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Title: High quality draft genome sequence of the slightly halophilic bacterium Halomonas zhanjiangensis type strain JSM 078169T (DSM 21076T) from a sea urchin in southern China

Abstract

Halomonas zhanjiangensis Chen et al. 2009 is a member of the genus Halomonas, family Halomonadaceae, class Gammaproteobacteria. Representatives of the genus Halomonas are a group of halophilic bacteria often isolated from salty environments. The type strain H. zhanjiangensis JSM 078169T was isolated from a sea urchin (Hemicentrotus pulcherrimus) collected from the South China Sea. The genome of strain JSM 078169T is the fourteenth sequenced genome in the genus Halomonas and the fifteenth in the family Halomonadaceae. The other thirteen genomes from the genus Halomonas are H. halocynthiae, H. venusta, H. alkaliphila, H. lutea, H. anticariensis, H. jeotgali, H. titanicae, H. desiderata, H. smyrnensis, H. salifodinae, H. boliviensis, H. elongata and H stevensii. Here, we describe the features of strain JSM 078169T , together with the complete genome sequence and annotation from a culture of DSM 21076T . The 4,060,520 bp long draft genome consists of 17 scaffolds with the 3,659 protein-coding and 80 RNA genes and is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.

Authors:
 [1];  [2];  [3];  [4];  [5];  [5];  [5];  [5];  [5];  [5];  [6];  [5];  [7];  [8];  [5];  [7];  [9];  [10]
  1. Yannan Univ., Kunming (China). Yannan Inst. of Microbiology. Ministry of Education and the Lab. for Conservation and Utilization of Bio-Resources. Key Lab. of Microbial Diversity in Southwest China; Zhejiang Academy of Agricultural Sciences (China). Inst. of Quality and Standard for Agro-products. State Key Lab. Breeding Base for Zhejiang Sustainable Plant Pest Control
  2. Zhejiang Academy of Agricultural Sciences (China). Inst. of Quality and Standard for Agro-products. State Key Lab. Breeding Base for Zhejiang Sustainable Plant Pest Control
  3. Chinese Academy of Sciences (CAS), Urumqi (China). Xinjiang Inst. of Ecology and Geography. Key Lab. of Biogeography and Bioresource in Arid Land; Chinese Academy of Sciences (CAS), Beijing (China)
  4. St. Petersburg State Univ. (Russia). Theodosius Dobzhansky Center for Genome Bioinformatics; St. Petersburg Academic Univ.. (Russia). Algorithmic Biology Lab.
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  6. Helmholtz Centre for Infection Research, Braunschweig (Germany). HZI
  7. Leibniz Inst. DSMZ, Braunschweig (Germany). German Collection of Microorganisms and Cell Cultures
  8. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center
  9. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia). Dept. of Biological Sciences
  10. Yannan Univ., Kunming (China). Yannan Inst. of Microbiology. Ministry of Education and the Lab. for Conservation and Utilization of Bio-Resources. Key Lab. of Microbial Diversity in Southwest China; Chinese Academy of Sciences (CAS), Urumqi (China). Xinjiang Inst. of Ecology and Geography. Key Lab. of Biogeography and Bioresource in Arid Land
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
OSTI Identifier:
1628694
Grant/Contract Number:  
AC02-05CH11231; AC52-07NA27344
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 9; Journal Issue: 3; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Genetics & Heredity; Microbiology; strictly aerobic; motile Gram-negative; chemoorganotrophic; slightly halophilic; Halomonadaceae

Citation Formats

Zhou, Yu, Li, Rui, Gao, Xiao-Yang, Lapidus, Alla, Han, James, Haynes, Matthew, Lobos, Elizabeth, Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N., Rohde, Manfred, Mavromatis, Konstantinos, Tindall, Brian J., Markowitz, Victor, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C., and Li, Wen-Jun. High quality draft genome sequence of the slightly halophilic bacterium Halomonas zhanjiangensis type strain JSM 078169T (DSM 21076T) from a sea urchin in southern China. United States: N. p., 2014. Web. doi:10.4056/sigs.5449586.
Zhou, Yu, Li, Rui, Gao, Xiao-Yang, Lapidus, Alla, Han, James, Haynes, Matthew, Lobos, Elizabeth, Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N., Rohde, Manfred, Mavromatis, Konstantinos, Tindall, Brian J., Markowitz, Victor, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C., & Li, Wen-Jun. High quality draft genome sequence of the slightly halophilic bacterium Halomonas zhanjiangensis type strain JSM 078169T (DSM 21076T) from a sea urchin in southern China. United States. https://doi.org/10.4056/sigs.5449586
Zhou, Yu, Li, Rui, Gao, Xiao-Yang, Lapidus, Alla, Han, James, Haynes, Matthew, Lobos, Elizabeth, Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N., Rohde, Manfred, Mavromatis, Konstantinos, Tindall, Brian J., Markowitz, Victor, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C., and Li, Wen-Jun. Fri . "High quality draft genome sequence of the slightly halophilic bacterium Halomonas zhanjiangensis type strain JSM 078169T (DSM 21076T) from a sea urchin in southern China". United States. https://doi.org/10.4056/sigs.5449586. https://www.osti.gov/servlets/purl/1628694.
@article{osti_1628694,
title = {High quality draft genome sequence of the slightly halophilic bacterium Halomonas zhanjiangensis type strain JSM 078169T (DSM 21076T) from a sea urchin in southern China},
author = {Zhou, Yu and Li, Rui and Gao, Xiao-Yang and Lapidus, Alla and Han, James and Haynes, Matthew and Lobos, Elizabeth and Huntemann, Marcel and Pati, Amrita and Ivanova, Natalia N. and Rohde, Manfred and Mavromatis, Konstantinos and Tindall, Brian J. and Markowitz, Victor and Woyke, Tanja and Klenk, Hans-Peter and Kyrpides, Nikos C. and Li, Wen-Jun},
abstractNote = {Halomonas zhanjiangensis Chen et al. 2009 is a member of the genus Halomonas, family Halomonadaceae, class Gammaproteobacteria. Representatives of the genus Halomonas are a group of halophilic bacteria often isolated from salty environments. The type strain H. zhanjiangensis JSM 078169T was isolated from a sea urchin (Hemicentrotus pulcherrimus) collected from the South China Sea. The genome of strain JSM 078169T is the fourteenth sequenced genome in the genus Halomonas and the fifteenth in the family Halomonadaceae. The other thirteen genomes from the genus Halomonas are H. halocynthiae, H. venusta, H. alkaliphila, H. lutea, H. anticariensis, H. jeotgali, H. titanicae, H. desiderata, H. smyrnensis, H. salifodinae, H. boliviensis, H. elongata and H stevensii. Here, we describe the features of strain JSM 078169T , together with the complete genome sequence and annotation from a culture of DSM 21076T . The 4,060,520 bp long draft genome consists of 17 scaffolds with the 3,659 protein-coding and 80 RNA genes and is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.},
doi = {10.4056/sigs.5449586},
journal = {Standards in Genomic Sciences},
number = 3,
volume = 9,
place = {United States},
year = {Fri Apr 11 00:00:00 EDT 2014},
month = {Fri Apr 11 00:00:00 EDT 2014}
}

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Halomonas zhanjiangensis sp. nov., a halophilic bacterium isolated from a sea urchin
journal, July 2009

  • Chen, Y. -G.; Zhang, Y. -Q.; Huang, H. -Y.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 11
  • DOI: 10.1099/ijs.0.010173-0

Halomonas muralis sp. nov., isolated from microbial biofilms colonizing the walls and murals of the Saint-Catherine chapel (Castle Herberstein, Austria)
journal, November 2002

  • Heyrman, J.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 52, Issue 6
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Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria
journal, January 2013

  • Williams, K. P.; Kelly, D. P.
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Halomonas indalinina sp. nov., a moderately halophilic bacterium isolated from a solar saltern in Cabo de Gata, Almeria, southern Spain
journal, February 2007

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Halomonas gomseomensis sp. nov., Halomonas janggokensis sp. nov., Halomonas salaria sp. nov. and Halomonas denitrificans sp. nov., moderately halophilic bacteria isolated from saline water
journal, April 2007

  • Kim, K. K.; Jin, L.; Yang, H. C.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 4
  • DOI: 10.1099/ijs.0.64767-0

Halomonas avicenniae sp. nov., isolated from the salty leaves of the black mangrove Avicennia germinans in Puerto Rico
journal, May 2007

  • Soto-Ramirez, N.; Sanchez-Porro, C.; Rosas, S.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 5
  • DOI: 10.1099/ijs.0.64818-0

Halomonas shengliensis sp. nov., a moderately halophilic, denitrifying, crude-oil-utilizing bacterium
journal, June 2007

  • Wang, Y. -N.; Cai, H.; Chi, C. -Q.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 6
  • DOI: 10.1099/ijs.0.64973-0

Halotalea alkalilenta gen. nov., sp. nov., a novel osmotolerant and alkalitolerant bacterium from alkaline olive mill wastes, and emended description of the family Halomonadaceae Franzmann et al. 1989, emend. Dobson and Franzmann 1996
journal, September 2007

  • Ntougias, Spyridon; Zervakis, Georgios I.; Fasseas, Constantinos
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 57, Issue 9
  • DOI: 10.1099/ijs.0.65078-0

Halomonas kribbensis sp. nov., a novel moderately halophilic bacterium isolated from a solar saltern in Korea
journal, October 2007

  • Jeon, C. O.; Lim, J. -M.; Lee, J. R.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 10
  • DOI: 10.1099/ijs.0.65285-0

A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581T: Ectoine metabolism from the Halomonas genome
journal, September 2010


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


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

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


Solexa Ltd
journal, June 2004


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

Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison
journal, January 2010

  • Auch, Alexander F.; von Jan, Mathias; Klenk, Hans-Peter
  • Standards in Genomic Sciences, Vol. 2, Issue 1
  • DOI: 10.4056/sigs.531120

Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs
journal, January 2010

  • Auch, Alexander F.; Klenk, Hans-Peter; Göker, Markus
  • Standards in Genomic Sciences, Vol. 2, Issue 1
  • DOI: 10.4056/sigs.541628

The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes
journal, July 2009

  • Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A.
  • Standards in Genomic Sciences, Vol. 1, Issue 1
  • DOI: 10.4056/sigs.632

Works referencing / citing this record:

Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments
journal, June 2016

  • Edbeib, Mohamed Faraj; Wahab, Roswanira Abdul; Huyop, Fahrul
  • World Journal of Microbiology and Biotechnology, Vol. 32, Issue 8
  • DOI: 10.1007/s11274-016-2081-9

Complete genome sequence of the halophilic PHA-producing bacterium Halomonas sp. SF2003: insights into its biotechnological potential
journal, March 2019

  • Thomas, Tatiana; Elain, Anne; Bazire, Alexis
  • World Journal of Microbiology and Biotechnology, Vol. 35, Issue 3
  • DOI: 10.1007/s11274-019-2627-8

Inheritance and Establishment of Gut Microbiota in Chickens
journal, October 2017


Exemplar Abstract for Halomonas zhanjiangensis Chen et al. 2009.
dataset, January 2013

  • Parker, Charles Thomas; Taylor, Dorothea; Garrity, George M.
  • NamesforLife
  • DOI: 10.1601/ex.14856

Inheritance and Establishment of Gut Microbiota in Chickens
journal, October 2017