skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Draft genome sequence of Halomonas lutea strain YIM 91125T (DSM 23508T) isolated from the alkaline Lake Ebinur in Northwest China

Journal Article · · Standards in Genomic Sciences
 [1];  [2];  [3];  [4];  [5];  [6];  [6];  [6];  [6];  [6];  [6];  [6];  [7];  [8];  [6];  [9];  [10];  [11]
  1. Chinese Academy of Sciences (CAS), Urumqi,(China). Xinjiang Institute of Ecology and Geography; Univ. of Chinese Academy of Sciences, Beijing (China)
  2. Yunnan Univ., Kunming (China)
  3. Yunnan Univ., Kunming (China); Qujing Affiliated Hospital of Kunming Medical University, Qujing (China)
  4. Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang (China)
  5. St. Petersburg State Univ., St. Petersburg (Russia). Theodosius Dobzhansky Center for Genome Bionformatics; St. Petersburg Academic Univ., St. Petersburg (Russia)
  6. DOE Joint Genome Institute, Walnut Creek, CA (United States)
  7. Leibniz Inst. DSMZ, Braunschweig (Germany)
  8. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  9. Leibniz Inst. DSMZ, Braunschweig (Germany); Newcastle Univ. Newcastle upon Tyne (United Kingdom)
  10. DOE Joint Genome Institute, Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)
  11. Chinese Academy of Sciences (CAS), Urumqi,(China). Xinjiang Institute of Ecology and Geography; Yunnan Univ., Kunming (China)
+ Show Author Affiliations

Species of the genus Halomonas are halophilic and their flexible adaption to changes of salinity and temperature brings considerable potential biotechnology applications, such as degradation of organic pollutants and enzyme production. The type strain Halomonas lutea YIM 91125T was isolated from a hypersaline lake in China. The genome of strain YIM 91125T becomes the twelfth species sequenced in Halomonas, and the thirteenth species sequenced in Halomonadaceae. We described the features of H. lutea YIM 91125T, together with the high quality draft genome sequence and annotation of its type strain. The 4,533,090 bp long genome of strain YIM 91125T with its 4,284 protein-coding and 84 RNA genes is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project. From the viewpoint of comparative genomics, H. lutea has a larger genome size and more specific genes, which indicated acquisition of function bringing better adaption to its environment. Finally, DDH analysis demonstrated that H. lutea is a distinctive species, and halophilic features and nitrogen metabolism related genes were discovered in its genome.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC02-05CH11231; AC52-07NA27344
OSTI ID:
1256080
Journal Information:
Standards in Genomic Sciences, Vol. 10, Issue 1; ISSN 1944-3277
Publisher:
BioMed CentralCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 11 works
Citation information provided by
Web of Science

References (49)

A dynamic and intricate regulatory network determines Pseudomonas aeruginosa virulence journal November 2012
The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes journal July 2009
Shifting the genomic gold standard for the prokaryotic species definition journal October 2009
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
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB journal July 2006
How Many Bootstrap Replicates Are Necessary? journal March 2010
Halomonas indalinina sp. nov., a moderately halophilic bacterium isolated from a solar saltern in Cabo de Gata, Almeria, southern Spain journal February 2007
Halomonas shengliensis sp. nov., a moderately halophilic, denitrifying, crude-oil-utilizing bacterium journal June 2007
The DNA Bank Network: The Start from a German Initiative journal March 2011
Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species journal November 2011
Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence journal July 2000
Halomonas avicenniae sp. nov., isolated from the salty leaves of the black mangrove Avicennia germinans in Puerto Rico journal May 2007
High-quality draft assemblies of mammalian genomes from massively parallel sequence data journal December 2010
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods journal May 2011
Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs journal January 2010
Basic local alignment search tool journal October 1990
Solexa Ltd journal June 2004
The minimum information about a genome sequence (MIGS) specification journal May 2008
Halomonas kribbensis sp. nov., a novel moderately halophilic bacterium isolated from a solar saltern in Korea journal October 2007
Gene Ontology: tool for the unification of biology journal May 2000
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata journal December 2011
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. journal June 1990
Prodigal: prokaryotic gene recognition and translation initiation site identification journal March 2010
Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains journal August 2014
Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison journal January 2010
Halomonas muralis sp. nov., isolated from microbial biofilms colonizing the walls and murals of the Saint-Catherine chapel (Castle Herberstein, Austria) journal November 2002
The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation journal December 2012
Halomonas lutea sp. nov., a moderately halophilic bacterium isolated from a salt lake journal September 2008
Multiple sequence alignment using partial order graphs journal March 2002
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs journal February 2008
IMG ER: a system for microbial genome annotation expert review and curation journal June 2009
En route to a genome-based classification of Archaea and Bacteria? journal June 2010
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea journal December 2009
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes journal May 2010
Phylogeny of the family Halomonadaceae based on 23S and 165 rDNA sequence analyses. journal January 2002
Biology of Moderately Halophilic Aerobic Bacteria journal June 1998
Characterization of a Haloalkalophilic Strictly Aerobic Bacterium, Isolated from Pantelleria Island journal October 1996
Validation of publication of new names and new combinations previously effectively published outside the IJSEM journal November 2005
Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies journal September 1996
Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects journal May 2013
Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project journal December 2013
Genome Sequence of Halomonas sp. Strain A3H3, Isolated from Arsenic-Rich Marine Sediments journal October 2013
Genome-wide identification, structural analysis and expression profiles of GRAS gene family in orchardgrass journal February 2020
Halomonadaceae fam. nov., a New Family of the Class Proteobacteria to Accommodate the Genera Halomonas and Deleya journal November 1988
Halomonas desiderata sp. nov, a new alkaliphilic, halotolerant and denitrifying bacterium isolated from a municipal sewage works journal August 1996
Dietary palmitic acid promotes a prometastatic memory via Schwann cells journal November 2021
The neighbor-joining method: a new method for reconstructing phylogenetic trees. journal July 1987
Halomonas elongata, a New Genus and Species of Extremely Salt-Tolerant Bacteria journal April 1980
Phylogenetic Inferences and Taxonomic Consequences of 16S Ribosomal DNA Sequence Comparison of Chromohalobacter marismortui, Volcaniella eurihalina, and Deleya salina and Reclassification of V. eurihalina as Halomonas eurihalina comb. nov. journal October 1995

Cited By (9)

Complete genome sequence of the halophilic PHA-producing bacterium Halomonas sp. SF2003: insights into its biotechnological potential journal March 2019
Endophytic bacterial microbiome associated with leaves of genetically modified (AtAREB1) and conventional (BR 16) soybean plants journal March 2018
Enhanced long-term nitrogen removal by organotrophic anammox bacteria under different C/N ratio constraints: quantitative molecular mechanism and microbial community dynamics journal January 2016
Genomic profiling of four cultivated Candidatus Nitrotoga spp. predicts broad metabolic potential and environmental distribution journal July 2018
Exploring the unmapped DNA and RNA reads in a songbird genome journal January 2019
The MG-RAST metagenomics database and portal in 2015 journal December 2015
Complete genome sequence of the Sulfodiicoccus acidiphilus strain HS-1T, the first crenarchaeon that lacks polB3, isolated from an acidic hot spring in Ohwaku-dani, Hakone, Japan journal July 2019
Characterization of rhizobia isolates obtained from nodules of wild genotypes of common bean journal January 2017
A genome-scale metabolic reconstruction of Lysinibacillus sphaericus unveils unexploited biotechnological potentials journal June 2017

Similar Records

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
Journal Article · Fri Apr 11 00:00:00 EDT 2014 · Standards in Genomic Sciences · OSTI ID:1256080
+15 more
Complete genome sequence of Jiangella gansuensis strain YIM 002T (DSM 44835T), the type species of the genus Jiangella and source of new antibiotic compounds
Journal Article · Fri Feb 03 00:00:00 EST 2017 · Standards in Genomic Sciences · OSTI ID:1256080
+16 more
Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11T and Bradyrhizobium yuanmingense CCBAU 10071T
Journal Article · Tue Dec 05 00:00:00 EST 2017 · Standards in Genomic Sciences · OSTI ID:1256080
+2 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Halomonas lutea
Aerobic
Gram-negative
Chemoorganotrophic
Moderately halophilic
Lake Ebinur