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

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. DDH analysis demonstrated that H. lutea is a distinctive species, and halophilic features and nitrogen metabolism related genes were discovered in its genome.

[1]  I-Min A. Chen,et al.  The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata , 2007, Nucleic Acids Res..

[2]  Natalia N. Ivanova,et al.  A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea , 2009, Nature.

[3]  Chris F. Taylor,et al.  The minimum information about a genome sequence (MIGS) specification , 2008, Nature Biotechnology.

[4]  G. Garrity,et al.  Gammaproteobacteria class. nov. , 2015 .

[5]  F. Plewniak,et al.  Genome Sequence of Halomonas sp. Strain A3H3, Isolated from Arsenic-Rich Marine Sediments , 2013, Genome Announcements.

[6]  O. Kandler,et al.  Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Hans-Peter Klenk,et al.  Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs , 2010, Standards in genomic sciences.

[8]  I-Min A. Chen,et al.  IMG ER: a system for microbial genome annotation expert review and curation , 2009, Bioinform..

[9]  H. Klenk,et al.  Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects , 2013, Standards in genomic sciences.

[10]  K. Strimmer,et al.  Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies , 1996 .

[11]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[12]  J. S. Marron,et al.  BlackOPs: increasing confidence in variant detection through mappability filtering , 2013, Nucleic acids research.

[13]  Shukun Tang,et al.  Halomonas lutea sp. nov., a moderately halophilic bacterium isolated from a salt lake. , 2008, International journal of systematic and evolutionary microbiology.

[14]  Rick Stevens,et al.  Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains , 2014, PLoS biology.

[15]  Natalia N. Ivanova,et al.  The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes , 2009, Standards in genomic sciences.

[16]  S. Bennett.  Solexa Ltd. , 2004, Pharmacogenomics.

[17]  Aidan C. Parte,et al.  LPSN—list of prokaryotic names with standing in nomenclature , 2013, Nucleic Acids Res..

[18]  K. Schleifer,et al.  Phylogeny of the family Halomonadaceae based on 23S and 165 rDNA sequence analyses. , 2002, International journal of systematic and evolutionary microbiology.

[19]  J. Euzéby.  Validation of publication of new names and new combinations previously effectively published outside the IJSEM. , 2005, International journal of systematic and evolutionary microbiology.

[20]  C. Litchfield,et al.  Halomonas elongata, a New Genus and Species of Extremely Salt-Tolerant Bacteria , 1980 .

[21]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[22]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[23]  K. Mathee,et al.  A dynamic and intricate regulatory network determines Pseudomonas aeruginosa virulence , 2012, Nucleic acids research.

[24]  Hans-Peter Klenk,et al.  Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison , 2010, Standards in genomic sciences.

[25]  J. Chun,et al.  Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. , 2012, International journal of systematic and evolutionary microbiology.

[26]  Christopher J. Lee,et al.  Multiple sequence alignment using partial order graphs , 2002, Bioinform..

[27]  N. Soto-Ramírez,et al.  Halomonas avicenniae sp. nov., isolated from the salty leaves of the black mangrove Avicennia germinans in Puerto Rico. , 2007, International journal of systematic and evolutionary microbiology.

[28]  G. Garrity,et al.  Proteobacteria phyl. nov. , 2015 .

[29]  H. Klenk,et al.  En route to a genome-based classification of Archaea and Bacteria? , 2010, Systematic and applied microbiology.

[30]  G. Garrity.  Bergey’s Manual® of Systematic Bacteriology , 2012, Springer New York.

[31]  P. de Vos,et al.  Halomonas muralis sp. nov., isolated from microbial biofilms colonizing the walls and murals of the Saint-Catherine chapel (Castle Herberstein, Austria). , 2002, International journal of systematic and evolutionary microbiology.

[32]  I-Min A. Chen,et al.  The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata , 2011, Nucleic Acids Res..

[33]  Ju-Young Park,et al.  Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. , 2000, International journal of systematic and evolutionary microbiology.

[34]  sung-taik lee,et al.  Halomonas gomseomensis sp. nov., Halomonas janggokensis sp. nov., Halomonas salaria sp. nov. and Halomonas denitrificans sp. nov., moderately halophilic bacteria isolated from saline water. , 2007, International journal of systematic and evolutionary microbiology.

[35]  George M. Garrity,et al.  Standards in Genomic Sciences , 2009, Standards in genomic sciences.

[36]  Alexandros Stamatakis,et al.  How Many Bootstrap Replicates Are Necessary? , 2009, RECOMB.

[37]  Chang-Qiao Chi,et al.  Halomonas shengliensis sp. nov., a moderately halophilic, denitrifying, crude-oil-utilizing bacterium. , 2007, International journal of systematic and evolutionary microbiology.

[38]  A. Gnirke,et al.  High-quality draft assemblies of mammalian genomes from massively parallel sequence data , 2010, Proceedings of the National Academy of Sciences.

[39]  Thomas S. Brettin,et al.  The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation , 2012, PloS one.

[40]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[41]  George M. Garrity,et al.  Oceanospirillales ord. nov. , 2015 .

[42]  C. Jeon,et al.  Halomonas kribbensis sp. nov., a novel moderately halophilic bacterium isolated from a solar saltern in Korea. , 2007, International journal of systematic and evolutionary microbiology.

[43]  Validation of publication of new names and new combinations previously effectively published outside the IJSEM. , 2003, International journal of systematic and evolutionary microbiology.

[44]  Anton Güntsch,et al.  The DNA bank network: the start from a german initiative. , 2011, Biopreservation and biobanking.

[45]  S. Fuentes,et al.  Halomonas indalinina sp. nov., a moderately halophilic bacterium isolated from a solar saltern in Cabo de Gata, Almeria, southern Spain. , 2007, International journal of systematic and evolutionary microbiology.

[46]  A. Gambacorta,et al.  Characterization of a Haloalkalophilic Strictly Aerobic Bacterium, Isolated from Pantelleria Island , 1996 .

[47]  P. H. A. Sneath,et al.  Sergey's Manual of Systematic Bacteriology — Volume 2 , 1987, 1987.

[48]  George Garrity,et al.  Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project , 2014, Standards in Genomic Sciences.

[49]  Antonio Ventosa,et al.  Biology of Moderately Halophilic Aerobic Bacteria , 1998, Microbiology and Molecular Biology Reviews.

[50]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[51]  Natalia N. Ivanova,et al.  GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes , 2010, Nature Methods.

[52]  Eoin L. Brodie,et al.  Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB , 2006, Applied and Environmental Microbiology.

[53]  R. Rosselló-Móra,et al.  Shifting the genomic gold standard for the prokaryotic species definition , 2009, Proceedings of the National Academy of Sciences.

[54]  J. J. Nieto,et al.  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. , 1995, International journal of systematic bacteriology.

[55]  C. Jeon,et al.  Halomonas koreensis sp. nov., a novel moderately halophilic bacterium isolated from a solar saltern in Korea. , 2004, International journal of systematic and evolutionary microbiology.

[56]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[57]  E. Stackebrandt,et al.  Halomonadaceae fam. nov., a New Family of the Class Proteobacteria to Accommodate the Genera Halomonas and Deleya , 1988 .

[58]  B. Tindall,et al.  Halomonas desiderata sp. nov, a new alkaliphilic, halotolerant and denitrifying bacterium isolated from a municipal sewage works , 1996 .