mon . "High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk". United States. https://doi.org/10.1186/s40793-017-0242-6. https://www.osti.gov/servlets/purl/1379843.
Copy to clipboard
@article{osti_1379843,
title = {High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk},
author = {Laviad-Shitrit, Sivan and Göker, Markus and Huntemann, Marcel and Clum, Alicia and Pillay, Manoj and Palaniappan, Krishnaveni and Varghese, Neha and Mikhailova, Natalia and Stamatis, Dimitrios and Reddy, T. B. K. and Daum, Chris and Shapiro, Nicole and Markowitz, Victor and Ivanova, Natalia and Woyke, Tanja and Klenk, Hans-Peter and Kyrpides, Nikos C. and Halpern, Malka},
abstractNote = {Chryseobacterium bovis DSM 19482 T (Hantsis-Zacharov et al., Int J Syst Evol Microbiol 58:1024-1028, 2008) is a Gram-negative, rod shaped, non-motile, facultative anaerobe, chemoorganotroph bacterium. C. bovis is a member of the Flavobacteriaceae, a family within the phylum Bacteroidetes. It was isolated when psychrotolerant bacterial communities in raw milk and their proteolytic and lipolytic traits were studied. Here we describe the features of this organism, together with the draft genome sequence and annotation. The DNA G + C content is 38.19%. The chromosome length is 3,346,045 bp. It encodes 3236 proteins and 105 RNA genes. The C. bovis genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes study.},
doi = {10.1186/s40793-017-0242-6},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 12,
place = {United States},
year = {Mon May 08 00:00:00 EDT 2017},
month = {Mon May 08 00:00:00 EDT 2017}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1186/s40793-017-0242-6
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:

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
journal, January 2014

Chryseobacterium bovis sp. nov., isolated from raw cow's milk
journal, April 2008

  • Hantsis-Zacharov, E.; Senderovich, Y.; Halpern, M.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 4
  • DOI: 10.1099/ijs.0.65500-0

How Many Bootstrap Replicates Are Necessary?
journal, March 2010

  • Pattengale, Nicholas D.; Alipour, Masoud; Bininda-Emonds, Olaf R. P.
  • Journal of Computational Biology, Vol. 17, Issue 3
  • DOI: 10.1089/cmb.2009.0179

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
journal, October 2015

  • Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos
  • Standards in Genomic Sciences, Vol. 10, Issue 1
  • DOI: 10.1186/s40793-015-0077-y

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

The DNA Bank Network: The Start from a German Initiative
journal, March 2011

  • Gemeinholzer, Birgit; Dröge, Gabriele; Zetzsche, Holger
  • Biopreservation and Biobanking, Vol. 9, Issue 1
  • DOI: 10.1089/bio.2010.0029

NOTES: New Perspectives in the Classification of the Flavobacteria: Description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev.
journal, October 1994

  • Vandamme, P.; Bernardet, J. -F.; Segers, P.
  • International Journal of Systematic Bacteriology, Vol. 44, Issue 4
  • DOI: 10.1099/00207713-44-4-827

Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects
journal, May 2013

  • Göker, Markus; Klenk, Hans-Peter
  • Standards in Genomic Sciences, Vol. 8, Issue 2
  • DOI: 10.4056/sigs.3446951

High-quality draft assemblies of mammalian genomes from massively parallel sequence data
journal, December 2010

  • Gnerre, S.; MacCallum, I.; Przybylski, D.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 4
  • DOI: 10.1073/pnas.1017351108

Solexa Ltd
journal, June 2004

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

Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy
journal, January 2014

  • Meier-Kolthoff, Jan P.; Hahnke, Richard L.; Petersen, Jörn
  • Standards in Genomic Sciences, Vol. 9, Issue 1
  • DOI: 10.1186/1944-3277-9-2

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

The Genomic Standards Consortium
journal, June 2011

Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
journal, June 1990

  • Woese, C. R.; Kandler, O.; Wheelis, M. L.
  • Proceedings of the National Academy of Sciences, Vol. 87, Issue 12
  • DOI: 10.1073/pnas.87.12.4576

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

Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project
journal, December 2013

  • Kyrpides, Nikos C.; Woyke, Tanja; Eisen, Jonathan A.
  • Standards in Genomic Sciences, Vol. 9, Issue 3
  • DOI: 10.4056/sigs.5068949

Genome sequence-based species delimitation with confidence intervals and improved distance functions
journal, January 2013

  • Meier-Kolthoff, Jan P.; Auch, Alexander F.; Klenk, Hans-Peter
  • BMC Bioinformatics, Vol. 14, Issue 1
  • DOI: 10.1186/1471-2105-14-60

Chryseobacterium haifense sp. nov., a psychrotolerant bacterium isolated from raw milk
journal, October 2007

  • Hantsis-Zacharov, E.; Halpern, M.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 10
  • DOI: 10.1099/ijs.0.65115-0

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

Culturable Psychrotrophic Bacterial Communities in Raw Milk and Their Proteolytic and Lipolytic Traits
journal, September 2007

  • Hantsis-Zacharov, E.; Halpern, M.
  • Applied and Environmental Microbiology, Vol. 73, Issue 22
  • DOI: 10.1128/AEM.00866-07

TNT, a free program for phylogenetic analysis
journal, October 2008

Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains
journal, August 2014

IMG 4 version of the integrated microbial genomes comparative analysis system
journal, October 2013

  • Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt963

MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004

  • Edgar, R. C.
  • Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
  • DOI: 10.1093/nar/gkh340

Whole-Genome Sequence of Chryseobacterium oranimense, a Colistin-Resistant Bacterium Isolated from a Cystic Fibrosis Patient in France
journal, January 2015

  • Sharma, Poonam; Gupta, Sushim Kumar; Diene, Seydina M.
  • Antimicrobial Agents and Chemotherapy, Vol. 59, Issue 3
  • DOI: 10.1128/AAC.02417-14

The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation
journal, December 2012

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008

Chryseobacterium oranimense sp. nov., a psychrotolerant, proteolytic and lipolytic bacterium isolated from raw cow's milk
journal, November 2008

  • Hantsis-Zacharov, E.; Shaked, T.; Senderovich, Y.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 11
  • DOI: 10.1099/ijs.0.65819-0

Mating pair stabilization mediates bacterial conjugation species specificity
journal, June 2022

Dietary palmitic acid promotes a prometastatic memory via Schwann cells
journal, November 2021

High-quality draft assemblies of mammalian genomes from massively parallel sequence data
journal, December 2010

  • Gnerre, S.; MacCallum, I.; Przybylski, D.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 4
  • DOI: 10.1073/pnas.1017351108

The DNA Bank Network: The Start from a German Initiative
journal, March 2011

  • Gemeinholzer, Birgit; Dröge, Gabriele; Zetzsche, Holger
  • Biopreservation and Biobanking, Vol. 9, Issue 1
  • DOI: 10.1089/bio.2010.0029

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

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

IMG 4 version of the integrated microbial genomes comparative analysis system
journal, October 2013

  • Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt963

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

NOTES: New Perspectives in the Classification of the Flavobacteria: Description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev.
journal, October 1994

  • Vandamme, P.; Bernardet, J. -F.; Segers, P.
  • International Journal of Systematic Bacteriology, Vol. 44, Issue 4
  • DOI: 10.1099/00207713-44-4-827

Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family.
journal, May 2002

  • Bernardet, Jean-Francois; Holmes, Barry; Nakagawa, Yasuyoshi
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 52, Issue 3
  • DOI: 10.1099/00207713-52-3-1049

Chryseobacterium haifense sp. nov., a psychrotolerant bacterium isolated from raw milk
journal, October 2007

  • Hantsis-Zacharov, E.; Halpern, M.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 10
  • DOI: 10.1099/ijs.0.65115-0

Chryseobacterium bovis sp. nov., isolated from raw cow's milk
journal, April 2008

  • Hantsis-Zacharov, E.; Senderovich, Y.; Halpern, M.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 4
  • DOI: 10.1099/ijs.0.65500-0

Chryseobacterium oranimense sp. nov., a psychrotolerant, proteolytic and lipolytic bacterium isolated from raw cow's milk
journal, November 2008

  • Hantsis-Zacharov, E.; Shaked, T.; Senderovich, Y.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 11
  • DOI: 10.1099/ijs.0.65819-0

Genome sequence-based species delimitation with confidence intervals and improved distance functions
journal, January 2013

  • Meier-Kolthoff, Jan P.; Auch, Alexander F.; Klenk, Hans-Peter
  • BMC Bioinformatics, Vol. 14, Issue 1
  • DOI: 10.1186/1471-2105-14-60

Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy
journal, January 2014

  • Meier-Kolthoff, Jan P.; Hahnke, Richard L.; Petersen, Jörn
  • Standards in Genomic Sciences, Vol. 9, Issue 1
  • DOI: 10.1186/1944-3277-9-2

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
journal, October 2015

  • Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos
  • Standards in Genomic Sciences, Vol. 10, Issue 1
  • DOI: 10.1186/s40793-015-0077-y

Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains
journal, August 2014

The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation
journal, December 2012

Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects
journal, May 2013

  • Göker, Markus; Klenk, Hans-Peter
  • Standards in Genomic Sciences, Vol. 8, Issue 2
  • DOI: 10.4056/sigs.3446951

Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project
journal, December 2013

  • Kyrpides, Nikos C.; Woyke, Tanja; Eisen, Jonathan A.
  • Standards in Genomic Sciences, Vol. 9, Issue 3
  • DOI: 10.4056/sigs.5068949
    Sort by:
    [ × clear filter / sort ]

    Works referencing / citing this record:

    Complete Genome Sequence of Chryseobacterium camelliae Dolsongi-HT1, a Green Tea Isolate with Keratinolytic Activity
    journal, January 2018

      Sort by:
      [ × clear filter / sort ]

      Similar Records in DOE PAGES and OSTI.GOV collections: